Publications

2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000

2014


Amamoto, R., Arlotta, P. Development-Inspired Reprogramming of the Central Nervous System. Science. In preparation. Science. 2014 Jan 31;343(6170):1239882. doi: 10.1126/science.1239882. PMID: 24482482


Choi Y, Mango SE. Hunting for Darwin's gemmules and Lamarck's fluid: Transgenerational signaling and histone methylation. Biochim Biophys Acta. 2014 May 21. pii: S1874-9399(14)00117-5. doi: 10.1016/j.bbagrm.2014.05.011. [Epub ahead of print] PMID: 24859459


Goodman BS, Reck-Peterson SL. Engineering defined motor ensembles with DNA origami. Methods Enzymol. 2014;540:169-88. doi: 10.1016/B978-0-12-397924-7.00010-8. PMID: 4630107


Gornstein E, Schwarz TL. The paradox of paclitaxel neurotoxicity: Mechanisms and unanswered questions. Neuropharmacology. 2014 Jan;76 Pt A:175-83. doi: 10.1016/j.neuropharm.2013.08.016. Epub 2013 Aug 24. PMID: 23978385


Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Yoshida S, Graham RR, Manoharan A, Ortmann W, Bhangale T, Denny JC, Carroll RJ, Eyler AE, Greenberg JD, Kremer JM, Pappas DA, Jiang L, Yin J, Ye L, Su DF, Yang J, Xie G, Keystone E, Westra HJ, Esko T, Metspalu A, Zhou X, Gupta N, Mirel D, Stahl EA, Diogo D, Cui J, Liao K, Guo MH, Myouzen K, Kawaguchi T, Coenen MJ, van Riel PL, van de Laar MA, Guchelaar HJ, Huizinga TW, Dieudé P, Mariette X, Bridges SL Jr, Zhernakova A, Toes RE, Tak PP, Miceli-Richard C, Bang SY, Lee HS, Martin J, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Rantapää-Dahlqvist S, Arlestig L, Choi HK, Kamatani Y, Galan P, Lathrop M; RACI consortium; GARNET consortium, Eyre S, Bowes J, Barton A, de Vries N, Moreland LW, Criswell LA, Karlson EW, Taniguchi A, Yamada R, Kubo M, Liu JS, Bae SC, Worthington J, Padyukov L, Klareskog L, Gregersen PK, Raychaudhuri S, Stranger BE, De Jager PL, Franke L, Visscher PM, Brown MA, Yamanaka H, Mimori T, Takahashi A, Xu H, Behrens TW, Siminovitch KA, Momohara S, Matsuda F, Yamamoto K, Plenge RM. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 2014 Feb 20;506(7488):376-81. doi: 10.1038/nature12873. Epub 2013 Dec 25. PMID: 24390342 PMCID: PMC3944098


Ho BT, Dong TG, Mekalanos JJ. A view to a kill: the bacterial type VI secretion system. Cell Host Microbe. 2014 Jan 15;15(1):9-21. doi: 10.1016/j.chom.2013.11.008. Epub 2013 Dec 11. PMID: 24332978 PMCID: PMC3936019


Bröcker MJ, Ho JM, Church GM, Söll D, O'Donoghue P. Recoding the genetic code with selenocysteine. Angew Chem Int Ed Engl. 2014 Jan 3;53(1):319-23. doi: 10.1002/anie.201308584. PMID: 24511637


Colak S, Zimberlin CD, Fessler E, Hogdal L, Prasetyanti PR, Grandela CM, Letai A, Medema JP. Decreased mitochondrial priming determines chemoresistance of colon cancer stem cells. Cell Death Differ. 2014 Mar 28. doi: 10.1038/cdd.2014.37. [Epub ahead of print] PMID: 24682005


Yang L, Mali P, Kim-Kiselak C, Church G. CRISPR-Cas-Mediated Targeted Genome Editing in Human Cells. Methods Mol Biol. 2014;1114:245-67. doi: 10.1007/978-1-62703-761-7_16. PMID: 24557908


Lee D, Boscolo E, Durham JT, Mulliken JB, Herman IM, Bischoff J. Propranolol Targets Contractility of Infantile Hemangioma-derived Pericytes. Br J Dermatol. 2014 Apr 10. doi: 10.1111/bjd.13048. [Epub ahead of print] PMID: 24720697


David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, Ling AV, Devlin AS, Varma Y, Fischbach MA, Biddinger SB, Dutton RJ, Turnbaugh PJ. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014 Jan 23;505(7484):559-63. doi: 10.1038/nature12820. Epub 2013 Dec 11. PMID: 24336217 PMCID: PMC3957428


Nizza ST, Campbell JJ. CD11b+ migratory dendritic cells mediate CD8 T cell cross-priming and cutaneous imprinting after topical immunization. PLoS One. 2014 Mar 11;9(3):e91054. doi: 10.1371/journal.pone.0091054. eCollection 2014. PMID: 24618819 PMCID: PMC3949685 read article


Davila SJ, Olive AJ, Starnbach MN. Integrin α4β1 is necessary for CD4+ T cell-mediated protection against genital Chlamydia trachomatis infection. J Immunol. 2014 May 1;192(9):4284-93. doi: 10.4049/jimmunol.1303238. Epub 2014 Mar 21. PMID: 24659687 PMCID: PMC3995848


Olive AJ, Haff MG, Emanuele MJ, Sack LM, Barker JR, Elledge SJ, Starnbach MN. Chlamydia trachomatis-induced alterations in the host cell proteome are required for intracellular growth. Cell Host Microbe. 2014 Jan 15;15(1):113-24. doi: 10.1016/j.chom.2013.12.009. PMID: 24439903 PMCID: PMC3932326


Järås M, Miller PG, Chu LP, Puram RV, Fink EC, Schneider RK, Al-Shahrour F, Peña P, Breyfogle LJ, Hartwell KA, McConkey ME, Cowley GS, Root DE, Kharas MG, Mullally A, Ebert BL. Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia. J Exp Med. 2014 Apr 7;211(4):605-12. doi: 10.1084/jem.20131033. Epub 2014 Mar 10. PMID: 24616378 PMCID: PMC3978274


Raiser DM, Narla A, Ebert BL. The emerging importance of ribosomal dysfunction in the pathogenesis of hematologic disorders. Leuk Lymphoma. 2014 Mar;55(3):491-500. doi: 10.3109/10428194.2013.812786. Epub 2013 Aug 28. PMID: 23863123


Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, Pedamallu CS, Sivachenko A, Rosenberg M, Chmielecki J, Lawrence MS, DeLuca DS, Getz G, Meyerson M. A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. PLoS One. 2014 Jan 31;9(1):e87361. doi: 10.1371/journal.pone.0087361. eCollection 2014. PMID: 24498085 PMCID: PMC3909098 read article


Berger AH, Imielinski M, Duke F, Wala J, Kaplan N, Shi GX, Andres DA, Meyerson M. Oncogenic RIT1 mutations in lung adenocarcinoma. Oncogene. 2014 Jan 27. doi: 10.1038/onc.2013.581. [Epub ahead of print] PMID: 24469055


top

2013


Amamoto, R., Arlotta, P. Reshaping the Brain: Direct Lineage Conversion in the Nervous System. F1000Prime Rep. 2013 Sep 2;5:33. eCollection 2013. PMID: 24049637 PMCID: PMC3768326 read article


Su X, Arellano-Santoyo H, Portran D, Gaillard J, Vantard M, Thery M, Pellman D. Microtubule-sliding activity of a kinesin-8 promotes spindle assembly and spindle-length control. Nat Cell Biol. 2013 Aug;15(8):948-57. doi: 10.1038/ncb2801. Epub 2013 Jul 14. PMID:23851487 PMCID: PMC3767134 read article


Atkins BD, Yoshida S, Saito K, Wu CF, Lew DJ, Pellman D. Inhibition of Cdc42 during mitotic exit is required for cytokinesis. J Cell Biol. 2013 Jul 22;202(2):231-40. doi: 10.1083/jcb.201301090. PMID: 23878274 PMCID: PMC3718968 read article


Duncan MB, Yang C, Tanjore H, Boyle PM, Keskin D, Sugimoto H, Zeisberg M, Olsen BR, Kalluri R. Type XVIII collagen is essential for survival during acute liver injury in mice. Dis Model Mech. 2013 Jul;6(4):942-51. doi: 10.1242/dmm.011577. Epub 2013 Apr 4. PMID: 23580202 PMCID: PMC3701214 read article


Kim SG, Buel GR, and Blenis J. 2013. Nutrient regulation of the mTOR Complex 1 signaling pathway. Mol Cells. 2013 Jun;35(6):463-73. doi: 10.1007/s10059-013-0138-2. Epub 2013 May 20. PMID: 23694989 PMCID: PMC3887879


Buel GR, Kim SG, and Blenis J. 2013. mTORC1 Signaling Aids in CADalyzing Pyrimidine Biosynthesis. Cell Metab. 2013 May 7;17(5):633-5. doi: 10.1016/j.cmet.2013.04.018. PMID: 23663734


Kim SG, Hoffman GR, Poulogiannis G, Buel GR, Jang YJ, Lee KW, Kim BY, Erikson RL, Cantley LC, Choo AY, and Blenis J. 2013. Metabolic stress controls mTORC1 lysosomal localization and dimerization by regulating the TTT-RUVBL1/2 complex. Mol Cell. 2013 Jan 10;49(1):172-85. doi: 10.1016/j.molcel.2012.10.003. Epub 2012 Nov 8. PMID: 23142078 PMCID: PMC3545014
 read article


Harris JM; Esain V; Frechette GM; Harris LJ; Cox AG; Cortes M; Garnaas MK; Carroll KJ; Cutting CC; Khan T; Elks PM; Renshaw SA; Dickinson BC; Chang CJ; Murphy MP; Paw BH; Vander Heiden MG; Goessling W; North TE. Glucose metabolism impacts the spatiotemporal onset and magnitude of HSC induction in vivo. Blood. 2013 Mar 28;121(13):2483-93. doi: 10.1182/blood-2012-12-471201. Epub 2013 Jan 22. PMID: 23341543 PMCID: PMC3612858 read article


Jemielity S, Wang JJ, Chan YK, Ahmed AA, Li W, Monahan S, Bu X, Farzan M, Freeman GJ, Umetsu DT, Dekruyff RH, Choe H. TIM-family proteins promote infection of multiple enveloped viruses through virion-associated phosphatidylserine. PLoS Pathog. 2013 Mar;9(3):e1003232. doi: 10.1371/journal.ppat.1003232. Epub 2013 Mar 28. PMID:23555248. PMCID:PMC3610696. read article


Buchwalter G, Hickey MM, Cromer A, Selfors LM, Gunawardane RN, Frishman J, Jeselsohn R, Lim E, Chi D, Fu X, Schiff R, Brown M, Brugge JS. PDEF Promotes Luminal Differentiation and Acts as a Survival Factor for ER-Positive Breast Cancer Cells. Cancer Cell. 2013 Jun 10;23(6):753-67. doi: 10.1016/j.ccr.2013.04.026. PMID:23764000. PMCID:PMC3711136.


Ciarlo CA, Zon LI. A model for primary melanoma of the CNS implicates NRAS. Cancer Discov. 2013 Apr;3(4):382-3. doi: 10.1158/2159-8290.CD-13-0076. PMID: 23580282


Fang R, Chen F, Dong Z, Hu D, Barbera AJ, Clark EA, Fang J, Yang Y, Mei P, Rutenberg M, Li Z, Zhang Y, Xu Y, Yang H, Wang P, Simon MD, Zhou Q, Li J, Marynick MP, Li X, Lu H, Kaiser UB, Kingston RE, Xu Y, Shi YG. LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation. Mol Cell. 2013 Feb 7;49(3):558-70. doi: 10.1016/j.molcel.2012.11.019. Epub 2012 Dec 20. PMID: 23260659 PMCID: PMC3625064 read article


Kung J, Colognori D, Lee J. (2013) Long noncoding RNAs: past, present, and future. Genetics. 2013 Mar;193(3):651-69. doi: 10.1534/genetics.112.146704. PMID: 23463798. PMCID:PMC3583990. read article


Csibi A, Fendt SM, Li C, Poulogiannis G, Choo AY, Chapski DJ, Jeong SM, Dempsey JM, Parkhitko A, Morrison T, Henske EP, Haigis MC, Cantley LC, Stephanopoulos G, Yu J, Blenis J. The mTORC1 pathway stimulates glutamine metabolism and cell proliferation by repressing SIRT4. Cell. 2013 May 9;153(4):840-54. doi: 10.1016/j.cell.2013.04.023. PMID: 23663782 PMCID: PMC3684628


Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A. Charting a dynamic DNA methylation landscape of the human genome. Nature. 2013 Aug 22;500(7463):477-81. doi: 10.1038/nature12433. Epub 2013 Aug 7. PMID: 23925113 PMCID: PMC3821869 read article


CA. Gifford*, MJ. Ziller*, H Gu, C Trapnell, J Donaghey, A Tsankov, AK. Shalek, DR Kelley, R Issner, X Zhang, M Coyne, JL Fostel, L Holmes, J Meldrim, C Epstein, H Park, A Regev, O Kohlbacher, J Rinn, A Gnirke, BE Bernstein and A Meissner. Transcriptional and Epigenetic Dynamics During Specification of Human Embryonic Stem Cells. Cell. 2013 May 23;153(5):1149-63. doi: 10.1016/j.cell.2013.04.037. Epub 2013 May 9. PMID: 23664763 PMCID: PMC3709577


Zangi L, Lui KO, von Gise A, Ma Q, Ebina W, Ptaszek LM, Später D, Xu H, Tabebordbar M, Gorbatov R, Sena B, Nahrendorf M, Briscoe DM, Li RA, Wagers AJ, Rossi DJ, Pu WT, Chien KR. Modified mRNA directs the fate of heart progenitor cells and induces vascular regeneration after myocardial infarction. Nat Biotechnol. 2013 Oct;31(10):898-907. doi: 10.1038/nbt.2682. Epub 2013 Sep 8. PMID: 24013197


Torella JP, Ford TJ, Kim SN, Chen AM, Way JC, Silver PA. Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11290-5. doi: 10.1073/pnas.1307129110. Epub 2013 Jun 24. PMID: 23798438 PMCID: PMC3710846 read article


Froberg JE, Yang L, Lee JT. Guided by RNAs: X-inactivation as a model for lncRNA function. J Mol Biol. 2013 Oct 9;425(19):3698-706. doi: 10.1016/j.jmb.2013.06.031. Epub 2013 Jun 28. PMID: 23816838 PMCID: PMC3771680


Harris JM, Esain V, Frechette GM, Harris LJ, Cox AG, Cortes M, Garnaas MK, Carroll KJ, Cutting CC, Khan T, Elks PM, Renshaw SA, Dickinson BC, Chang CJ, Murphy MP, Paw BH, Vander Heiden MG, Goessling W, North TE. Glucose metabolism impacts the spatiotemporal onset and magnitude of HSC induction in vivo. Blood. 2013 Mar 28;121(13):2483-93. doi: 10.1182/blood-2012-12-471201. Epub 2013 Jan 22. PMID: 23341543 PMCID: PMC3612858 read article


Laurent G, German NJ, Saha AK, de Boer VC, Davies M, Koves TR, Dephoure N, Fischer F, Boanca G, Vaitheesvaran B, Lovitch SB, Sharpe AH, Kurland IJ, Steegborn C, Gygi SP, Muoio DM, Ruderman NB, Haigis MC. SIRT4 coordinates the balance between lipid synthesis and catabolism by repressing malonyl CoA decarboxylase. Mol Cell. 2013 Jun 6;50(5):686-98. doi: 10.1016/j.molcel.2013.05.012. PMID: 23746352 PMCID: PMC3721068


Jeong SM, Xiao C, Finley LW, Lahusen T, Souza AL, Pierce K, Li YH, Wang X, Laurent G, German NJ, Xu X, Li C, Wang RH, Lee J, Csibi A, Cerione R, Blenis J, Clish CB, Kimmelman A, Deng CX, Haigis MC. SIRT4 has tumor-suppressive activity and regulates the cellular metabolic response to DNA damage by inhibiting mitochondrial glutamine metabolism. Cancer Cell. 2013 Apr 15;23(4):450-63. doi: 10.1016/j.ccr.2013.02.024. Epub 2013 Apr 4. PMID: 23562301 PMCID: PMC3650305


Yang MH, Laurent G, Bause AS, Spang R, German N, Haigis MC, Haigis KM. HDAC6 and SIRT2 regulate the acetylation state and oncogenic activity of mutant K-RAS. Mol Cancer Res. 2013 Sep;11(9):1072-7. doi: 10.1158/1541-7786.MCR-13-0040-T. Epub 2013 May 30. PMID: 23723075 PMCID: PMC3778089


Abazeed ME, Adams DJ, Hurov KE, Tamayo P, Creighton CJ, Sonkin D, Giacomelli AO, Du C, Fries DF, Wong KK, Mesirov JP, Loeffler JS, Schreiber SL, Hammerman PS, Meyerson M. Integrative radiogenomic profiling of squamous cell lung cancer. Cancer Res. 2013 Oct 15;73(20):6289-98. doi: 10.1158/0008-5472.CAN-13-1616. Epub 2013 Aug 26. PMID: 23980093 PMCID: PMC3856255


Hagerstrand D, Tong A, Schumacher SE, Ilic N, Shen RR, Cheung HW, Vazquez F, Shrestha Y, Kim SY, Giacomelli AO, Rosenbluh J, Schinzel AC, Spardy NA, Barbie DA, Mermel CH, Weir BA, Garraway LA, Tamayo P, Mesirov JP, Beroukhim R, Hahn WC. Systematic interrogation of 3q26 identifies TLOC1 and SKIL as cancer drivers. Cancer Discov. 2013 Sep;3(9):1044-57. doi: 10.1158/2159-8290.CD-12-0592. Epub 2013 Jun 13. PMID: 23764425 PMCID: PMC3770815


Wilson-Grady JT, Haas W, Gygi SP. Quantitative comparison of the fasted and re-fed mouse liver phosphoproteomes using lower pH reductive dimethylation. Methods. 2013 Jun 15;61(3):277-86. doi: 10.1016/j.ymeth.2013.03.031. Epub 2013 Apr 6. PMID: 23567750


Wilson-Grady JT, Haas W, Gygi SP. Quantitative comparison of the fasted and re-fed mouse liver phosphoproteomes using lower pH reductive dimethylation. Methods. 2013 Jun 15;61(3):277-86. doi: 10.1016/j.ymeth.2013.03.031. Epub 2013 Apr 6. PMID: 3567750


Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RN, Hill AV, Vannberg FO, Rinn JL; 1000 Genomes Project, Lander ES, Schaffner SF, Sabeti PC. Identifying recent adaptations in large-scale genomic data. Cell. 2013 Feb 14;152(4):703-13. doi: 10.1016/j.cell.2013.01.035. PMID: 23415221 PMCID: PMC3674781 read article


Guo MH, Stoler J, Lui J, Nilsson O, Bianchi DW, Hirschhorn JN, Dauber A. Redefining the progeroid form of Ehlers-Danlos syndrome: report of the fourth patient with B4GALT7 deficiency and review of the literature. Am J Med Genet A. 2013 Oct;161(10):2519-27. doi: 10.1002/ajmg.a.36128. Epub 2013 Aug 16. PMID: 23956117
PMCID: PMC3788078


Hanson KK, Ressurreição AS, Buchholz K, Prudêncio M, Herman-Ornelas JD, Rebelo M, Beatty WL, Wirth DF, Hänscheid T, Moreira R, Marti M, Mota MM. Torins are potent antimalarials that block replenishment of Plasmodium liver stage parasitophorous vacuole membrane proteins. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):E2838-47. doi: 10.1073/pnas.1306097110. Epub 2013 Jul 8. PMID: 23836641


Hinshaw SM, Harrison SC. An Iml3-Chl4 heterodimer links the core centromere to factors required for accurate chromosome segregation. Cell Rep. 2013 Oct 17;5(1):29-36. doi: 10.1016/j.celrep.2013.08.036. Epub 2013 Sep 26. PMID:24075991 PMCID:PMC3888643


Ho BT, Basler M, Mekalanos JJ. Type 6 secretion system-mediated immunity to type 4 secretion system-mediated gene transfer. Science. 2013 Oct 11;342(6155):250-3. doi: 10.1126/science.1243745. PMID: 24115441


Dong TG, Ho BT, Yoder-Himes DR, Mekalanos JJ. Identification of T6SS-dependent effector and immunity proteins by Tn-seq in Vibrio cholerae. Proc Natl Acad Sci U S A. 2013 Feb 12;110(7):2623-8. doi: 10.1073/pnas.1222783110. Epub 2013 Jan 29. PMID: 23362380 PMCID: PMC3574944 read article


Basler M, Ho BT, Mekalanos JJ. Tit-for-tat: type VI secretion system counterattack during bacterial cell-cell interactions. Cell. 2013 Feb 14;152(4):884-94. doi: 10.1016/j.cell.2013.01.042. PMID: 23415234 PMCID: PMC3616380 read article


Shneider MM, Buth SA, Ho BT, Basler M, Mekalanos JJ, Leiman PG. PAAR-repeat proteins sharpen and diversify the type VI secretion system spike. Nature. 2013 Aug 15;500(7462):350-3. doi: 10.1038/nature12453. Epub 2013 Aug 7. PMID: 23925114 PMCID: PMC3792578 read article


Hogdal LJ, Letai A. BCL-2 inhibition: stemming the tide of myeloid malignancies. Cell Stem Cell. 2013 Mar 7;12(3):269-70. doi: 10.1016/j.stem.2013.02.006. PMID: 23472867 PMCID: PMC3705714 read article


Gu X, Yu JJ, Ilter D, Blenis N, Henske EP, Blenis J. Integration of mTOR and estrogen-ERK2 signaling in lymphangioleiomyomatosis pathogenesis. Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):14960-5. doi: 10.1073/pnas.1309110110. Epub 2013 Aug 27. PMID: 23983265 PMCID: PMC3773757 read article


Duncan MB, Yang C, Tanjore H, Boyle PM, Keskin D, Sugimoto H, Zeisberg M, Olsen BR, Kalluri R. Type XVIII collagen is essential for survival during acute liver injury in mice. Dis Model Mech. 2013 Jul;6(4):942-51. doi: 10.1242/dmm.011577. Epub 2013 Apr 4. PMID: 23580202 PMCID: PMC3701214 read article


Li CM, Chen G, Dayton TL, Kim-Kiselak C, Hoersch S, Whittaker CA, Bronson RT, Beer DG, Winslow MM, Jacks T. Differential Tks5 isoform expression contributes to metastatic invasion of lung adenocarcinoma. Genes Dev. 2013 Jul 15;27(14):1557-67. doi: 10.1101/gad.222745.113. PMID: 23873940 PMCID: PMC3731545 read article


Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G. Optimization of scarless human stem cell genome editing. PMID: 23907390 PMCID: PMC3799423 read article


Kowalko JE, Rohner N, Rompani SB, Peterson BK, Linden TA, Yoshizawa M, Kay EH, Weber J, Hoekstra HE, Jeffery WR, Borowsky R, Tabin CJ. Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms. Curr Biol. 2013 Oct 7;23(19):1874-83. doi: 10.1016/j.cub.2013.07.056. Epub 2013 Sep 12. PMID: 24035545 PMCID: PMC3904651


Rohner N, Jarosz DF, Kowalko JE, Yoshizawa M, Jeffery WR, Borowsky RL, Lindquist S, Tabin CJ. Cryptic variation in morphological evolution: HSP90 as a capacitor for loss of eyes in cavefish. Science. 2013 Dec 13;342(6164):1372-5. doi: 10.1126/science.1240276. PMID: 24337296


Kowalko JE, Rohner N, Linden TA, Rompani SB, Warren WC, Borowsky R, Tabin CJ, Jeffery WR, Yoshizawa M. Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus. Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16933-8. doi: 10.1073/pnas.1317192110. Epub 2013 Oct 1. PMID: 24085851 PMCID: PMC3801050


Oksenych V, Kumar V, Liu X, Guo C, Schwer B, Zha S, Alt FW. Functional redundancy between the XLF and DNA-PKcs DNA repair factors in V(D)J recombination and nonhomologous DNA end joining. Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2234-9. doi: 10.1073/pnas.1222573110. Epub 2013 Jan 23. PMID: 23345432 PMCID: PMC3568359 read article


Kung JT, Colognori D, Lee JT. Long noncoding RNAs: past, present, and future.Genetics. 2013 Mar;193(3):651-69. doi: 10.1534/genetics.112.146704. PMID: 23463798 PMCID: PMC3583990 read article


Kung JT, Lee JT. RNA in the loop. Dev Cell. 2013 Mar 25;24(6):565-7. doi: 10.1016/j.devcel.2013.03.009. PMID: 23537627 PMCID: PMC3777248 read article


Lee RS, Roberts CW. Rhabdoid tumors: an initial clue to the role of chromatin remodeling in cancer. Brain Pathol. 2013 Mar;23(2):200-5. doi: 10.1111/bpa.12021. PMID: 23432645


Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, Dicara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau D-A, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Lee RS, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CWM, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013 Jul 11;499(7457):214-8. doi: 10.1038/nature12213. Epub 2013 Jun 16. PMID: 23770567 PMCID: PMC3919509 read article


Lim ET, Raychaudhuri S, Sanders SJ, Stevens C, Sabo A, MacArthur DG, Neale BM, Kirby A, Ruderfer DM, Fromer M, Lek M, Liu L, Flannick J, Ripke S, Nagaswamy U, Muzny D, Reid JG, Hawes A, Newsham I, Wu Y, Lewis L, Dinh H, Gross S, Wang LS, Lin CF, Valladares O, Gabriel SB, dePristo M, Altshuler DM, Purcell SM; NHLBI Exome Sequencing Project, State MW, Boerwinkle E, Buxbaum JD, Cook EH, Gibbs RA, Schellenberg GD, Sutcliffe JS, Devlin B, Roeder K, Daly MJ. Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders. Neuron. 2013 Jan 23;77(2):235-42. doi: 10.1016/j.neuron.2012.12.029. PMID: 23352160 PMCID: PMC3613849 read article


He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, State MW, Devlin B, Roeder K. Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes. PLoS Genet. 2013;9(8):e1003671. doi: 10.1371/journal.pgen.1003671. Epub 2013 Aug 15. PMID: 23966865 PMCID: PMC3744441 read article


Yu TW, Chahrour MH, Coulter ME, Jiralerspong S, Okamura-Ikeda K, Ataman B, Schmitz-Abe K, Harmin DA, Adli M, Malik AN, D'Gama AM, Lim ET, Sanders SJ, Mochida GH, Partlow JN, Sunu CM, Felie JM, Rodriguez J, Nasir RH, Ware J, Joseph RM, Hill RS, Kwan BY, Al-Saffar M, Mukaddes NM, Hashmi A, Balkhy S, Gascon GG, Hisama FM, LeClair E, Poduri A, Oner O, Al-Saad S, Al-Awadi SA, Bastaki L, Ben-Omran T, Teebi AS, Al-Gazali L, Eapen V, Stevens CR, Rappaport L, Gabriel SB, Markianos K, State MW, Greenberg ME, Taniguchi H, Braverman NE, Morrow EM, Walsh CA. Using whole-exome sequencing to identify inherited causes of autism. Neuron. 2013 Jan 23;77(2):259-73. doi: 10.1016/j.neuron.2012.11.002. PMID: 23352163 PMCID: PMC3694430 read article


Liu L, Sabo A, Neale BM, Nagaswamy U, Stevens C, Lim E, Bodea CA, Muzny D, Reid JG, Banks E, Coon H, Depristo M, Dinh H, Fennel T, Flannick J, Gabriel S, Garimella K, Gross S, Hawes A, Lewis L, Makarov V, Maguire J, Newsham I, Poplin R, Ripke S, Shakir K, Samocha KE, Wu Y, Boerwinkle E, Buxbaum JD, Cook EH Jr, Devlin B, Schellenberg GD, Sutcliffe JS, Daly MJ, Gibbs RA, Roeder K. Analysis of rare, exonic variation amongst subjects with autism spectrum disorders and population controls. PLoS Genet. 2013 Apr;9(4):e1003443. doi: 10.1371/journal.pgen.1003443. Epub 2013 Apr 11. PMID: 23593035 PMCID: PMC3623759 read article


Margolin DH, Kousi M, Chan YM, Lim ET, Schmahmann JD, Hadjivassiliou M, Hall JE, Adam I, Dwyer A, Plummer L, Aldrin SV, O'Rourke J, Kirby A, Lage K, Milunsky A, Milunsky JM, Chan J, Hedley-Whyte ET, Daly MJ, Katsanis N, Seminara SB. Ataxia, dementia, and hypogonadotropism caused by disordered ubiquitination. N Engl J Med. 2013 May 23;368(21):1992-2003. doi: 10.1056/NEJMoa1215993. Epub 2013 May 8. PMID: 23656588 PMCID: PMC3738065 read article


Mannstadt M, Harris M, Bravenboer B, Chitturi S, Dreijerink KM, Lambright DG, Lim ET, Daly MJ, Gabriel S, Jüppner H. Germline mutations affecting Gα11 in hypoparathyroidism. N Engl J Med. 2013 Jun 27;368(26):2532-4. doi: 10.1056/NEJMc1300278. PMID: 23802536 PMCID: PMC3750735 read article


Liu LY, Fox CS, North TE, Goessling W. Functional validation of GWAS gene candidates for abnormal liver function during zebrafish liver development. Dis Model Mech. 2013 Sep;6(5):1271-8. doi: 10.1242/dmm.011726. Epub 2013 Jun 27. PMID: 23813869 PMCID: PMC3759346 read article


Morgan AM, Lo J, Fisher DE. How does pheomelanin synthesis contribute to melanomagenesis?: Two distinct mechanisms could explain the carcinogenicity of pheomelanin synthesis. Bioessays. 2013 Aug;35(8):672-6. doi: 10.1002/bies.201300020. Epub 2013 May 7. PMID: 23650156


Doan T, Coleman J, Marquis KA, Meeske AJ, Burton BM, Karatekin E, Rudner DZ. FisB mediates membrane fission during sporulation in Bacillus subtilis. Genes Dev. 2013 Feb 1;27(3):322-34. doi: 10.1101/gad.209049.112. PMID: 23388828 PMCID: PMC3576517 read article


Montero-Diez C, Deighan P, Osmundson J, Darst SA, Hochschild A. Phage-encoded inhibitor of Staphylococcus aureus transcription exerts context-dependent effects on promoter function in a modified Escherichia coli-based transcription system. J Bacteriol. 2013 Aug;195(16):3621-8. doi: 10.1128/JB.00499-13. Epub 2013 Jun 7. PMID: 23749973 PMCID: PMC3754564 read article


Son J, Lyssiotis CA, Ying H, Wang X, Hua S, Ligorio M, Perera RM, Ferrone CR, Mullarky E, Shyh-Chang N, Kang Y, Fleming JB, Bardeesy N, Asara JM, Haigis MC, DePinho RA, Cantley LC, Kimmelman AC. Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature. 2013 Apr 4;496(7443):101-5. doi: 10.1038/nature12040. Epub 2013 Mar 27. PMID: 23535601 PMCID: PMC3656466
 read article


Nedelcu D, Liu J, Xu Y, Jao C, Salic A. Oxysterol binding to the extracellular domain of Smoothened in Hedgehog signaling. Nat Chem Biol. 2013 Sep;9(9):557-64. doi: 10.1038/nchembio.1290. Epub 2013 Jul 7. PMID: 23831757 PMCID: PMC3749252 read article


Shyh-Chang N, Daley GQ, Cantley LC. Stem cell metabolism in tissue development and aging. Development. 2013 Jun;140(12):2535-47. doi: 10.1242/dev.091777. PMID: 23715547 PMCID: PMC3666381


Shyh-Chang N, Daley GQ. Lin28: primal regulator of growth and metabolism in stem cells. Cell Stem Cell. 2013 Apr 4;12(4):395-406. doi: 10.1016/j.stem.2013.03.005. PMID: 23561442 PMCID: PMC3652335 read article


Shyh-Chang N, Locasale JW, Lyssiotis CA, Zheng Y, Teo RY, Ratanasirintrawoot S, Zhang J, Onder T, Unternaehrer JJ, Zhu H, Asara JM, Daley GQ, Cantley LC. Influence of threonine metabolism on S-adenosylmethionine and histone methylation. Science. 2013 Jan 11;339(6116):222-6. doi: 10.1126/science.1226603. Epub 2012 Nov 1. PMID: 23118012 PMCID: PMC3652341 read article


Shyh-Chang N, Zhu H, Yvanka de Soysa T, Shinoda G, Seligson MT, Tsanov KM, Nguyen L, Asara JM, Cantley LC, Daley GQ. Lin28 enhances tissue repair by reprogramming cellular metabolism. Cell. 2013 Nov 7;155(4):778-92. doi: 10.1016/j.cell.2013.09.059. PMID: 24209617 PMCID: PMC3917449


Shinoda G, Shyh-Chang N, Soysa TY, Zhu H, Seligson MT, Shah SP, Abo-Sido N, Yabuuchi A, Hagan JP, Gregory RI, Asara JM, Cantley LC, Moss EG, Daley GQ. Fetal deficiency of lin28 programs life-long aberrations in growth and glucose metabolism. Stem Cells. 2013 Aug;31(8):1563-73. doi: 10.1002/stem.1423. PMID: 23666760 PMCID: PMC3775935 read article


Son J, Lyssiotis CA, Ying H, Wang X, Hua S, Ligorio M, Perera RM, Ferrone CR, Mullarky E, Shyh-Chang N, Kang Y, Fleming JB, Bardeesy N, Asara JM, Haigis MC, DePinho RA, Cantley LC, Kimmelman AC. Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature. 2013 Apr 4;496(7443):101-5. doi: 10.1038/nature12040. Epub 2013 Mar 27. PMID: 23535601 PMCID: PMC3656466 read article


Vander Lugt B, Tubo NJ, Nizza ST, Boes M, Malissen B, Fuhlbrigge RC, Kupper TS, Campbell JJ. CCR7 plays no appreciable role in trafficking of central memory CD4 T cells to lymph nodes. J Immunol. 2013 Sep 15;191(6):3119-27. doi: 10.4049/jimmunol.1200938. Epub 2013 Aug 9. PMID: 23935190 PMCID: PMC3784989


Lienert F, Torella JP, Chen JH, Norsworthy M, Richardson RR, Silver PA. Two- and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic Acids Res. 2013 Nov;41(21):9967-75. doi: 10.1093/nar/gkt758. Epub 2013 Aug 27. PMID: 23982518 PMCID: PMC3834826 read article


McCluskey AJ, Olive AJ, Starnbach MN, Collier RJ. Targeting HER2-positive cancer cells with receptor-redirected anthrax protective antigen. Mol Oncol. 2013 Jun;7(3):440-51. doi: 10.1016/j.molonc.2012.12.003. Epub 2012 Dec 19. PMID: 23290417 PMCID: PMC3621010


Reiling JH, Olive AJ, Sanyal S, Carette JE, Brummelkamp TR, Ploegh HL, Starnbach MN, Sabatini DM. A CREB3-ARF4 signalling pathway mediates the response to Golgi stress and susceptibility to pathogens. Nat Cell Biol. 2013 Dec;15(12):1473-85. doi: 10.1038/ncb2865. Epub 2013 Nov 3. PMID: 24185178 PMCID: PMC3965854 read article


McLaughlin SK, Olsen SN, Dake B, De Raedt T, Lim E, Bronson RT, Beroukhim R, Polyak K, Brown M, Kuperwasser C, Cichowski K. The RasGAP gene, RASAL2, is a tumor and metastasis suppressor. Cancer Cell. 2013 Sep 9;24(3):365-78. doi: 10.1016/j.ccr.2013.08.004. PMID: 24029233 PMCID: PMC3822334


Paik EJ, Mahony S, White RM, Price EN, Dibiase A, Dorjsuren B, Mosimann C, Davidson AJ, Gifford D, Zon LI. A cdx4-sall4 regulatory module controls the transition from mesoderm formation to embryonic hematopoiesis. Stem Cell Reports. 2013 Nov 7;1(5):425-36. doi: 10.1016/j.stemcr.2013.10.001. eCollection 2013. PMID: 24286030 PMCID: PMC3841246


Pasquina LW, Santa Maria JP, Walker S. Teichoic acid biosynthesis as an antibiotic target. Curr Opin Microbiol. 2013 Oct;16(5):531-7. doi: 10.1016/j.mib.2013.06.014. Epub 2013 Jul 31. PMID: 23916223 PMCID: PMC3834221


Perry KJ, Higgins DE. A differential fluorescence-based genetic screen identifies Listeria monocytogenes determinants required for intracellular replication. J Bacteriol. 2013 Aug;195(15):3331-40. doi: 10.1128/JB.00210-13. Epub 2013 May 17. PMID: 23687268 PMCID: PMC3719552  read article


Snuderl M, Batista A, Kirkpatrick ND, Ruiz de Almodovar C, Riedemann L, Walsh EC, Anolik R, Huang Y, Martin JD, Kamoun W, Knevels E, Schmidt T, Farrar CT, Vakoc BJ, Mohan N, Chung E, Roberge S, Peterson T, Bais C, Zhelyazkova BH, Yip S, Hasselblatt M, Rossig C, Niemeyer E, Ferrara N, Klagsbrun M, Duda DG, Fukumura D, Xu L, Carmeliet P, Jain RK. Targeting placental growth factor/neuropilin 1 pathway inhibits growth and spread of medulloblastoma. Cell. 2013 Feb 28;152(5):1065-76. doi: 10.1016/j.cell.2013.01.036. PMID: 23452854 PMCID: PMC3587980 read article


Miller PG, Al-Shahrour F, Hartwell KA, Chu LP, Järås M, Puram RV, Puissant A, Callahan KP, Ashton J, McConkey ME, Poveromo LP, Cowley GS, Kharas MG, Labelle M, Shterental S, Fujisaki J, Silberstein L, Alexe G, Al-Hajj MA, Shelton CA, Armstrong SA, Root DE, Scadden DT, Hynes RO, Mukherjee S, Stegmaier K, Jordan CT, Ebert BL. In Vivo RNAi screening identifies a leukemia-specific dependence on integrin beta 3 signaling. Cancer Cell. 2013 Jul 8;24(1):45-58. doi: 10.1016/j.ccr.2013.05.004. Epub 2013 Jun 13. PMID: 23770013 PMCID: PMC3746037


Hartwell KA, Miller PG, Mukherjee S, Kahn AR, Stewart AL, Logan DJ, Negri JM, Duvet M, Järås M, Puram R, Dancik V, Al-Shahrour F, Kindler T, Tothova Z, Chattopadhyay S, Hasaka T, Narayan R, Dai M, Huang C, Shterental S, Chu LP, Haydu JE, Shieh JH, Steensma DP, Munoz B, Bittker JA, Shamji AF, Clemons PA, Tolliday NJ, Carpenter AE, Gilliland DG, Stern AM, Moore MA, Scadden DT, Schreiber SL, Ebert BL, Golub TR. Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nat Chem Biol. 2013 Dec;9(12):840-8. doi: 10.1038/nchembio.1367. Epub 2013 Oct 27. PMID: 24161946 PMCID: PMC4009363


Puram SV, Bonni A. Cell-intrinsic drivers of dendrite morphogenesis. Development. 2013 Dec;140(23):4657-71. doi: 10.1242/dev.087676. PMID: 24255095 PMCID: PMC3833426


Puram SV, Kim AH, Park HY, Anckar J, Bonni A. The ubiquitin receptor S5a/Rpn10 links centrosomal proteasomes with dendrite development in the mammalian brain. Cell Rep. 2013 Jul 11;4(1):19-30. doi: 10.1016/j.celrep.2013.06.006. Epub 2013 Jul 3. PMID: 23831032


Abyzov A1, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L; 1000 Genomes Project Consortium, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Res. 2013 Dec;23(12):2042-52. doi: 10.1101/gr.154625.113. Epub 2013 Sep 11. PMID: 24026178 PMCID: PMC3847774
 read article


Shyh-Chang N, Locasale JW, Lyssiotis CA, Zheng Y, Teo RY, Ratanasirintrawoot S, Zhang J, Onder T, Unternaehrer JJ, Zhu H, Asara JM, Daley GQ, Cantley LC. Influence of threonine metabolism on S-adenosylmethionine and histone methylation. Science. 2013 Jan 11;339(6116):222-6. doi: 10.1126/science.1226603. Epub 2012 Nov 1. PMID: 23118012 PMCID: PMC3652341 read article


Ricoult SJ, Manning BD. The multifaceted role of mTORC1 in the control of lipid metabolism. EMBO Rep. 2013 Mar 1;14(3):242-51. doi: 10.1038/embor.2013.5. Epub 2012 Feb 12. PMID: 23399656 PMCID: PMC3589096 read article


Howell JJ, Ricoult SJ, Ben-Sahra I, Manning BD. A growing role for mTOR in promoting anabolic metabolism. Biochem Soc Trans. 2013 Aug;41(4):906-12. doi: 10.1042/BST20130041. PMID: 23863154


Praetorius C, Grill C, Stacey SN, Metcalf AM, Gorkin DU, Robinson KC, Van Otterloo E, Kim RS, Bergsteinsdottir K, Ogmundsdottir MH, Magnusdottir E, Mishra PJ, Davis SR, Guo T, Zaidi MR, Helgason AS, Sigurdsson MI, Meltzer PS, Merlino G, Petit V, Larue L, Loftus SK, Adams DR, Sobhiafshar U, Emre NC, Pavan WJ, Cornell R, Smith AG, McCallion AS, Fisher DE, Stefansson K, Sturm RA, Steingrimsson E. A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway. Cell. 2013 Nov 21;155(5):1022-33. doi: 10.1016/j.cell.2013.10.022. PMID: 24267888 PMCID: PMC3873608


White R, Rose K, Zon L. Zebrafish cancer: the state of the art and the path forward. Nat Rev Cancer. 2013 Sep;13(9):624-36. doi: 10.1038/nrc3589. PMID: 23969693


Liu L, Sabo A, Neale BM, Nagaswamy U, Stevens C, Lim E, Bodea CA, Muzny D, Reid JG, Banks E, Coon H, Depristo M, Dinh H, Fennel T, Flannick J, Gabriel S, Garimella K, Gross S, Hawes A, Lewis L, Makarov V, Maguire J, Newsham I, Poplin R, Ripke S, Shakir K, Samocha KE, Wu Y, Boerwinkle E, Buxbaum JD, Cook EH Jr, Devlin B, Schellenberg GD, Sutcliffe JS, Daly MJ, Gibbs RA, Roeder K. Analysis of rare, exonic variation amongst subjects with autism spectrum disorders and population controls. PLoS Genet. 2013 Apr;9(4):e1003443. doi: 10.1371/journal.pgen.1003443. Epub 2013 Apr 11. PMID: 23593035 PMCID: PMC3623759 read article


Verzi MP, Shin H, San Roman AK, Liu XS, Shivdasani RA. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding. Mol Cell Biol. 2013 Jan;33(2):281-92. doi: 10.1128/MCB.01185-12. Epub 2012 Nov 5. PMID: 23129810 PMCID: PMC3554120 read article


Sarkar A, Hochedlinger K. The sox family of transcription factors: versatile regulators of stem and progenitor cell fate. Cell Stem Cell. 2013 Jan 3;12(1):15-30. doi: 10.1016/j.stem.2012.12.007. PMID: 23290134 PMCID: PMC3608206 read article


Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP. ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res. 2013 Apr;23(4):665-78. doi: 10.1101/gr.143586.112. Epub 2012 Dec 26. PMID: 23269662 PMCID: PMC3613583 read article


Emerling BM, Hurov JB, Poulogiannis G, Tsukazawa KS, Choo-Wing R, Wulf GM, Bell EL, Shim HS, Lamia KA, Rameh LE, Bellinger G, Sasaki AT, Asara JM, Yuan X, Bullock A, Denicola GM, Song J, Brown V, Signoretti S, Cantley LC. Depletion of a putatively druggable class of phosphatidylinositol kinases inhibits growth of p53-null tumors. Cell. 2013 Nov 7;155(4):844-57. doi: 10.1016/j.cell.2013.09.057. PMID: 24209622


Tabebordbar M, Wang ET, Wagers AJ. Skeletal muscle degenerative diseases and strategies for therapeutic muscle repair. Annu Rev Pathol. 2013 Jan 24;8:441-75. doi: 10.1146/annurev-pathol-011811-132450. Epub 2012 Nov 1. PMID: 23121053


Xu C, Tabebordbar M, Iovino S, Ciarlo C, Liu J, Castiglioni A, Price E, Liu M, Barton ER, Kahn CR, Wagers AJ, Zon LI. A zebrafish embryo culture system defines factors that promote vertebrate myogenesis across species. Cell. 2013 Nov 7;155(4):909-21. doi: 10.1016/j.cell.2013.10.023. PMID: 24209627 PMCID: PMC3902670


Tang JC, Szikra T, Kozorovitskiy Y, Teixiera M, Sabatini BL, Roska B, Cepko CL. A nanobody-based system using fluorescent proteins as scaffolds for cell-specific gene manipulation. Cell. 2013 Aug 15;154(4):928-39. doi: 10.1016/j.cell.2013.07.021. PMID: 23953120


Yen J, White RM, Wedge DC, Van Loo P, de Ridder J, Capper A, Richardson J, Jones D, Raine K, Watson IR, Wu CJ, Cheng J, Martincorena I, Nik-Zainal S, Mudie L, Moreau Y, Marshall J, Ramakrishna M, Tarpey P, Shlien A, Whitmore I, Gamble S, Latimer C, Langdon E, Kaufman C, Dovey M, Taylor A, Menzies A, McLaren S, O'Meara S, Butler A, Teague J, Lister J, Chin L, Campbell P, Adams DJ, Zon LI, Patton EE, Stemple DL, Futreal PA. The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models. Genome Biol. 2013;14(10):R113. PMID: 24148783


Choi S, Chatzigeorgiou M, Taylor KP, Schafer WR, Kaplan JM. Analysis of NPR-1 reveals a circuit mechanism for behavioral quiescence in C. elegans. Neuron. 2013 Jun 5;78(5):869-80. doi: 10.1016/j.neuron.2013.04.002. PMID: 23764289 PMCID: PMC3683153


Thomas MP, Lieberman J. Live or let die: posttranscriptional gene regulation in cell stress and cell death. Immunol Rev. 2013 May;253(1):237-52. doi: 10.1111/imr.12052. PMID: 23550650


Shyh-Chang N1, Zhu H, Yvanka de Soysa T, Shinoda G, Seligson MT, Tsanov KM, Nguyen L, Asara JM, Cantley LC, Daley GQ. Lin28 enhances tissue repair by reprogramming cellular metabolism. Cell. 2013 Nov 7;155(4):778-92. doi: 10.1016/j.cell.2013.09.059. PMID: 24209617 PMCID: PMC3917449


Tseng WA, Thein T, Kinnunen K, Lashkari K, Gregory MS, D'Amore PA, Ksander BR. NLRP3 inflammasome activation in retinal pigment epithelial cells by lysosomal destabilization: implications for age-related macular degeneration. Invest Ophthalmol Vis Sci. 2013 Jan 7;54(1):110-20. doi: 10.1167/iovs.12-10655. PMID: 23221073 PMCID: PMC3544415 read article


Xu J, Bauer DE, Kerenyi MA, Vo TD, Hou S, Hsu YJ, Yao H, Trowbridge JJ, Mandel G, Orkin SH. Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6518-23. doi: 10.1073/pnas.1303976110. Epub 2013 Apr 1. PMID: 23576758 PMCID: PMC3631619 read article


Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R. Pan-cancer patterns of somatic copy number alteration. Nat Genet. 2013 Sep 26;45(10):1134-1140. doi: 10.1038/ng.2760. [Epub ahead of print] PMID: 24071852 PMCID: PMC3966983


Wang SR, Carmichael H, Andrew SF, Miller TC, Moon JE, Derr MA, Hwa V, Hirschhorn JN, Dauber A. Large-scale pooled next-generation sequencing of 1077 genes to identify genetic causes of short stature. J Clin Endocrinol Metab. 2013 Aug;98(8):E1428-37. doi: 10.1210/jc.2013-1534. Epub 2013 Jun 14. PMID: 23771920 PMCID: PMC3733853


Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G. Optimization of scarless human stem cell genome editing. Nucleic Acids Res. 2013 Oct;41(19):9049-61. doi: 10.1093/nar/gkt555. Epub 2013 Jul 31. PMID: 23907390 PMCID: PMC3799423 read article


Walker SR, Nelson EA, Yeh JE, Pinello L, Yuan GC, Frank DA. STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6. Mol Cell Biol. 2013 Aug;33(15):2879-90. doi: 10.1128/MCB.01620-12. Epub 2013 May 28. PMID: 23716595 PMCID: PMC3719667 read article


Yeh JE, Toniolo P2, Frank DA. JAK2-STAT5 signaling: A novel mechanism of resistance to targeted PI3K/mTOR inhibition. JAKSTAT. 2013 Oct 1;2(4):e24635. doi: 10.4161/jkst.24635. Epub 2013 Apr 15. PMID: 24470973 PMCID: PMC3891630 read article


Yeh JE, Toniolo PA, Frank DA. Targeting transcription factors: promising new strategies for cancer therapy. Curr Opin Oncol. 2013 Nov;25(6):652-8. doi: 10.1097/01.cco.0000432528.88101.1a. PMID: 24048019


Yu Y, Munger K. Human papillomavirus type 16 E7 oncoprotein inhibits the anaphase promoting complex/cyclosome activity by dysregulating EMI1 expression in mitosis. Virology. 2013 Nov;446(1-2):251-9. doi: 10.1016/j.virol.2013.08.013. Epub 2013 Sep 5. PMID: 24074588 PMCID: PMC3799973


top

2012


Adamson B, Smogorzewska A, Sigoillot FD, King RW, Elledge SJ. A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nat Cell Biol. 2012 Feb 19;14(3):318-28. doi: 10.1038/ncb2426. PMID: 22344029 PMCID: PMC3290715 read article


Sigoillot FD, Lyman S, Huckins JF, Adamson B, Chung E, Quattrochi B, King RW. A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nat Methods. 2012 Feb 19;9(4):363-6. doi: 10.1038/nmeth.1898. PMID: 22343343 PMCID: PMC3482495 read article


Ciccia A, Nimonkar AV, Hu Y, Hajdu I, Achar YJ, Izhar L, Petit SA, Adamson B, Yoon JC, Kowalczykowski SC, Livingston DM, Haracska L, Elledge SJ. Polyubiquitinated PCNA recruits the ZRANB3 translocase to maintain genomic integrity after replication stress. Mol Cell. 2012 Aug 10;47(3):396-409. doi: 10.1016/j.molcel.2012.05.024. Epub 2012 Jun 14. PMID: 22704558 PMCID: PMC3613862 read article


Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, Dewerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV, Silver PA. A BioBrick compatible strategy for genetic modification of plants. J Biol Eng. 2012 Jun 20;6(1):8. doi: 10.1186/1754-1611-6-8. PMID: 22716313 PMCID: PMC3537565 read article


Dulak AM, Schumacher SE, van Lieshout J, Imamura Y, Fox C, Shim B, Ramos AH, Saksena G, Baca SC, Baselga J, Tabernero J, Barretina J, Enzinger PC, Corso G, Roviello F, Lin L, Bandla S, Luketich JD, Pennathur A, Meyerson M, Ogino S, Shivdasani RA, Beer DG, Godfrey TE, Beroukhim R, Bass AJ. Gastrointestinal adenocarcinomas of the esophagus, stomach, and colon exhibit distinct patterns of genome instability and oncogenesis. Cancer Res. 2012 Sep 1;72(17):4383-93. Epub 2012 Jul 2. PMID: 22751462 PMCID: PMC3432726 read article


Baca SC, Garraway LA. The genomic landscape of prostate cancer. Front Endocrinol (Lausanne). 2012 May 16;3:69. doi: 10.3389/fendo.2012.00069. eCollection 2012. PMID: 22649426 PMCID: PMC3355898 read article


Hafler BP, Surzenko N, Beier KT, Punzo C, Trimarchi JM, Kong JH, Cepko CL. Transcription factor Olig2 defines subpopulations of retinal progenitor cells biased toward specific cell fates. Proc Natl Acad Sci U S A. 2012 May 15;109(20):7882-7. Epub 2012 Apr 27. PubMed PMID: 22543161; PubMed Central PMCID: PMC3356608.


Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21301-6. doi: 10.1073/pnas.1213818110. Epub 2012 Dec 11. PMID: 23236188 PMCID: PMC3535588 read article


Bowen ME, Henke K, Siegfried KR, Warman ML, Harris MP. (2012) Efficient mapping and cloning of mutations in zebrafish by low-coverage whole-genome sequencing. Genetics 190(3):1017-24. PMCID:PMC3296239.


Kurek KC, Luks VL, Ayturk UM, Alomari AI, Fishman SJ, Spencer SA, Mulliken JB, Bowen ME, Yamamoto GL, Kozakewich HP, Warman ML. (2012) Somatic mosaic activating mutations in PIK3CA cause CLOVES syndrome. Am J Hum Genet 90(6):1108-15. PMCID:PMC3370283.


Boyle PM, Silver PA. Parts plus pipes: synthetic biology approaches to metabolic engineering. Metab Eng. 2012 May;14(3):223-32. doi: 10.1016/j.ymben.2011.10.003. Epub 2011 Oct 25. PMID: 22037345 PMCID: PMC3293987 read article


Agapakis CM, Boyle PM, Silver PA. Natural strategies for the spatial optimization of metabolism in synthetic biology. Nat Chem Biol. 2012 May 17;8(6):527-35. doi: 10.1038/nchembio.975. PMID: 22596204


Ray, R.S., Corcoran, A.E., Brust, R.B., Nattie, E., Dymecki, S.M. Egr2-neurons control the adult respiratory response to hypercapnia. Brain Res. 2013 May 20;1511:115-25. doi: 10.1016/j.brainres.2012.12.017. Epub 2012 Dec 19. PMID: 23261662 PMCID: PMC3947592


Engleka, K., Manderfield, L., Brust, R.B., Lu, M.M., Dymecki, S.M., and Epstein J.A. Islet1 Derivatives in the Heart are of Both Neural Crest and Second Heard Field Origin. Circ Res. 2012 Mar 30;110(7):922-6. doi: 10.1161/CIRCRESAHA.112.266510. Epub 2012 Mar 6. PMID: 22394517 PMCID: PMC3355870 read article


Burrill DR, Inniss MC, Boyle PM, Silver PA. Synthetic memory circuits for tracking human cell fate. Genes Dev. 2012 Jul 1;26(13):1486-97. doi: 10.1101/gad.189035.112. PMID: 22751502 PMCID: PMC3403016 read article


Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, Dewerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV, Silver PA. A BioBrick compatible strategy for genetic modification of plants. J Biol Eng. 2012 Jun 20;6(1):8. doi: 10.1186/1754-1611-6-8. PMID: 22716313 PMCID: PMC3537565 read article


Cooney JD; Hildick-Smith GJ; Shafizadeh E; McBride PF; Carroll KJ; Anderson H; Shaw GC; Tamplin OK; Branco DS; Dalton AJ; Shah DI; Wong C; Gallagher PG; Zon LI; North TE; Paw, BH. Teleost growth factor idendependence (gfi) genes differentially regulate successive waves of hematopoiesis. Dev Biol. 2013 Jan 15;373(2):431-41. doi: 10.1016/j.ydbio.2012.08.015. Epub 2012 Aug 29. PMID: 22960038 PMCID: PMC3532562
 read article


Chan YK, Huang IC, Farzan M. IFITM proteins restrict antibody-dependent enhancement of dengue virus infection. PLoS One. 2012;7(3):e34508. doi: 10.1371/journal.pone.0034508. Epub 2012 Mar 30. PMID: 22479637; PMCID: PMC3316688.  read article


Lui JC, Nilsson O, Chan Y, Palmer CD, Andrade AC, Hirschhorn JN, Baron J. Synthesizing genome-wide association studies and expression microarray reveals novel genes that act in the human growth plate to modulate height. Hum Mol Genet. 2012 Dec 1;21(23):5193-201. doi: 10.1093/hmg/dds347. Epub 2012 Aug 21. PMID: 22914739 PMCID: PMC3490510
 read article


Cherry AB, Daley GQ. Reprogramming cellular identity for regenerative medicine. Cell. 2012 Mar 16;148(6):1110-22. doi: 10.1016/j.cell.2012.02.031. PMID: 22424223; PMCID: PMC3354575.  read article


Chiang CW, Liu CT, Lettre G, Lange LA, Jorgensen NW, Keating BJ, Vedantam S, Nock NL, Franceschini N, Reiner AP, Demerath EW, Boerwinkle E, Rotter JI, Wilson JG, North KE, Papanicolaou GJ, Cupples LA, Murabito JM, Consortium G, Hirschhorn JN. Ultraconserved Elements in the Human Genome: Association and Transmission Analyses of Highly Constrained SNPs. Genetics. 2012 Jun 19. [Epub ahead of print] PubMed PMID: 22714408.


Stadtfeld, M., Apostolou, E., Ferrari, F., Choi, J., Walsh, R.M., Chen, T., Oi, S., Kim, S.Y., Bestor, T., Shioda, T., et al. (2012). Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nat Genet. 2012 Mar 4;44(4):398-405, S1-2. doi: 10.1038/ng.1110. PMID: 22387999 PMCID: PMC3538378 read article


He A, Ma Q, Cao J, von Gise A, Zhou P, Xie H, Zhang B, Hsing M, Christodoulou DC, Cahan P, Daley GQ, Kong SW, Orkin SH, Seidman CE, Seidman JG, Pu WT. Polycomb repressive complex 2 regulates normal development of the mouse heart. Circ Res. 2012 Feb 3;110(3):406-15. Epub 2011 Dec 8. PubMed PMID: 22158708; PubMed Central PMCID: PMC3282145.


Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, Ma C, Barbara A, Veenstra GJ, Xu G, Kaiser UB, Liu XS, Sugrue SP, He X, Min J, Kato Y, Shi YG. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development. Cell. 2012 Dec 7;151(6):1200-13. doi: 10.1016/j.cell.2012.11.014. PMID: 23217707 PMCID: PMC3705565 read article


Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM. Genome-scale promoter engineering by coselection MAGE. Nat Methods. 2012 Jun;9(6):591-3. doi: 10.1038/nmeth.1971. Epub 2012 Apr 8. PubMed PMID: 22484848 PMCID: PMC3428217 read article


Folco EG, Lee CS, Dufu K, Yamazaki T, Reed R. The proteins PDIP3 and ZC11A associate with the human TREX complex in an ATP-dependent manner and function in mRNA export. PLoS One. 2012;7(8):e43804. doi: 10.1371/journal.pone.0043804. Epub 2012 Aug 23. PMID: 22928037 PMCID: PMC3426524 read article


Silveira-Neto AP, Leal LF, Emerman AB, Henderson KD, Piskounova E, Henderson BE, Gregory RI, Silveira LF, Hirschhorn JN, Nguyen TT, Beneduzzi D, Tusset C, Reis AC, Brito VN, Mendonca BB, Palmert MR, Antonini SR, Latronico AC. Absence of functional LIN28B mutations in a large cohort of patients with idiopathic central precocious puberty. Horm Res Paediatr. 2012;78(3):144-50. doi: 10.1159/000342212. Epub 2012 Sep 6. PMID: 22964795. PMCID: PMC3526815. read article


Finley LW, Lee J, Souza A, Rowe G, Clish CB, Arany Z, Haigis MC. Skeletal muscle transcriptional coactivator PGC-1α mediates mitochondrial, but not metabolic, changes during calorie restriction. Proc Natl Acad Sci USA 2012 Feb 3. PMCID: PMC3286952


Ford KM, D'Amore PA. Molecular regulation of vascular endothelial growth factor expression in the retinal pigment epithelium. Mol Vis. 2012;18:519-27. Epub 2012 Mar 1. PMID: 22419845 PMCID: PMC3298425 read article


Ford KM, Saint-Geniez M, Walshe TE, D'Amore PA. Expression and role of VEGF--a in the ciliary body. Invest Ophthalmol Vis Sci. 2012 Nov 7;53(12):7520-7. doi: 10.1167/iovs.12-10098. PMID: 23081980 PMCID: PMC3493183 read article


Garnaas MK, Cutting CC, Meyers A, Kelsey PB Jr, Harris JM, North TE, Goessling W. Rargb regulates organ laterality in a zebrafish model of right atrial isomerism. Dev Biol. 2012 Dec 15;372(2):178-89. doi: 10.1016/j.ydbio.2012.09.001. Epub 2012 Sep 13.PMID: 22982668 PMCID: PMC3697125
 read article


Pattaro C1, Köttgen A, Teumer A, Garnaas M, Böger CA, Fuchsberger C, Olden M, Chen MH, Tin A, Taliun D, Li M, Gao X, Gorski M, Yang Q, Hundertmark C, Foster MC, O'Seaghdha CM, Glazer N, Isaacs A, Liu CT, Smith AV, O'Connell JR, Struchalin M, Tanaka T, Li G, Johnson AD, Gierman HJ, Feitosa M, Hwang SJ, Atkinson EJ, Lohman K, Cornelis MC, Johansson Å, Tönjes A, Dehghan A, Chouraki V, Holliday EG, Sorice R, Kutalik Z, Lehtimäki T, Esko T, Deshmukh H, Ulivi S, Chu AY, Murgia F, Trompet S, Imboden M, Kollerits B, Pistis G; CARDIoGRAM Consortium; ICBP Consortium; CARe Consortium; Wellcome Trust Case Control Consortium 2 (WTCCC2), Harris TB, Launer LJ, Aspelund T, Eiriksdottir G, Mitchell BD, Boerwinkle E, Schmidt H, Cavalieri M, Rao M, Hu FB, Demirkan A, Oostra BA, de Andrade M, Turner ST, Ding J, Andrews JS, Freedman BI, Koenig W, Illig T, Döring A, Wichmann HE, Kolcic I, Zemunik T, Boban M, Minelli C, Wheeler HE, Igl W, Zaboli G, Wild SH, Wright AF, Campbell H, Ellinghaus D, Nöthlings U, Jacobs G, Biffar R, Endlich K, Ernst F, Homuth G, Kroemer HK, Nauck M, Stracke S, Völker U, Völzke H, Kovacs P, Stumvoll M, Mägi R, Hofman A, Uitterlinden AG, Rivadeneira F, Aulchenko YS, Polasek O, Hastie N, Vitart V, Helmer C, Wang JJ, Ruggiero D, Bergmann S, Kähönen M, Viikari J, Nikopensius T, Province M, Ketkar S, Colhoun H, Doney A, Robino A, Giulianini F, Krämer BK, Portas L, Ford I, Buckley BM, Adam M, Thun GA, Paulweber B, Haun M, Sala C, Metzger M, Mitchell P, Ciullo M, Kim SK, Vollenweider P, Raitakari O, Metspalu A, Palmer C, Gasparini P, Pirastu M, Jukema JW, Probst-Hensch NM, Kronenberg F, Toniolo D, Gudnason V, Shuldiner AR, Coresh J, Schmidt R, Ferrucci L, Siscovick DS, van Duijn CM, Borecki I, Kardia SL, Liu Y, Curhan GC, Rudan I, Gyllensten U, Wilson JF, Franke A, Pramstaller PP, Rettig R, Prokopenko I, Witteman JC, Hayward C, Ridker P, Parsa A, Bochud M, Heid IM, Goessling W, Chasman DI, Kao WH, Fox CS. Genome-wide association and functional follow-up reveals new loci for kidney function. PLoS Genet. 2012;8(3):e1002584. doi: 10.1371/journal.pgen.1002584. Epub 2012 Mar 29. PMID: 22479191 PMCID: PMC3315455
 read article


Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin-Tse CA, Cooney JD, Anderson H, King MJ, Stottmann RW, Garnaas MK, Ha S, Drummond IA, Paw BH, North TE, Beier DR, Goessling W, Sunyaev SR. Mutation mapping and identification by whole-genome sequencing. Genome Res. 2012 Aug;22(8):1541-8. doi: 10.1101/gr.135541.111. Epub 2012 May 3. PMID: 22555591 PMCID: PMC3409267 read article


Shaik S, Nucera C, Inuzuka H, Gao D, Garnaas M, Frechette G, Harris L, Wan L, Fukushima H, Husain A, Nose V, Fadda G, Sadow PM, Goessling W, North T, Lawler J, Wei W. SCF(β-TRCP) suppresses angiogenesis and thyroid cancer cell migration by promoting ubiquitination and destruction of VEGF receptor 2. J Exp Med. 2012 Jul 2;209(7):1289-307. doi: 10.1084/jem.20112446. Epub 2012 Jun 18. PMID: 22711876
PMCID: PMC3405505
 read article


Derr ND1, Goodman BS, Jungmann R, Leschziner AE, Shih WM, Reck-Peterson SL. Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold. Science. 2012 Nov 2;338(6107):662-5. doi: 10.1126/science.1226734. Epub 2012 Oct 11. PMID: 23065903 PMCID: PMC3840815 read article


Goodman BS, Derr ND, Reck-Peterson SL. Engineered, harnessed, and hijacked: synthetic uses for cytoskeletal systems. Trends Cell Biol. 2012 Dec;22(12):644-52. doi: 10.1016/j.tcb.2012.09.005. Epub 2012 Oct 8. PMID: 23059001 PMCID: PMC3505249 read article


Qiu W, Derr ND, Goodman BS, Villa E, Wu D, Shih W, Reck-Peterson SL. Dynein achieves processive motion using both stochastic and coordinated stepping. Nat Struct Mol Biol. 2012 Jan 8;19(2):193-200. doi: 10.1038/nsmb.2205. PMID: 22231401 PMCID: PMC3272163 read article


Chiang WC, Tishkoff DX, Yang B, Wilson-Grady J, Yu X, Mazer T, Eckersdorff M, Gygi SP, Lombard DB, Hsu AL. C. elegans SIRT6/7 homolog SIR-2.4 promotes DAF-16 relocalization and function during stress. PLoS Genet. 2012 Sep;8(9):e1002948. doi: 10.1371/journal.pgen.1002948. Epub 2012 Sep 13. PMID: 23028355 PMCID: PMC3441721 read article


Haas JT, Miao J, Chanda D, Wang Y, Zhao E, Haas ME, Hirschey M, Vaitheesvaran B, Farese RV Jr, Kurland IJ, Graham M, Crooke R, Foufelle F, Biddinger SB. Hepatic Insulin Signaling Is Required for Obesity-Dependent Expression of SREBP-1c mRNA but Not for Feeding-Dependent Expression. Cell Metab. 2012 Jun 6;15(6):873-84. doi: 10.1016/j.cmet.2012.05.002. PMID: 22682225 PMCID: PMC3383842.  read article


Holoch D, Moazed D. RNAi in fission yeast finds new targets and new ways of targeting at the nuclear periphery. Genes Dev. 2012 Apr 15;26(8):741-5. doi: 10.1101/gad.191155.112. PMID: 22508721 PMCID: PMC3337448 read article


Blum B, Hrvatin SS, Schuetz C, Bonal C, Rezania A, Melton DA. Functional beta-cell maturation is marked by an increased glucose threshold and by expression of urocortin 3. Nat Biotechnol. 2012 Feb 26;30(3):261-4. doi: 10.1038/nbt.2141. PubMed PMID: 22371083.


Hu X, Daly M. What have we learned from six years of GWAS in autoimmune diseases, and what is next? Curr Opin Immunol. 2012 Oct;24(5):571-5. doi: 10.1016/j.coi.2012.09.001. Epub 2012 Sep 24. PMID: 23017373


Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D'Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Gearry R, Georges M, Gieger C, Glas J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TH, Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W, Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M, Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber S, Simms LA, Sventoraityte J, Targan SR, Taylor KD, Tremelling M, Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier RJ, Zeissig S, Zhang B, Zhang CK, Zhao H; International IBD Genetics Consortium (IIBDGC), Silverberg MS, Annese V, Hakonarson H, Brant SR, Radford-Smith G, Mathew CG, Rioux JD, Schadt EE, Daly MJ, Franke A, Parkes M, Vermeire S, Barrett JC, Cho JH. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012 Nov 1;491(7422):119-24. doi: 10.1038/nature11582. PMID 23128233 PMCID: PMC3491803 read article


Eyre S, Bowes J, Diogo D, Lee A, Barton A, Martin P, Zhernakova A, Stahl E, Viatte S, McAllister K, Amos CI, Padyukov L, Toes RE, Huizinga TW, Wijmenga C, Trynka G, Franke L, Westra HJ, Alfredsson L, Hu X, Sandor C, de Bakker PI, Davila S, Khor CC, Heng KK, Andrews R, Edkins S, Hunt SE, Langford C, Symmons D; Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate; Wellcome Trust Case Control Consortium, Concannon P, Onengut-Gumuscu S, Rich SS, Deloukas P, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Ärlsetig L, Martin J, Rantapää-Dahlqvist S, Plenge RM, Raychaudhuri S, Klareskog L, Gregersen PK, Worthington J. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat Genet. 2012 Dec;44(12):1336-40. doi: 10.1038/ng.2462. Epub 2012 Nov 11. PMID: 23143596 PMCID: PMC3605761 read article


Zhang W, Mendoza MC, Pei X, Ilter D, Mahoney SJ, Zhang Y, Ma D, Blenis J, Wang Y. Down-regulation of CMTM8 induces epithelial-to-mesenchymal transition-like changes via c-MET/extracellular signal-regulated kinase (ERK) signaling. J Biol Chem. 2012 Apr 6;287(15):11850-8. doi: 10.1074/jbc.M111.258236. Epub 2012 Feb 15. PMID: 22337876 PMCID: PMC3320933 read article


Burrill DR, Inniss MC, Boyle PM, Silver PA. Synthetic memory circuits for tracking human cell fate. Genes Dev. 2012 Jul 1;26(13):1486-97. doi: 10.1101/gad.189035.112.
PMID: 22751502 PMCID: PMC3403016
 read article


Boyle PM, Burrill DR, Inniss MC, Agapakis CM, Deardon A, Dewerd JG, Gedeon MA, Quinn JY, Paull ML, Raman AM, Theilmann MR, Wang L, Winn JC, Medvedik O, Schellenberg K, Haynes KA, Viel A, Brenner TJ, Church GM, Shah JV, Silver PA. A BioBrick compatible strategy for genetic modification of plants. J Biol Eng. 2012 Jun 20;6(1):8. doi: 10.1186/1754-1611-6-8. PMID: 22716313 PMCID: PMC3537565 read article


Rajani DK, Walch M, Martinvalet D, Thomas MP, Lieberman J. Alterations in RNA processing during immune-mediated programmed cell death. Proc Natl Acad Sci U S A. 2012 May 29;109(22):8688-93. doi: 10.1073/pnas.1201327109. Epub 2012 May 15. PMID: 22589304 PMCID: PMC3365155 read article


Collins B, Kane EA, Reeves DC, Akabas MH, Blau J. Balance of activity between LN(v)s and glutamatergic dorsal clock neurons promotes robust circadian rhythms in Drosophila. Neuron. 2012 May 24;74(4):706-18. doi: 10.1016/j.neuron.2012.02.034. PMID: 22632728 PMCID: PMC3361687 read article


Gershow M, Berck M, Mathew D, Luo L, Kane EA, Carlson JR, Samuel AD. Controlling airborne cues to study small animal navigation. Nat Methods. 2012 Jan 15;9(3):290-6. doi: 10.1038/nmeth.1853. PMID: 22245808 PMCID: PMC3513333
 read article


Cooke VG, LeBleu VS, Keskin D, Khan Z, O'Connell JT, Teng Y, Duncan MB, Xie L, Maeda G, Vong S, Sugimoto H, Rocha RM, Damascena A, Brentani RR, Kalluri R. Pericyte depletion results in hypoxia-associated epithelial-to-mesenchymal transition and metastasis mediated by met signaling pathway. Cancer Cell. 2012 Jan 17;21(1):66-81. doi: 10.1016/j.ccr.2011.11.024. PMID: 22264789 PMCID: PMC3999522 read article


Wood KC, Konieczkowski DJ, Johannessen CM, Boehm JS, Tamayo P, Botvinnik OB, Mesirov JP, Hahn WC, Root DE, Garraway LA, Sabatini DM. MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma. Sci Signal. 2012 May 15;5(224):rs4. doi: 10.1126/scisignal.2002612. PMID: 22589389 PMCID: PMC3498828 read article


Kung JT, Gelbart ME. Getting a head start: the importance of personal genetics education in high schools. Yale J Biol Med. 2012 Mar;85(1):87-92. Epub 2012 Mar 29. PMID: 22461746 PMCID: PMC3313542 read article


Tukachinsky H, Kuzmickas RP, Jao CY, Liu J, Salic A. Dispatched and scube mediate the efficient secretion of the cholesterol-modified hedgehog ligand. Cell Rep. 2012 Aug 30;2(2):308-20. doi: 10.1016/j.celrep.2012.07.010. Epub 2012 Aug 16. PMID: 22902404 PMCID: PMC3682496 read article


Kwiatkowski N, Deng X, Wang J, Tan L, Villa F, Santaguida S, Huang HC, Mitchison T, Musacchio A, Gray N. Selective aurora kinase inhibitors identified using a taxol-induced checkpoint sensitivity screen. ACS Chem Biol. 2012 Jan 20;7(1):185-96. doi: 10.1021/cb200305u. Epub 2011 Oct 21. PMID: 21992004 PMCID: PMC3262907 read article


Driscoll B, Kikuchi A, Lau AN, Lee J, Reddy R, Jesudason E, Kim CF, Warburton D. Isolation and characterization of distal lung progenitor cells. Methods Mol Biol. 2012;879:109-22. doi: 10.1007/978-1-61779-815-3_7. PMID: 22610556 PMCID: PMC3710291 read article


Lau AN, Goodwin M, Kim CF, Weiss DJ. Stem cells and regenerative medicine in lung biology and diseases. Mol Ther. 2012 Jun;20(6):1116-30. doi: 10.1038/mt.2012.37. Epub 2012 Mar 6. PMID: 22395528 PMCID: PMC3369292 read article


Tropea KA, Leder E, Aslam M, Lau AN, Raiser DM, Lee JH, Balasubramaniam V, Fredenburgh LE, Alex Mitsialis S, Kourembanas S, Kim CF. Bronchioalveolar stem cells increase after mesenchymal stromal cell treatment in a mouse model of bronchopulmonary dysplasia. Am J Physiol Lung Cell Mol Physiol. 2012 May;302(9):L829-37. doi: 10.1152/ajplung.00347.2011. Epub 2012 Feb 10. PMID: 22328358 PMCID: PMC3362163. read article


Sugimoto H, LeBleu VS, Bosukonda D, Keck P, Taduri G, Bechtel W, Okada H, Carlson W Jr, Bey P, Rusckowski M, Tampe B, Tampe D, Kanasaki K, Zeisberg M, Kalluri R. Activin-like kinase 3 is important for kidney regeneration and reversal of fibrosis. Nat Med. 2012 Feb 5;18(3):396-404. doi: 10.1038/nm.2629. PubMed PMID: 22306733.


Cooke VG, LeBleu VS, Keskin D, Khan Z, O'Connell JT, Teng Y, Duncan MB, Xie L, Maeda G, Vong S, Sugimoto H, Rocha RM, Damascena A, Brentani RR, Kalluri R. Pericyte depletion results in hypoxia-associated epithelial-to-mesenchymal transition and metastasis mediated by met signaling pathway. Cancer Cell. 2012 Jan 17;21(1):66-81. PubMed PMID: 22264789.


Lee RS, Stewart C, Carter SL, Ambrogio L, Cibulskis K, Sougnez C, Lawrence MS, Auclair D, Mora J, Golub TR, Biegel JA, Getz G, Roberts CW. A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers. J Clin Invest. 2012 Aug 1;122(8):2983-8. doi: 10.1172/JCI64400. Epub 2012 Jul 17. PMID: 22797305 PMCID:PMC3408754 read article


Landreville S, Agapova OA, Matatall KA, Kneass ZT, Onken MD, Lee RS, Bowcock AM, Harbour JW. Histone deacetylase inhibitors induce growth arrest and differentiation in uveal melanoma. Clin Cancer Res. 2012 Jan 15;18(2):408-16. doi: 10.1158/1078-0432.CCR-11-0946. Epub 2011 Oct 28. PMID: 22038994 PMCID: PMC3261307 read article


Chahrour MH, Yu TW, Lim ET, Ataman B, Coulter ME, Hill RS, Stevens CR, Schubert CR; ARRA Autism Sequencing Collaboration, Greenberg ME, Gabriel SB, Walsh CA. Whole-exome sequencing and homozygosity analysis implicate depolarization-regulated neuronal genes in autism. PLoS Genet. 2012;8(4):e1002635. doi: 10.1371/journal.pgen.1002635. Epub 2012 Apr 12. PMID: 22511880 PMCID: PMC3325173 read article


Staropoli JF, Karaa A, Lim ET, Kirby A, Elbalalesy N, Romansky SG, Leydiker KB, Coppel SH, Barone R, Xin W, MacDonald ME, Abdenur JE, Daly MJ, Sims KB, Cotman SL. A homozygous mutation in KCTD7 links neuronal ceroid lipofuscinosis to the ubiquitin-proteasome system. Am J Hum Genet. 2012 Jul 13;91(1):202-8. doi: 10.1016/j.ajhg.2012.05.023. Epub 2012 Jun 28. PMID: 22748208 PMCID: PMC3397260 read article


Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH Jr, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012 Apr 4;485(7397):242-5. doi: 10.1038/nature11011. PMID: 22495311 PMCID: PMC3613847 read article


Haas JT, Winter HS, Lim E, Kirby A, Blumenstiel B, DeFelice M, Gabriel S, Jalas C, Branski D, Grueter CA, Toporovski MS, Walther TC, Daly MJ, Farese RV Jr. DGAT1 mutation is linked to a congenital diarrheal disorder. J Clin Invest. 2012 Dec 3;122(12):4680-4. doi: 10.1172/JCI64873. Epub 2012 Nov 1. PMID: 23114594 PMCID: PMC3533555 read article


Patten IS, Rana S, Shahul S, Rowe GC, Jang C, Liu L, Hacker MR, Rhee JS, Mitchell J, Mahmood F, Hess P, Farrell C, Koulisis N, Khankin EV, Burke SD, Tudorache I, Bauersachs J, del Monte F, Hilfiker-Kleiner D, Karumanchi SA, Arany Z. Cardiac angiogenic imbalance leads to peripartum cardiomyopathy. Nature. 2012 May 9;485(7398):333-8. doi: 10.1038/nature11040. PMID: 22596155 PMCID: PMC3356917.  read article


Mitra D, Luo X, Morgan A, Wang J, Hoang MP, Lo J, Guerrero CR, Lennerz JK, Mihm MC, Wargo JA, Robinson KC, Devi SP, Vanover JC, D'Orazio JA, McMahon M, Bosenberg MW, Haigis KM, Haber DA, Wang Y, Fisher DE. An ultraviolet-radiation-independent pathway to melanoma carcinogenesis in the red hair/fair skin background. Nature. 2012 Nov 15;491(7424):449-53. doi: 10.1038/nature11624. Epub 2012 Oct 31. PMID: 23123854 PMCID: PMC3521494 read article


Lohmueller JJ, Armel TZ, Silver PA. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Res. 2012 Jun;40(11):5180-7. doi: 10.1093/nar/gks142. Epub 2012 Feb 9. PMID: 22323524 PMCID: PMC3367183 read article


Garg A, Lohmueller JJ, Silver PA, Armel TZ. Engineering synthetic TAL effectors with orthogonal target sites. Nucleic Acids Res. 2012 Aug;40(15):7584-95. doi: 10.1093/nar/gks404. Epub 2012 May 11. PMID: 22581776 PMCID: PMC3424557 read article


Madigan CA, Cheng TY, Layre E, Young DC, McConnell MJ, Debono CA, Murry JP, Wei JR, Barry CE 3rd, Rodriguez GM, Matsunaga I, Rubin EJ, Moody DB. Lipidomic discovery of deoxysiderophores reveals a revised mycobactin biosynthesis pathway in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1257-62. Epub 2012 Jan 9. PubMed PMID: 22232695; PubMed Central PMCID: PMC3268331.


Majczenko K, Davidson AE, Camelo-Piragua S, Agrawal PB, Manfready RA, Li X, Joshi S, Xu J, Peng W, Beggs AH, Li JZ, Burmeister M, Dowling JJ. Dominant mutation of CCDC78 in a unique congenital myopathy with prominent internal nuclei and atypical cores. Am J Hum Genet. 2012 Aug 10;91(2):365-71. doi: 10.1016/j.ajhg.2012.06.012. Epub 2012 Jul 19. PMID: 22818856 PMCID: PMC3415545 read article


Lawlor MW, Alexander MS, Viola MG, Meng H, Joubert R, Gupta V, Motohashi N, Manfready RA, Hsu CP, Huang P, Buj-Bello A, Kunkel LM, Beggs AH, Gussoni E. Myotubularin-deficient myoblasts display increased apoptosis, delayed proliferation, and poor cell engraftment. Am J Pathol. 2012 Sep;181(3):961-8. doi: 10.1016/j.ajpath.2012.05.016. Epub 2012 Jul 27. PMID: 22841819 PMCID PMC3432426
 read article


Mitra D, Luo X, Morgan A, Wang J, Hoang MP, Lo J, Guerrero CR, Lennerz JK, Mihm MC, Wargo JA, Robinson KC, Devi SP, Vanover JC, D'Orazio JA, McMahon M, Bosenberg MW, Haigis KM, Haber DA, Wang Y, Fisher DE. An ultraviolet-radiation-independent pathway to melanoma carcinogenesis in the red hair/fair skin background. Nature. 2012 Nov 15;491(7424):449-53. doi: 10.1038/nature11624. Epub 2012 Oct 31. PMID: 23123854 PMCID: PMC3521494 read article


Osmundson J, Montero-Diez C, Westblade LF, Hochschild A, Darst SA. Promoter-specific transcription inhibition in Staphylococcus aureus by a phage protein. Cell. 2012 Nov 21;151(5):1005-16. doi: 10.1016/j.cell.2012.10.034. PMID: 23178120 PMCID: PMC3604623 read article


Ng MR, Besser A, Danuser G, Brugge JS. Substrate stiffness regulates cadherin-dependent collective migration through myosin-II contractility. J Cell Biol. 2012 Oct 29;199(3):545-63. doi: 10.1083/jcb.201207148. Epub 2012 Oct 22. PMID: 23091067 PMCID: PMC3483134 read article


Gondek DC, Olive AJ, Stary G, Starnbach MN. CD4+ T cells are necessary and sufficient to confer protection against Chlamydia trachomatis infection in the murine upper genital tract. J Immunol. 2012 Sep 1;189(5):2441-9. doi: 10.4049/jimmunol.1103032. Epub 2012 Aug 1. PMID: 22855710 PMCID: PMC3690950 read article


Rosmarin DM, Carette JE, Olive AJ, Starnbach MN, Brummelkamp TR, Ploegh HL. Attachment of Chlamydia trachomatis L2 to host cells requires sulfation. Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):10059-64. doi: 10.1073/pnas.1120244109. Epub 2012 Jun 6. PMID: 22675117 PMCID: PMC3382535 read article


Larman HB, Xu GJ, Pavlova NN, Elledge SJ. Construction of a rationally designed antibody platform for sequencing-assisted selection. Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18523-8. doi: 10.1073/pnas.1215549109. Epub 2012 Oct 11. PMID: 23064642 PMCID: PMC3494914 read article


Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, Theurillat JP, Nickerson E, Auclair D, Li L, Place C, Dicara D, Ramos AH, Lawrence MS, Cibulskis K, Sivachenko A, Voet D, Saksena G, Stransky N, Onofrio RC, Winckler W, Ardlie K, Wagle N, Wargo J, Chong K, Morton DL, Stemke-Hale K, Chen G, Noble M, Meyerson M, Ladbury JE, Davies MA, Gershenwald JE, Wagner SN, Hoon DS, Schadendorf D, Lander ES, Gabriel SB, Getz G, Garraway LA, Chin L. A landscape of driver mutations in melanoma. Cell. 2012 Jul 20;150(2):251-63. doi: 10.1016/j.cell.2012.06.024. PMID: 22817889 PMCID: PMC3600117
 read article


Puram SV, Yeung CM, Jahani-Asl A, Lin C, de la Iglesia N, Konopka G, Jackson-Grusby L, Bonni A. STAT3-iNOS Signaling Mediates EGFRvIII-Induced Glial Proliferation and Transformation. J Neurosci. 2012 Jun 6;32(23):7806-18. doi: 10.1523/JNEUROSCI.3243-11.2012. PMID: 22674257 PMCID: PMC3409246 read article


Blackburn JS, Liu S, Raiser DM, Martinez SA, Feng H, Meeker ND, Gentry J, Neuberg D, Look AT, Ramaswamy S, Bernards A, Trede NS, Langenau DM. Notch signaling expands a pre-malignant pool of T-cell acute lymphoblastic leukemia clones without affecting leukemia-propagating cell frequency. Leukemia. 2012 Sep;26(9):2069-78. doi: 10.1038/leu.2012.116. Epub 2012 Apr 27. PMID: 22538478 PMCID: PMC3435461 read article


Tropea KA, Leder E, Aslam M, Lau AN, Raiser DM, Lee JH, Balasubramaniam V, Fredenburgh LE, Alex Mitsialis S, Kourembanas S, Kim CF. Bronchioalveolar stem cells increase after mesenchymal stromal cell treatment in a mouse model of bronchopulmonary dysplasia. Am J Physiol Lung Cell Mol Physiol. 2012 May 1;302(9):L829-37. doi: 10.1152/ajplung.00347.2011. Epub 2012 Feb 10. PMID: 22328358 PMCID: PMC3362163 read article


Moore FE, Reyon D, Sander JD, Martinez SA, Blackburn JS, Khayter C, Ramirez CL, Joung JK, Langenau DM. Improved Somatic Mutagenesis in Zebrafish Using Transcription Activator-Like Effector Nucleases (TALENs). PLoS One. 2012;7(5):e37877. Epub 2012 May 24. PubMed PMID: 22655075; PubMed Central PMCID: PMC3360007.


Ramirez CL, Certo MT, Mussolino C, Goodwin MJ, Cradick TJ, McCaffrey AP, Cathomen T, Scharenberg AM, Joung JK. Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects. Nucleic Acids Res. 2012 Jul 1;40(12):5560-5568. Epub 2012 Feb 28. PubMed PMID: 22373919; PubMed Central PMCID: PMC3384306.


Redwine WB, Hernández-López R, Zou S, Huang J, Reck-Peterson SL, Leschziner AE. Structural basis for microtubule binding and release by dynein. Science. 2012 Sep 21;337(6101):1532-6. PMID: 22997337 PMCID: PMC3919166 read article


Mitra D, Luo X, Morgan A, Wang J, Hoang MP, Lo J, Guerrero CR, Lennerz JK, Mihm MC, Wargo JA, Robinson KC, Devi SP, Vanover JC, D'Orazio JA, McMahon M, Bosenberg MW, Haigis KM, Haber DA, Wang Y, Fisher DE. An ultraviolet-radiation-independent pathway to melanoma carcinogenesis in the red hair/fair skin background. Nature. 2012 Nov 15;491(7424):449-53. doi: 10.1038/nature11624. Epub 2012 Oct 31. PMID: 23123854 PMCID: PMC3521494 read article


Robinton DA, Daley GQ. The promise of induced pluripotent stem cells in research and therapy. Nature. 2012 Jan 18;481(7381):295-305. doi: 10.1038/nature10761. Review. PubMed PMID: 22258608 PMCID: PMC3652331 read article


Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH Jr, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012 Apr 4;485(7397):242-5. doi: 10.1038/nature11011. PMID: 22495311 PMCID: PMC3613847 read article


Beliveau BJ, Joyce EF, Apostolopoulos N, Yilmaz F, Fonseka CY, McCole RB, Chang Y, Li JB, Senaratne TN, Williams BR, Rouillard JM, Wu CT. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes. Proc Natl Acad Sci U S A. 2012 Dec 26;109(52):21301-6. doi: 10.1073/pnas.1213818110. Epub 2012 Dec 11. PMID: 23236188 PMCID: PMC3535588 read article


Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Jänne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell. 2012 Sep 14;150(6):1107-20. doi: 10.1016/j.cell.2012.08.029. PMID: 22980975 PMCID: PMC3557932 read article


Sikorski TW, Joo YJ, Ficarro SB, Askenazi M, Buratowski S, Marto JA. Proteomic analysis demonstrates activator- and chromatin-specific recruitment to promoters. J Biol Chem. 2012 Oct 12;287(42):35397-408. doi: 10.1074/jbc.M112.391581. Epub 2012 Aug 17. PMID: 22902623 PMCID: PMC3471693 read article


Akopian V, Chan MM, Clement K, Galonska C, Gifford CA, Lehtola E, Liao J, Samavarchi-Tehrani P, Sindhu C, Smith ZD, Tsankov AM, Webster J, Zhang Y, Ziller MJ, Meissner A. Epigenomics and chromatin dynamics. Genome Biol. 2012 Feb 24;13(2):313. doi: 10.1186/gb-2012-13-2-313. PMID: 22364154 PMCID: PMC3334565 read article


Sindhu C, Samavarchi-Tehrani P, Meissner A. Transcription factor-mediated epigenetic reprogramming. J Biol Chem. 2012 Sep 7;287(37):30922-31. doi: 10.1074/jbc.R111.319046. Epub 2012 Sep 5. PMID: 22952239 PMCID: PMC3438925 read article


Taylor AM, Humphries JM, White RM, Murphey RD, Burns CE, Zon LI. Hematopoietic defects in rps29 mutant zebrafish depend upon p53 activation. Exp Hematol. 2012 Mar;40(3):228-237.e5. doi: 10.1016/j.exphem.2011.11.007.. Epub 2011 Nov 25. PMID: 22120640 PMCID: PMC3310385 read article


Tamplin OJ, White RM, Jing L, Kaufman CK, Lacadie SA, Li P, Taylor AM, Zon LI. Small molecule screening in zebrafish: swimming in potential drug therapies. Wiley Interdiscip Rev Dev Biol. 2012 May-Jun;1(3):459-68. doi: 10.1002/wdev.37. Epub 2012 Feb 28. PMID: 23801494


Rajani DK, Walch M, Martinvalet D, Thomas MP, Lieberman J. Alterations in RNA processing during immune-mediated programmed cell death. Proc Natl Acad Sci U S A. 2012 May 29;109(22):8688-93. doi: 10.1073/pnas.1201327109. Epub 2012 May 15. PMID: 22589304 PMCID: PMC3365155 read article


Thompson DB, Cronican JJ, Liu DR. Engineering and identifying supercharged proteins for macromolecule delivery into mammalian cells. Methods Enzymol. 2012;503:293-319. doi: 10.1016/B978-0-12-396962-0.00012-4. PMID: 22230574 PMCID: PMC3505079 read article


Thompson DB, Villaseñor R, Dorr BM, Zerial M, Liu DR. Cellular uptake mechanisms and endosomal trafficking of supercharged proteins. Chem Biol. 2012 Jul 27;19(7):831-43. doi: 10.1016/j.chembiol.2012.06.014. PMID: 22840771 PMCID: PMC3408882 read article


Tsanov KM, Nishi Y, Peterson KA, Liu J, Baetscher M, McMahon AP. An embryonic stem cell-based system for rapid analysis of transcriptional enhancers. Genesis. 2012 May;50(5):443-50. doi: 10.1002/dvg.20820. Epub 2012 Jan 17. PMID: 22083581 PMCID: PMC3334447.  read article


Vo TT, Ryan J, Carrasco R, Neuberg D, Rossi DJ, Stone RM, Deangelo DJ, Frattini MG, Letai A. Relative mitochondrial priming of myeloblasts and normal HSCs determines chemotherapeutic success in AML. Cell. 2012 Oct 12;151(2):344-55. doi: 10.1016/j.cell.2012.08.038. PMID: 23063124 PMCID: PMC3534747 read article


Williams LA, Davis-Dusenbery BN, Eggan KC. SnapShot: directed differentiation of pluripotent stem cells. Cell. 2012 May 25;149(5):1174-1174.e1. doi: 10.1016/j.cell.2012.05.015. PMID: 22632979


Wivagg CN, Hung DT. Resuscitation-promoting factors are required for β-lactam tolerance and the permeability barrier in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2012 Mar;56(3):1591-4. doi: 10.1128/AAC.06027-11. Epub 2011 Dec 12. PMID: 22155826 PMCID: PMC3294900 read article


Stanley SA, Grant SS, Kawate T, Iwase N, Shimizu M, Wivagg C, Silvis M, Kazyanskaya E, Aquadro J, Golas A, Fitzgerald M, Dai H, Zhang L, Hung DT. Identification of novel inhibitors of M. tuberculosis growth using whole cell based high-throughput screening. ACS Chem Biol. 2012 Aug 17;7(8):1377-84. doi: 10.1021/cb300151m. Epub 2012 May 21. PMID: 22577943 PMCID: PMC3560293
 read article


Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM. A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A. 2012 Jul 24;109(30):11920-7. doi: 10.1073/pnas.1201904109. Epub 2012 Jul 13. PMID: 22797899 PMCID: PMC3409785 read article


Kim H, Yang K, Dejsuphong D, D'Andrea AD. Regulation of Rev1 by the Fanconi anemia core complex. Nat Struct Mol Biol. 2012 Jan 22;19(2):164-70. doi: 10.1038/nsmb.2222. PubMed PMID: 22266823; PubMed Central PMCID: PMC3280818.


Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM. A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A. 2012 Jul 13. [Epub ahead of print] PubMed PMID: 22797899.


Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM. Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res. 2012 Jun 26. [Epub ahead of print] PubMed PMID: 22740649.


Yu Y, Munger K. Human papillomavirus type 16 E7 oncoprotein engages but does not abrogate the mitotic spindle assembly checkpoint. Virology. 2012 Oct 10;432(1):120-6. doi: 10.1016/j.virol.2012.06.006. Epub 2012 Jun 28. PMID: 22748180 PMCID: PMC3402702 read article


Zeng X, King RW. An APC/C inhibitor stabilizes cyclin B1 by prematurely terminating ubiquitination. Nat Chem Biol. 2012 Feb 26;8(4):383-92. doi: 10.1038/nchembio.801. PubMed PMID: 22366722; PubMed Central PMCID: PMC3307893.


Christofferson DE, Li Y, Hitomi J, Zhou W, Upperman C, Zhu H, Gerber SA, Gygi S, Yuan J .A novel role for RIP1 kinase in mediating TNFα production. Cell Death Dis. 2012 Jun 14;3:e320. doi: 10.1038/cddis.2012.64. PMID: 22695613 PMCID: PMC3388236 read article


Zhou W, Yuan J. Cell biology: Death by deacetylation. Nature. 2012 Dec 13;492(7428):194-5. doi: 10.1038/nature11761. Epub 2012 Nov 28. PMID:23201692


top

2011


Barstow B, Agapakis CM, Boyle PM, Grandl G, Silver PA, Wintermute EH. A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism. J Biol Eng. 2011 May 26;5:7. doi: 10.1186/1754-1611-5-7. PMID: 21615937 PMCID: PMC3130634 read article


Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC, Silver PA. Towards a synthetic chloroplast. PLoS One. 2011 Apr 20;6(4):e18877. doi: 10.1371/journal.pone.0018877. PMID: 21533097 PMCID: PMC3080389 read article


Pathak N, Austin CA, Drummond IA. Tubulin tyrosine ligase-like genes ttll3 and ttll6 maintain zebrafish cilia structure and motility. J Biol Chem. 2011 Apr 1;286(13):11685-95. doi: 10.1074/jbc.M110.209817. Epub 2011 Jan 24. PMID: 21262966 PMCID: PMC3064220 read article


Beier KT, Saunders A, Oldenburg IA, Miyamichi K, Akhtar N, Luo L, Whelan SP, Sabatini B, Cepko CL. Anterograde or retrograde transsynaptic labeling of CNS neurons with vesicular stomatitis virus vectors. Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15414-9. Epub 2011 Aug 8. PubMed PMID: 21825165; PubMed Central PMCID: PMC3174680.


Cronican JJ, Beier KT, Davis TN, Tseng JC, Li W, Thompson DB, Shih AF, May EM, Cepko CL, Kung AL, Zhou Q, Liu DR. A class of human proteins that deliver functional proteins into mammalian cells in vitro and in vivo. Chem Biol. 2011 Jul 29;18(7):833-8. PubMed PMID: 21802004; PubMed Central PMCID: PMC3154086.


Beier KT, Samson ME, Matsuda T, Cepko CL. Conditional expression of the TVA receptor allows clonal analysis of descendents from Cre-expressing progenitor cells. Dev Biol. 2011 May 15;353(2):309-20. Epub 2011 Mar 21. PubMed PMID: 21397594; PubMed Central PMCID: PMC3100772.


Bowen ME, Boyden ED, Holm IA, Campos-Xavier B, Bonafé L, et al. (2011) Loss-of-function mutations in PTPN11 cause Metachondromatosis, but not Ollier disease or Maffucci syndrome. PLoS Genetics 7(4):e1002050. PMCID:PMC3077396.


Burrill DR, Boyle PM, Silver PA. A new approach to an old problem: synthetic biology tools for human disease and metabolism. Cold Spring Harb Symp Quant Biol. 2011;76:145-54. doi: 10.1101/sqb.2011.76.010686. Epub 2011 Dec 14. PMID: 22169233


Senapedis WT, Kennedy CJ, Boyle PM, Silver PA. Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain. Mol Biol Cell. 2011 May 15;22(10):1791-805. doi: 10.1091/mbc.E10-10-0854. Epub 2011 Apr 1. PMID: 21460183 PMCID: PMC3093329
 read article


Barstow B, Agapakis CM, Boyle PM, Grandl G, Silver PA, Wintermute EH. A synthetic system links FeFe-hydrogenases to essential E. coli sulfur metabolism. J Biol Eng. 2011 May 26;5:7. doi: 10.1186/1754-1611-5-7. PMID: 21615937 PMCID: PMC3130634 read article


Ray, R.S.*, Corcoran, A.E.*, Brust, R.D.*, Kim, J.C., Richerson, G.B., Nattie, E., Dymecki, S.M. Impaired Respiratory and Body Temperature Control Upon Acute Serotonergic Neuron Inhibition. Science. 2011 Jul 29;333(6042):637-42. doi: 10.1126/science.1205295. PMID: 21798952 PMCID: PMC3729433 *- These authors contributed equally to this work. read article


Burrill DR, Silver PA. Synthetic circuit identifies subpopulations with sustained memory of DNA damage. Genes Dev. 2011 Mar 1;25(5):434-9. doi: 10.1101/gad.1994911. PMID: 21363961 PMCID: PMC3049284 read article


Burrill DR, Silver PA. Recording cellular experiences of DNA damage. Cell Cycle. 2011 Aug 1;10(15):2410-1. Epub 2011 Aug 1. PMID: 21670599


Meerbrey KL, Hu G, Kessler JD, Roarty K, Li MZ, Fang JE, Herschkowitz JI, Burrows AE, Ciccia A, Sun T, Schmitt EM, Bernardi RJ, Fu X, Bland CS, Cooper TA, Schiff R, Rosen JM, Westbrook TF, Elledge SJ. The pINDUCER lentiviral toolkit for inducible RNA interference in vitro and in vivo. Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3665-70. doi: 10.1073/pnas.1019736108. Epub 2011 Feb 9. PMID: 21307310 PMCID: PMC3048138 read article


Alkuraya FS, Cai X, Emery C, Mochida GH, Al-Dosari MS, Felie JM, Hill RS, Barry BJ, Partlow JN, Gascon GG, Kentab A, Jan M, Shaheen R, Feng Y, Walsh CA. Human mutations in NDE1 cause extreme microcephaly with lissencephaly [corrected]. Am J Hum Genet. 2011 May 13;88(5):536-47. doi: 10.1016/j.ajhg.2011.04.003. Epub 2011 Apr 28. PMID: 21529751 PMCID: PMC3146728 read article


Chan Y, Holmen OL, Dauber A, Vatten L, Havulinna AS, Skorpen F, Kvaløy K, Silander K, Nguyen TT, Willer C, Boehnke M, Perola M, Palotie A, Salomaa V, Hveem K, Frayling TM, Hirschhorn JN, Weedon MN. Common variants show predicted polygenic effects on height in the tails of the distribution, except in extremely short individuals. PLoS Genet. 2011 Dec;7(12):e1002439. doi: 10.1371/journal.pgen.1002439. Epub 2011 Dec 29. PMID: 22242009 PMCID: PMC3248463 read article


Dauber A, Yu Y, Turchin MC, Chiang CW, Meng YA, Demerath EW, Patel SR, Rich SS, Rotter JI, Schreiner PJ, Wilson JG, Shen Y, Wu BL, Hirschhorn JN. Genome-wide association of copy-number variation reveals an association between short stature and the presence of low-frequency genomic deletions. Am J Hum Genet. 2011 Dec 9;89(6):751-9. Epub 2011 Nov 23. PubMed PMID: 22118881; PubMed Central PMCID: PMC3234379.


Chiang CW, Gajdos ZK, Korn JM, Butler JL, Hackett R, Guiducci C, Nguyen TT, Wilks R, Forrester T, Henderson KD, Le Marchand L, Henderson BE, Haiman CA, Cooper RS, Lyon HN, Zhu X, McKenzie CA, Palmert MR, Hirschhorn JN. The efficacy of detecting variants with small effects on the Affymetrix 6.0 platform using pooled DNA. Hum Genet. 2011 Nov;130(5):607-21. Epub 2011 Mar 22. PubMed PMID: 21424828.


Zhu X, Young JH, Fox E, Keating BJ, Franceschini N, Kang S, Tayo B, Adeyemo A, Sun YV, Li Y, Morrison A, Newton-Cheh C, Liu K, Ganesh SK, Kutlar A, Vasan RS, Dreisbach A, Wyatt S, Polak J, Palmas W, Musani S, Taylor H, Fabsitz R, Townsend RR, Dries D, Glessner J, Chiang CW, Mosley T, Kardia S, Curb D, Hirschhorn JN, Rotimi C, Reiner A, Eaton C, Rotter JI, Cooper RS, Redline S, Chakravarti A, Levy D. Combined admixture mapping and association analysis identifies a novel blood pressure genetic locus on 5p13: contributions from the CARe consortium. Hum Mol Genet. 2011 Jun 1;20(11):2285-95. Epub 2011 Mar 21. PubMed PMID: 21422096; PubMed Central PMCID: PMC3090198.


Christodoulou DC, Gorham JM, Herman DS, Seidman JG. Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease. Curr Protoc Mol Biol. 2011 Apr;Chapter 4:Unit4.12. PubMed PMID: 21472699; PubMed Central PMCID: PMC3152986.


Alon S, Vigneault F, Eminaga S, Christodoulou DC, Seidman JG, Church GM, Eisenberg E. Barcoding bias in high-throughput multiplex sequencing of miRNA. Genome Res. 2011 Sep;21(9):1506-11. Epub 2011 Jul 12. PubMed PMID: 21750102; PubMed Central PMCID: PMC3166835.


Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol. 2011 Feb;29(2):149-53. Epub 2011 Jan 19. PubMed PMID: 21248753; PubMed Central PMCID: PMC3084533.  read article


Park KS, Liang MC, Raiser DM, Zamponi R, Roach RR, Curtis SJ, Walton Z, Schaffer BE, Roake CM, Zmoos AF, Kriegel C, Wong KK, Sage J, Kim CF. Characterization of the cell of origin for small cell lung cancer. Cell Cycle. 2011 Aug 15;10(16):2806-15. Epub 2011 Aug 15. PubMed PMID: 21822053; PubMed Central PMCID: PMC3219544.


Goessling W, Allen RS, Guan X, Jin P, Uchida N, Dovey M, Harris JM, Metzger ME, Bonifacino AC, Stroncek D, Stegner J, Armant M, Schlaeger T, Tisdale JF, Zon LI, Donahue RE, North TE. Prostaglandin E2 enhances human cord blood stem cell xenotransplants and shows long-term safety in preclinical nonhuman primate transplant models. Cell Stem Cell. 2011 Apr 8;8(4):445-58. doi: 10.1016/j.stem.2011.02.003. PMID: 21474107 PMCID: PMC3148081 read article


Trompouki E, Bowman TV, Lawton LN, Fan ZP, Wu DC, DiBiase A, Martin CS, Cech JN, Sessa AK, Leblanc JL, Li P, Durand EM, Mosimann C, Heffner GC, Daley GQ, Paulson RF, Young RA, Zon LI. Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell. 2011 Oct 28;147(3):577-89. PubMed PMID: 22036566; PubMed Central PMCID: PMC3219441.


Anderl S, Freeland M, Kwiatkowski DJ, Goto J. (2011)Therapeutic value of prenatal rapamycin treatment in a mouse brain model of tuberous sclerosis complex. Hum Mol Genet. 2011 Dec 1;20(23):4597-604. doi: 10.1093/hmg/ddr393. Epub 2011 Sep 1. PMID: 21890496 PMCID: PMC3209830 read article


Kim T, Escudero S, and Shivdasani RA. Intact function of Lgr5-expressing intestinal stem cells in the absence of paneth cells. Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3932-7. doi: 10.1073/pnas.1113890109. Epub 2012 Feb 21. PMID: 22355124 PMCID: PMC3309789 read article


Sukumaran B, Mastronunzio JE, Narasimhan S, Fankhauser S, Uchil PD, Levy R, Graham M, Colpitts TM, Lesser CF, Fikrig E. Anaplasma phagocytophilum AptA modulates Erk1/2 signalling. Cell Microbiol. 2011 Jan;13(1):47-61. doi: 10.1111/j.1462-5822.2010.01516.x. Epub 2010 Aug 27. PMID: 20716207 PMCID: PMC3005019 read article


Finley LW, Haas W, Desquiret-Dumas V, Wallace DC, Procaccio V, Gygi SP, Haigis MC. Succinate dehydrogenase is a direct target of sirtuin 3 deacetylase activity. PLoS One 2011;6(8):e23295. Epub 2011 Aug 17. PMID: 21858060. PMCID: PMC3157345.


Ford KM, Saint-Geniez M, Walshe T, Zahr A, D'Amore PA. Expression and role of VEGF in the adult retinal pigment epithelium. Invest Ophthalmol Vis Sci. 2011 Dec 9;52(13):9478-87. doi: 10.1167/iovs.11-8353. PMID: 22058334 PMCID: PMC3250352 read article


Liu CT, Garnaas MK, Tin A, Kottgen A, Franceschini N, Peralta CA, de Boer IH, Lu X, Atkinson E, Ding J, Nalls M, Shriner D, Coresh J, Kutlar A, Bibbins-Domingo K, Siscovick D, Akylbekova E, Wyatt S, Astor B, Mychaleckjy J, Li M, Reilly MP, Townsend RR, Adeyemo A, Zonderman AB, de Andrade M, Turner ST, Mosley TH, Harris TB; CKDGen Consortium, Rotimi CN, Liu Y, Kardia SL, Evans MK, Shlipak MG, Kramer H, Flessner MF, Dreisbach AW, Goessling W, Cupples LA, Kao WL, Fox CS. Genetic association for renal traits among participants of African ancestry reveals new loci for renal function. PLoS Genet. 2011 Sep;7(9):e1002264. Epub 2011 Sep 8. PubMed PMID: 21931561; PubMed Central PMCID: PMC3169523. read article


Puram SV, Kim AH, Ikeuchi Y, Wilson-Grady JT, Merdes A, Gygi SP, Bonni A. A CaMKIIβ signaling pathway at the centrosome regulates dendrite patterning in the brain. Nat Neurosci. 2011 Jul 3;14(8):973-83. doi: 10.1038/nn.2857. PMID: 21725312 PMCID: PMC3391735 read article


Grassian AR, Coloff JL, Brugge JS. Extracellular matrix regulation of metabolism and implications for tumorigenesis. Cold Spring Harb Symp Quant Biol. 2011;76:313-24. Epub 2011 Nov 21. PubMed PMID: 22105806.


Grassian AR, Metallo CM, Coloff JL, Stephanopoulos G, Brugge JS. Erk regulation of pyruvate dehydrogenase flux through PDK4 modulates cell proliferation. Genes Dev. 2011 Aug 15;25(16):1716-33. PubMed PMID: 21852536; PubMed Central PMCID: PMC3165936.


Locasale JW, Grassian AR, Melman T, Lyssiotis CA, Mattaini KR, Bass AJ, Heffron G, Metallo CM, Muranen T, Sharfi H, Sasaki AT, Anastasiou D, Mullarky E, Vokes NI, Sasaki M, Beroukhim R, Stephanopoulos G, Ligon AH, Meyerson M, Richardson AL, Chin L, Wagner G, Asara JM, Brugge JS, Cantley LC, Vander Heiden MG. Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis. Nat Genet. 2011 Jul 31;43(9):869-74. doi: 10.1038/ng.890. PubMed PMID: 21804546.


Castillo M, Hall JA, Correa-Medina M, Ueta C, Kang HW, Cohen DE, Bianco AC. Disruption of thyroid hormone activation in type 2 deiodinase knockout mice causes obesity with glucose intolerance and liver steatosis only at thermoneutrality. Diabetes. 2011 Apr;60(4):1082-9. doi: 10.2337/db10-0758. Epub 2011 Feb 18. PMID: 21335378 PMCID: PMC3064082 read article


Hayes GD, Riedel CG, Ruvkun G. The Caenorhabditis elegans SOMI-1 zinc finger protein and SWI/SNF promote regulation of development by the mir-84 microRNA. Genes Dev. 2011 Oct 1;25(19):2079-92. doi: 10.1101/gad.17153811. PMID: 21979920 PMCID: PMC3197206 read article


Pathania S, Nguyen J, Hill SJ, Scully R, Adelmant GO, Marto JA, Feunteun J, Livingston DM. BRCA1 is required for postreplication repair after UV-induced DNA damage. Mol Cell. 2011 Oct 21;44(2):235-51. Epub 2011 Sep 29.
PMID: 21963239. PMCID: PMC3200447. NIHMSID: NIHMS326474


Zheng J, Ho B, Mekalanos JJ. Genetic analysis of anti-amoebae and anti-bacterial activities of the type VI secretion system in Vibrio cholerae. PLoS One. 2011;6(8):e23876. doi: 10.1371/journal.pone.0023876. Epub 2011 Aug 31. PMID: 21909372 PMCID: PMC3166118 read article


Huynh MA, Ikeuchi Y, Netherton S, de la Torre-Ubieta L, Kanadia R, Stegmüller J, Cepko C, Bonni S, Bonni A. An isoform-specific SnoN1-FOXO1 repressor complex controls neuronal morphogenesis and positioning in the mammalian brain. Neuron. 2011 Mar 10;69(5):930-44. doi: 10.1016/j.neuron.2011.02.008. PMID: 21382553 PMCID: PMC3073069 read article


Lal A, Thomas MP, Altschuler G, Navarro F, O'Day E, Li XL, Concepcion C, Han YC, Thiery J, Rajani DK, Deutsch A, Hofmann O, Ventura A, Hide W, Lieberman J. Capture of microRNA-bound mRNAs identifies the tumor suppressor miR-34a as a regulator of growth factor signaling. PLoS Genet. 2011 Nov;7(11):e1002363. doi: 10.1371/journal.pgen.1002363. Epub 2011 Nov 10. PMID: 22102825 PMCID: PMC3213160 read article


Lahiri S, Shen K, Klein M, Tang A, Kane E, Gershow M, Garrity P, Samuel AD. Two alternating motor programs drive navigation in Drosophila larva. PLoS One. 2011;6(8):e23180. doi: 10.1371/journal.pone.0023180. Epub 2011 Aug 15. PMID: 21858019 PMCID: PMC3156121 read article


Kiely CM, Marguerat S, Garcia JF, Madhani HD, Bähler J, Winston F. Spt6 is required for heterochromatic silencing in the fission yeast Schizosaccharomyces pombe. Mol Cell Biol. 2011 Oct;31(20):4193-204. doi: 10.1128/MCB.05568-11. Epub 2011 Aug 15. PMID: 21844224 PMCID: PMC3187285 read article


Marotta LL, Almendro V, Marusyk A, Shipitsin M, Schemme J, Walker SR, Bloushtain-Qimron N, Kim JJ, Choudhury SA, Maruyama R, Wu Z, Gönen M, Mulvey LA, Bessarabova MO, Huh SJ, Silver SJ, Kim SY, Park SY, Lee HE, Anderson KS, Richardson AL, Nikolskaya T, Nikolsky Y, Liu XS, Root DE, Hahn WC, Frank DA, Polyak K. The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors. J Clin Invest. 2011 Jul;121(7):2723-35. doi: 10.1172/JCI44745. PMID: 21633165 PMCID: PMC3223826 read article


Sansregret L, Vadnais C, Livingstone J, Kwiatkowski N, Awan A, Cadieux C, Leduy L, Hallett MT, Nepveu A. Cut homeobox 1 causes chromosomal instability by promoting bipolar division after cytokinesis failure. Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1949-54. doi: 10.1073/pnas.1008403108. Epub 2011 Jan 18. PMID: 21245318 PMCID: PMC3033318 read article


Deng X, Yang Q, Kwiatkowski N, Sim T, McDermott U, Settleman JE, Lee JD, Gray NS. ACS Med Chem Lett. 2011 Mar 10;2(3):195-200. Epub 2011 Jan 12. PMID: 21412406 PMCID: PMC3055678 read article


Miduturu CV, Deng X, Kwiatkowski N, Yang W, Brault L, Filippakopoulos P, Chung E, Yang Q, Schwaller J, Knapp S, King RW, Lee JD, Herrgard S, Zarrinkar P, Gray NS. High-throughput kinase profiling: a more efficient approach toward the discovery of new kinase inhibitors. Chem Biol. 2011 Jul 29;18(7):868-79. doi: 10.1016/j.chembiol.2011.05.010. PMID: 21802008 PMCID: PMC3171802 read article


Zacharek SJ, Fillmore CM, Lau AN, Gludish DW, Chou A, Ho JW, Zamponi R, Gazit R, Bock C, Jäger N, Smith ZD, Kim TM, Saunders AH, Wong J, Lee JH, Roach RR, Rossi DJ, Meissner A, Gimelbrant AA, Park PJ, Kim CF. Lung stem cell self-renewal relies on BMI1-dependent control of expression at imprinted loci. Cell Stem Cell. 2011 Sep 2;9(3):272-81. doi: 10.1016/j.stem.2011.07.007. PMID: 21885022 PMCID: PMC3167236 read article


O'Connell JT, Sugimoto H, Cooke VG, MacDonald BA, Mehta AI, LeBleu VS, Dewar R, Rocha RM, Brentani RR, Resnick MB, Neilson EG, Zeisberg M, Kalluri R. VEGF-A and Tenascin-C produced by S100A4+ stromal cells are important for metastatic colonization. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):16002-7. Epub 2011 Sep 12. PubMed PMID: 21911392; PubMed Central PMCID: PMC3179047.


Bian X, Klemm RW, Liu TY, Zhang M, Sun S, Sui X, Liu X, Rapoport TA, Hu J. Structures of the atlastin GTPase provide insight into homotypic fusion of endoplasmic reticulum membranes. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3976-81. doi: 10.1073/pnas.1101643108. Epub 2011 Feb 22. PMID: 21368113 PMCID: PMC3054032 read article


Layre E, Sweet L, Hong S, Madigan CA, Desjardins D, Young DC, Cheng TY, Annand JW, Kim K, Shamputa IC, McConnell MJ, Debono CA, Behar SM, Minnaard AJ, Murray M, Barry CE 3rd, Matsunaga I, Moody DB. A comparative lipidomics platform for chemotaxonomic analysis of Mycobacterium tuberculosis. Chem Biol. 2011 Dec 23;18(12):1537-49. PubMed PMID: 22195556.


Huang S, Cheng TY, Young DC, Layre E, Madigan CA, Shires J, Cerundolo V, Altman JD, Moody DB. Discovery of deoxyceramides and diacylglycerols as CD1b scaffold lipids among diverse groove-blocking lipids of the human CD1 system. Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):19335-40. Epub 2011 Nov 15. PubMed PMID: 22087000; PubMed Central PMCID: PMC3228429.


De Raedt T, Walton Z, Yecies JL, Li D, Chen Y, Malone CF, Maertens O, Jeong SM, Bronson RT, Lebleu V, Kalluri R, Normant E, Haigis MC, Manning BD, Wong KK, Macleod KF, Cichowski K. Exploiting cancer cell vulnerabilities to develop a combination therapy for ras-driven tumors.Cancer Cell. 2011 Sep 13;20(3):400-13. doi: 10.1016/j.ccr.2011.08.014.PMID: 21907929 PMCID: PMC3233475.  read article


Yang DC, Peters NT, Parzych KR, Uehara T, Markovski M, Bernhardt TG. An ATP-binding cassette transporter-like complex governs cell-wall hydrolysis at the bacterial cytokinetic ring. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):E1052-60. Epub 2011 Oct 17. PubMed PMID: 22006326; PubMed Central PMCID: PMC3215046.


Cho H, McManus HR, Dove SL, Bernhardt TG. Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist. Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3773-8. doi: 10.1073/pnas.1018674108. Epub 2011 Feb 14. PMID: 21321206 PMCID: PMC3048121 read article


McManus HR, Dove SL. The CgrA and CgrC proteins form a complex that positively regulates cupA fimbrial gene expression in Pseudomonas aeruginosa. J Bacteriol. 2011 Nov;193(22):6152-61. doi: 10.1128/JB.05904-11. Epub 2011 Sep 16. PMID: 21926232 PMCID: PMC3209204 read article


Mullarky E, Mattaini KR, Vander Heiden MG, Cantley LC, Locasale JW. PHGDH amplification and altered glucose metabolism in human melanoma. Pigment Cell Melanoma Res. 2011 Dec;24(6):1112-5. doi: 10.1111/j.1755-148X.2011.00919.x. Epub 2011 Oct 28. PMID: 21981974


Locasale JW, Grassian AR, Melman T, Lyssiotis CA, Mattaini KR, Bass AJ, Heffron G, Metallo CM, Muranen T, Sharfi H, Sasaki AT, Anastasiou D, Mullarky E, Vokes NI, Sasaki M, Beroukhim R, Stephanopoulos G, Ligon AH, Meyerson M, Richardson AL, Chin L, Wagner G, Asara JM, Brugge JS, Cantley LC, Vander Heiden MG. Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis. Nat Genet. 2011 Jul 31;43(9):869-74. doi: 10.1038/ng.890. PMID: 21804546 PMCID: PMC3677549 read article


Helman E, Naxerova K, Kohane IS. DNA hypermethylation in lung cancer is targeted at differentiation-associated genes. Oncogene. 2012 Mar 1;31(9):1181-8. doi: 10.1038/onc.2011.307. Epub 2011 Aug 1. PubMed PMID: 21804601.


Liu J, Liao S, Huang Y, Samuel R, Shi T, Naxerova K, Huang P, Kamoun W, Jain RK, Fukumura D, Xu L. PDGF-D improves drug delivery and efficacy via vascular normalization, but promotes lymphatic metastasis by activating CXCR4 in breast cancer. Clin Cancer Res. 2011 Jun 1;17(11):3638-48. Epub 2011 Apr 1. PubMed PMID: 21459800; PubMed Central PMCID: PMC3107920.


Gallegos L, Ng MR, Brugge JS. The myosin-II-responsive focal adhesion proteome: a tour de force? Nat Cell Biol. 2011 Apr;13(4):344-6. doi: 10.1038/ncb0411-344. Epub 2011 Mar 20. PMID: 21460805


Iwanicki MP, Davidowitz RA, Ng MR, Besser A, Muranen T, Merritt M, Danuser G, Ince TA, Brugge JS. Ovarian cancer spheroids use myosin-generated force to clear the mesothelium. Cancer Discov. 2011 Jul;1(2):144-57. doi: 10.1158/2159-8274.CD-11-0010. PMID: 22303516 PMCID: PMC3269166 read article


Shyh-Chang N, Zheng Y, Locasale JW, Cantley LC. Human pluripotent stem cells decouple respiration from energy production. EMBO J. 2011 Dec 14;30(24):4851-2. doi: 10.1038/emboj.2011.436. PMID: 22166995 PMCID: PMC3242981 read article


Zhu H, Shyh-Chang N, Segrè AV, Shinoda G, Shah SP, Einhorn WS, Takeuchi A, Engreitz JM, Hagan JP, Kharas MG, Urbach A, Thornton JE, Triboulet R, Gregory RI; DIAGRAM Consortium; MAGIC Investigators, Altshuler D, Daley GQ. The Lin28/let-7 axis regulates glucose metabolism. Cell. 2011 Sep 30;147(1):81-94. doi: 10.1016/j.cell.2011.08.033. PMID: 21962509 PMCID: PMC3353524 read article


Olive AJ, Gondek DC, Starnbach MN. CXCR3 and CCR5 are both required for T cell-mediated protection against C. trachomatis infection in the murine genital mucosa. Mucosal Immunol. 2011 Mar;4(2):208-16. doi: 10.1038/mi.2010.58. Epub 2010 Sep 15. PMID: 20844481 PMCID: PMC3010299 read article


Coers J, Gondek DC, Olive AJ, Rohlfing A, Taylor GA, Starnbach MN. Compensatory T cell responses in IRG-deficient mice prevent sustained Chlamydia trachomatis infections. PLoS Pathog. 2011 Jun;7(6):e1001346. doi: 10.1371/journal.ppat.1001346. Epub 2011 Jun 23. PMID: 21731484 PMCID: PMC3121881 read article


Jiang J, Lazarus MB, Pasquina L, Sliz P, Walker S. A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase. Nat Chem Biol. 2011 Nov 13;8(1):72-7. doi: 10.1038/nchembio.711. PMID: 22082911 PMCID: PMC3241908  read article


Piskounova E, Polytarchou C, Thornton JE, LaPierre RJ, Pothoulakis C, Hagan JP, Iliopoulos D, Gregory RI. Lin28A and Lin28B inhibit let-7 microRNA biogenesis by distinct mechanisms. Cell. 2011 Nov 23;147(5):1066-79. PubMed PMID: 22118463; PubMed Central PMCID: PMC3227872.


Sharp JA, Plant JJ, Ohsumi TK, Borowsky M, Blower MD. Functional analysis of the microtubule-interacting transcriptome. Mol Biol Cell. 2011 Nov;22(22):4312-23. doi: 10.1091/mbc.E11-07-0629. Epub 2011 Sep 21. PMID: 21937723 PMCID: PMC3216657 read article


Medici D, Potenta S, Kalluri R. Transforming growth factor-β2 promotes Snail-mediated endothelial-mesenchymal transition through convergence of Smad-dependent and Smad-independent signalling. Biochem J. 2011 Aug 1;437(3):515-20. doi: 10.1042/BJ20101500. PMID: 21585337


Puram SV, Riccio A, Koirala S, Ikeuchi Y, Kim AH, Corfas G, Bonni A. A TRPC5-regulated calcium signaling pathway controls dendrite patterning in the mammalian brain. Genes Dev. 2011 Dec 15;25(24):2659-73. doi: 10.1101/gad.174060.111. Epub 2011 Dec 1. PMID: 22135323 PMCID: PMC3248686 read article


Puram SV, Kim AH, Ikeuchi Y, Wilson-Grady JT, Merdes A, Gygi SP, Bonni A. A CaMKIIβ signaling pathway at the centrosome regulates dendrite patterning in the brain. Nat Neurosci. 2011 Jul 3;14(8):973-83. doi: 10.1038/nn.2857. PMID: 21725312 PMCID: PMC3391735 read article


Puram SV, Bonni A. Novel functions for the anaphase-promoting complex in neurobiology. Semin Cell Dev Biol. 2011 Aug;22(6):586-94. doi: 10.1016/j.semcdb.2011.03.006. Epub 2011 Mar 23. PMID: 21439392 PMCID: PMC3177029 read article


Park KS, Liang MC, Raiser DM, Zamponi R, Roach RR, Curtis SJ, Walton Z, Schaffer BE, Roake CM, Zmoos AF, Kriegel C, Wong KK, Sage J, Kim CF. Characterization of the cell of origin for small cell lung cancer. Cell Cycle. 2011 Aug 15;10(16):2806-15. Epub 2011 Aug 15. PMID: 21822053 PMCID: PMC3219544 read article


Sebastiano V, Maeder ML, Angstman JF, Haddad B, Khayter C, Yeo DT, Goodwin MJ, Hawkins JS, Ramirez CL, Batista LF, Artandi SE, Wernig M, Joung JK. In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases. Stem Cells. 2011 Nov;29(11):1717-26. doi: 10.1002/stem.718. PubMed PMID: 21898685; PubMed Central PMCID: PMC3285772.


Pattanayak V, Ramirez CL, Joung JK, Liu DR. Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Nat Methods. 2011 Aug 7;8(9):765-70. doi: 10.1038/nmeth.1670. PubMed PMID: 21822273; PubMed Central PMCID: PMC3164905.


White RM, Cech J, Ratanasirintrawoot S, Lin CY, Rahl PB, Burke CJ, Langdon E, Tomlinson ML, Mosher J, Kaufman C, Chen F, Long HK, Kramer M, Datta S, Neuberg D, Granter S, Young RA, Morrison S, Wheeler GN, Zon LI. DHODH modulates transcriptional elongation in the neural crest and melanoma. Nature. 2011 Mar 24;471(7339):518-22. doi: 10.1038/nature09882. PMID: 21430780 PMCID: PMC3759979 read article


Manos PD, Ratanasirintrawoot S, Loewer S, Daley GQ, Schlaeger TM. Live-cell immunofluorescence staining of human pluripotent stem cells. Curr Protoc Stem Cell Biol. 2011 Dec;Chapter 1:Unit 1C.12. doi: 10.1002/9780470151808.sc01c12s19. PMID: 22135082


Mitra D, Robinson KC, Fisher DE. Melanoma and viagra: an unexpected connection. Pigment Cell Melanoma Res. 2011 Feb;24(1):16-8.


Coers J, Gondek DC, Olive AJ, Rohlfing A, Taylor GA, Starnbach MN. Compensatory T cell responses in IRG-deficient mice prevent sustained Chlamydia trachomatis infections. PLoS Pathog. 2011 Jun;7(6):e1001346. doi: 10.1371/journal.ppat.1001346. Epub 2011 Jun 23. PMID: 21731484 PMCID: PMC3121881 read article


Dong CK, Urgaonkar S, Cortese JF, Gamo FJ, Garcia-Bustos JF, Lafuente MJ, Patel V, Ross L, Coleman BI, Derbyshire ER, Clish CB, Serrano AE, Cromwell M, Barker RH Jr, Dvorin JD, Duraisingh MT, Wirth DF, Clardy J, Mazitschek R. Identification and validation of tetracyclic benzothiazepines as Plasmodium falciparum cytochrome bc1 inhibitors. Chem Biol. 2011 Dec 23;18(12):1602-10. doi: 10.1016/j.chembiol.2011.09.016. PMID: 22195562 PMCID: PMC3474356 read article


San Roman AK, Shivdasani RA. Boundaries, junctions and transitions in the gastrointestinal tract. Exp Cell Res. 2011 Nov 15;317(19):2711-8. doi: 10.1016/j.yexcr.2011.07.011. Epub 2011 Jul 23. PMID: 21802415 PMCID: PMC3210370 read article


Sarkar A, Hochedlinger K. A gutsy way to grow: intestinal stem cells as nutrient sensors. Cell. 2011 Oct 28;147(3):487-9. doi: 10.1016/j.cell.2011.10.006. PMID: 22036555


Arnold K, Sarkar A, Yram MA, Polo JM, Bronson R, Sengupta S, Seandel M, Geijsen N, Hochedlinger K. Sox2(+) adult stem and progenitor cells are important for tissue regeneration and survival of mice. Cell Stem Cell. 2011 Oct 4;9(4):317-29. doi: 10.1016/j.stem.2011.09.001. PMID: 21982232 PMCID: PMC3538360 read article


Sequist LV, Waltman BA, Dias-Santagata D, Digumarthy S, Turke AB, Fidias P, Bergethon K, Shaw AT, Gettinger S, Cosper AK, Akhavanfard S, Heist RS, Temel J, Christensen JG, Wain JC, Lynch TJ, Vernovsky K, Mark EJ, Lanuti M, Iafrate AJ, Mino-Kenudson M, Engelman JA. Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors. Sci Transl Med. 2011 Mar 23;3(75):75ra26. doi: 10.1126/scitranslmed.3002003. PMID: 21430269 PMCID: PMC3132801 read article


Yang X, Turke AB, Qi J, Song Y, Rexer BN, Miller TW, Jänne PA, Arteaga CL, Cantley LC, Engelman JA, Asara JM. Using tandem mass spectrometry in targeted mode to identify activators of class IA PI3K in cancer. Cancer Res. 2011 Sep 15;71(18):5965-75. doi: 10.1158/0008-5472.CAN-11-0445. Epub 2011 Jul 20. PMID: 21775521 PMCID: PMC3209668 read article


Chen X, Tukachinsky H, Huang CH, Jao C, Chu YR, Tang HY, Mueller B, Schulman S, Rapoport TA, Salic A. Processing and turnover of the Hedgehog protein in the endoplasmic reticulum. J Cell Biol. 2011 Mar 7;192(5):825-38. doi: 10.1083/jcb.201008090. Epub 2011 Feb 28. PMID: 21357747 PMCID: PMC3051819 read article


Dutt A, Ramos AH, Hammerman PS, Mermel C, Cho J, Sharifnia T, Chande A, Tanaka KE, Stransky N, Greulich H, Gray NS, Meyerson M. Inhibitor-sensitive FGFR1 amplification in human non-small cell lung cancer. PLoS One. 2011;6(6):e20351. doi: 10.1371/journal.pone.0020351. Epub 2011 Jun 7. PMID: 21666749 PMCID: PMC3110189 read article


Savin T, Kurpios NA, Shyer AE, Florescu P, Liang H, Mahadevan L, Tabin CJ. On the growth and form of the gut. Nature. 2011 Aug 3;476(7358):57-62. doi: 10.1038/nature10277. PMID: 21814276 PMCID: PMC3335276 read article


Zhou F, Sikorski TW, Ficarro SB, Webber JT, Marto JA. Online nanoflow reversed phase-strong anion exchange-reversed phase liquid chromatography-tandem mass spectrometry platform for efficient and in-depth proteome sequence analysis of complex organisms. Anal Chem. 2011 Sep 15;83(18):6996-7005. doi: 10.1021/ac200639v. Epub 2011 Aug 18. PMID: 21851055 PMCID: PMC3196608 read article


Sikorski TW, Ficarro SB, Holik J, Kim T, Rando OJ, Marto JA, Buratowski S. Sub1 and RPA associate with RNA polymerase II at different stages of transcription. Mol Cell. 2011 Nov 4;44(3):397-409. doi: 10.1016/j.molcel.2011.09.013. PMID: 22055186 PMCID: PMC3227220 read article


Broadbent KM, Park D, Wolf AR, Van Tyne D, Sims JS, Ribacke U, Volkman S, Duraisingh M, Wirth D, Sabeti PC, Rinn JL. A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs. Genome Biol. 2011 Jun 20;12(6):R56. doi: 10.1186/gb-2011-12-6-r56.PMID: 21689454
PMCID: PMC3218844
 read article


Tanner NA, Tolun G, Loparo JJ, Jergic S, Griffith JD, Dixon NE, van Oijen AM. E. coli DNA replication in the absence of free β clamps. EMBO J. 2011 May 4;30(9):1830-40. doi: 10.1038/emboj.2011.84. Epub 2011 Mar 25. PMID: 21441898 PMCID: PMC3101994 read article


Taylor AM, Zon LI. Modeling Diamond Blackfan anemia in the zebrafish. Semin Hematol. 2011 Apr;48(2):81-8. doi: 10.1053/j.seminhematol.2011.02.002. PMID: 21435504


Lal A, Thomas MP, Altschuler G, Navarro F, O'Day E, Li XL, Concepcion C, Han YC, Thiery J, Rajani DK, Deutsch A, Hofmann O, Ventura A, Hide W, Lieberman J. Capture of microRNA-bound mRNAs identifies the tumor suppressor miR-34a as a regulator of growth factor signaling. PLoS Genet. 2011 Nov;7(11):e1002363. doi: 10.1371/journal.pgen.1002363. Epub 2011 Nov 10. PMID: 22102825 PMCID: PMC3213160 read article


Cronican JJ, Beier KT, Davis TN, Tseng JC, Li W, Thompson DB, Shih AF, May EM, Cepko CL, Kung AL, Zhou Q, Liu DR. A class of human proteins that deliver functional proteins into mammalian cells in vitro and in vivo. Chem Biol. 2011 Jul 29;18(7):833-8. doi: 10.1016/j.chembiol.2011.07.003. PMID: 21802004 PMCID: PMC3154086 read article


Tse JC, Kalluri R. Waking up dormant tumors. Breast Cancer Res. 2011 Jun 10;13(3):310. doi: 10.1186/bcr2872. PMID: 21672272 PMCID: PMC3218930 read article


Chen X, Tukachinsky H, Huang CH, Jao C, Chu YR, Tang HY, Mueller B, Schulman S, Rapoport TA, Salic A. Processing and turnover of the Hedgehog protein in the endoplasmic reticulum. J Cell Biol. 2011 Mar 7;192(5):825-38. doi: 10.1083/jcb.201008090. Epub 2011 Feb 28. PMID: 21357747 PMCID: PMC3051819 read article


Ni Chonghaile T, Sarosiek KA, Vo TT, Ryan JA, Tammareddi A, Moore Vdel G, Deng J, Anderson KC, Richardson P, Tai YT, Mitsiades CS, Matulonis UA, Drapkin R, Stone R, Deangelo DJ, McConkey DJ, Sallan SE, Silverman L, Hirsch MS, Carrasco DR, Letai A. Pretreatment mitochondrial priming correlates with clinical response to cytotoxic chemotherapy. Science. 2011 Nov 25;334(6059):1129-33. doi: 10.1126/science.1206727. Epub 2011 Oct 27. PMID: 22033517 PMCID: PMC3280949
 read article


Vong S, Kalluri R. The role of stromal myofibroblast and extracellular matrix in tumor angiogenesis. Genes Cancer. 2011 Dec;2(12):1139-45. doi: 10.1177/1947601911423940. PMID: 22866205 PMCID: PMC3411128 read article


Camp AH, Wang AF, Losick R. A small protein required for the switch from {sigma}F to {sigma}G during sporulation in Bacillus subtilis.J Bacteriol. 2011 Jan;193(1):116-24. doi: 10.1128/JB.00949-10. Epub 2010 Oct 29. PMID: 21037003 PMCID: PMC3019954 read article


Wardwell LH, Huttenhower C, Garrett WS. Current concepts of the intestinal microbiota and the pathogenesis of infection. Curr Infect Dis Rep. 2011 Feb;13(1):28-34. doi: 10.1007/s11908-010-0147-7. PMID: 21308452 PMCID: PMC3077078 read article


Wu MP, Gussoni E. Carbamylated erythropoietin does not alleviate signs of dystrophy in mdx mice. Muscle Nerve. 2011 Jan;43(1):88-93. doi: 10.1002/mus.21785. PMID: 21171099 PMCID: PMC3057654 read article


Yang K, Moldovan GL, Vinciguerra P, Murai J, Takeda S, D'Andrea AD. Regulation of the Fanconi anemia pathway by a SUMO-like delivery network. Genes Dev. 2011 Sep 1;25(17):1847-58. PubMed PMID: 21896657; PubMed Central PMCID: PMC3175720.


Murai J, Yang K, Dejsuphong D, Hirota K, Takeda S, D'Andrea AD. The USP1/UAF1 complex promotes double-strand break repair through homologous recombination. Mol Cell Biol. 2011 Jun;31(12):2462-9. Epub 2011 Apr 11. PubMed PMID: 21482670; PubMed Central PMCID: PMC3133424.


Loh YH, Yang L, Yang JC, Li H, Collins JJ, Daley GQ. Genomic approaches to deconstruct pluripotency. Annu Rev Genomics Hum Genet. 2011;12:165-85. doi: 10.1146/annurev-genom-082410-101506. PMID: 21801025 PMCID: PMC3652340  read article


Lehtinen MK, Zappaterra MW, Chen X, Yang YJ, Hill AD, Lun M, Maynard T, Gonzalez D, Kim S, Ye P, D'Ercole AJ, Wong ET, LaMantia AS, Walsh CA. The cerebrospinal fluid provides a proliferative niche for neural progenitor cells. Neuron. 2011 Mar 10;69(5):893-905. doi: 10.1016/j.neuron.2011.01.023. PMID: 21382550 PMCID: PMC3085909 read article


top

2010


Chou DM, Adamson B, Dephoure NE, Tan X, Nottke AC, Hurov KE, Gygi SP, Colaiácovo MP, Elledge SJ. A chromatin localization screen reveals poly (ADP ribose)-regulated recruitment of the repressive polycomb and NuRD complexes to sites of DNA damage. Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18475-80. doi: 10.1073/pnas.1012946107. Epub 2010 Oct 11. PMID: 20937877 PMCID: PMC2972950 read article


O'Connell BC, Adamson B, Lydeard JR, Sowa ME, Ciccia A, Bredemeyer AL, Schlabach M, Gygi SP, Elledge SJ, Harper JW. A genome-wide camptothecin sensitivity screen identifies a mammalian MMS22L-NFKBIL2 complex required for genomic stability. Mol Cell. 2010 Nov 24;40(4):645-57. doi: 10.1016/j.molcel.2010.10.022. Epub 2010 Nov 4. PMID: 21055985 PMCID: PMC3006237 read article


Agapakis CM, Silver PA. Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway. Bioeng Bugs. 2010 Nov-Dec;1(6):413-8. doi: 10.4161/bbug.1.6.12462. PMID: 21468209 PMCID: PMC3056092 read article


Agapakis CM, Ducat DC, Boyle PM, Wintermute EH, Way JC, Silver PA. Insulation of a synthetic hydrogen metabolism circuit in bacteria. J Biol Eng. 2010 Feb 25;4:3. doi: 10.1186/1754-1611-4-3. PMID: 20184755 PMCID: PMC2847965 read article


Whited JL, Lehoczky JA, Austin CA, Tabin CJ. Dynamic expression of two thrombospondins during axolotl limb regeneration. Dev Dyn. 2011 May;240(5):1249-58. doi: 10.1002/dvdy.22548. Epub 2011 Feb 1. PMID: 21360624 PMCID: PMC3081376 read article


Hellman NE, Liu Y, Merkel E, Austin C, Le Corre S, Beier DR, Sun Z, Sharma N, Yoder BK, Drummond IA. The zebrafish foxj1a transcription factor regulates cilia function in response to injury and epithelial stretch. Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18499-504. doi: 10.1073/pnas.1005998107. Epub 2010 Oct 11. PMID: 20937855 PMCID: PMC2972951 read article


Ching MS, Shen Y, Tan WH, Jeste SS, Morrow EM, Chen X, Mukaddes NM, Yoo SY, Hanson E, Hundley R, Austin C, Becker RE, Berry GT, Driscoll K, Engle EC, Friedman S, Gusella JF, Hisama FM, Irons MB, Lafiosca T, LeClair E, Miller DT, Neessen M, Picker JD, Rappaport L, Rooney CM, Sarco DP, Stoler JM, Walsh CA, Wolff RR, Zhang T, Nasir RH, Wu BL; Children's Hospital Boston Genotype Phenotype Study Group. Deletions of NRXN1 (neurexin-1) predispose to a wide spectrum of developmental disorders. Am J Med Genet B Neuropsychiatr Genet. 2010 Jun 5;153B(4):937-47. doi: 10.1002/ajmg.b.31063. PMID: 20468056 PMCID: PMC3001124 read article


Kim S, Lehtinen MK, Sessa A, Zappaterra MW, Cho SH, Gonzalez D, Boggan B, Austin CA, Wijnholds J, Gambello MJ, Malicki J, LaMantia AS, Broccoli V, Walsh CA. The apical complex couples cell fate and cell survival to cerebral cortical development. Neuron. 2010 Apr 15;66(1):69-84. doi: 10.1016/j.neuron.2010.03.019. PMID: 20399730 PMCID: PMC2872122 read article


Huttlin EL, Jedrychowski MP, Elias JE, Goswami T, Rad R, Beausoleil SA, Villén J, Haas W, Sowa ME, Gygi SP. A tissue-specific atlas of mouse protein phosphorylation and expression. Cell. 2010 Dec 23;143(7):1174-89. doi: 10.1016/j.cell.2010.12.001. PMID: 21183079 PMCID: PMC3035969 read article


Aguiar M, Haas W, Beausoleil SA, Rush J, Gygi SP. Gas-phase rearrangements do not affect site localization reliability in phosphoproteomics data sets. J Proteome Res. 2010 Jun 4;9(6):3103-7. doi: 10.1021/pr1000225. PMID: 20377248 PMCID: PMC2912977 read article


Cronican JJ, Thompson DB, Beier KT, McNaughton BR, Cepko CL, Liu DR. Potent delivery of functional proteins into Mammalian cells in vitro and in vivo using a supercharged protein. ACS Chem Biol. 2010 Aug 20;5(8):747-52. PubMed PMID: 20545362; PubMed Central PMCID: PMC2924640.


Agapakis CM, Ducat DC, Boyle PM, Wintermute EH, Way JC, Silver PA. Insulation of a synthetic hydrogen metabolism circuit in bacteria. J Biol Eng. 2010 Feb 25;4:3. doi: 10.1186/1754-1611-4-3. PMID: 20184755 PMCID: PMC2847965
 read article


Burrill DR, Silver PA. Making cellular memories. Cell. 2010 Jan 8;140(1):13-8. doi: 10.1016/j.cell.2009.12.034. PMID: 20085698 PMCID: PMC2882105 read article


Burrows AE, Smogorzewska A, Elledge SJ. Polybromo-associated BRG1-associated factor components BRD7 and BAF180 are critical regulators of p53 required for induction of replicative senescence. Proc Natl Acad Sci U S A. 2010 Aug 10;107(32):14280-5. doi: 10.1073/pnas.1009559107. Epub 2010 Jul 26. PMID: 20660729 PMCID: PMC2922604 read article


Derti A, Cenik C, Kraft P, Roth FP. Absence of evidence for MHC-dependent mate selection within HapMap populations. PLoS Genet. 2010 Apr 29;6(4):e1000925. PubMed PMID: 20442868; PubMed Central PMCID: PMC2861700.


Cenik C, Derti A, Mellor JC, Berriz GF, Roth FP. Genome-wide functional analysis of human 5' untranslated region introns. Genome Biol. 2010;11(3):R29. Epub 2010 Mar 11. PubMed PMID: 20222956; PubMed Central PMCID: PMC2864569.


Chao MC, Rubin EJ. Letting sleeping dos lie: does dormancy play a role in tuberculosis? Annu Rev Microbiol. 2010;64:293-311. Review. PubMed PMID: 20825351.


Hett EC, Chao MC, Rubin EJ. Interaction and modulation of two antagonistic cell wall enzymes of mycobacteria. PLoS Pathog. 2010 Jul 29;6(7):e1001020. PubMed PMID: 20686708; PubMed Central PMCID: PMC2912383.


Chen AC, Guo LY, Ostaszewski BL, Selkoe DJ, LaVoie MJ. Aph-1 associates directly with full-length and C-terminal fragments of gamma-secretase substrates. J Biol Chem. 2010 Apr 9;285(15):11378-91. Epub 2010 Feb 9. PubMed PMID: 20145246; PubMed Central PMCID: PMC2857016.


Chiang CW, Gajdos ZK, Korn JM, Kuruvilla FG, Butler JL, Hackett R, Guiducci C, Nguyen TT, Wilks R, Forrester T, Haiman CA, Henderson KD, Le Marchand L, Henderson BE, Palmert MR, McKenzie CA, Lyon HN, Cooper RS, Zhu X, Hirschhorn JN. Rapid assessment of genetic ancestry in populations of unknown origin by genome-wide genotyping of pooled samples. PLoS Genet. 2010 Mar 5;6(3):e1000866. PubMed PMID: 20221249; PubMed Central PMCID: PMC2832667.


Kang SJ, Chiang CW, Palmer CD, Tayo BO, Lettre G, Butler JL, Hackett R, Adeyemo AA, Guiducci C, Berzins I, Nguyen TT, Feng T, Luke A, Shriner D, Ardlie K, Rotimi C, Wilks R, Forrester T, McKenzie CA, Lyon HN, Cooper RS, Zhu X, Hirschhorn JN. Genome-wide association of anthropometric traits in African- and African-derived populations. Hum Mol Genet. 2010 Jul 1;19(13):2725-38. Epub 2010 Apr 16. PubMed PMID: 20400458; PubMed Central PMCID: PMC2883343.


Nowak RJ, Cuny GD, Choi S, Lansbury PT, Ray SS. Improving binding specificity of pharmacological chaperones that target mutant superoxide dismutase-1 linked to familial amyotrophic lateral sclerosis using computational methods. J Med Chem. 2010 Apr 8;53(7):2709-18. PubMed PMID: 20232802.


Prisic S, Dankwa S, Schwartz D, Chou MF, Locasale JW, Kang CM, Bemis G, Church GM, Steen H, Husson RN. Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7521-6. Epub 2010 Apr 5. PubMed PMID: 20368441.


Christofferson DE, Yuan J. Necroptosis as an alternative form of programmed cell death. Curr Opin Cell Biol. 2010 Apr;22(2):263-8. doi: 10.1016/j.ceb.2009.12.003. Epub 2010 Jan 4. PMID: 20045303 PMCID: PMC2854308 read article


Christofferson DE, Yuan J. Cyclophilin A release as a biomarker of necrotic cell death. Cell Death Differ. 2010 Dec;17(12):1942-3. doi: 10.1038/cdd.2010.123. Epub 2010 Oct 8. PMID: 20930851 PMCID: PMC2981659 read article


Zhang H, Zhang X, Clark E, Mulcahey M, Huang S, Shi YG. TET1 is a DNA-binding protein that modulates DNA methylation and gene transcription via hydroxylation of 5-methylcytosine. Cell Res. 2010 Dec;20(12):1390-3. doi: 10.1038/cr.2010.156. Epub 2010 Nov 16. PMID: 21079648


Curtis SJ, Sinkevicius KW, Li D, Lau AN, Roach RR, Zamponi R, Woolfenden AE, Kirsch DG, Wong KK, Kim CF. Primary tumor genotype is an important determinant in identification of lung cancer propagating cells. Cell Stem Cell. 2010 Jul 2;7(1):127-33. PubMed PMID: 20621056; PubMed Central PMCID: PMC2908996.


Dufu K Livingstone MJ, Seebacher J, Gygi SP, Wilson SA, Reed R. ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. Genes Dev. 2010 Sep 15;24(18):2043-53. doi: 10.1101/gad.1898610. PMID: 20844015 PMCID: PMC2939366 read article


Li W, Schulman S, Dutton RJ, Boyd D, Beckwith J, Rapoport TA. Structure of a bacterial homologue of vitamin K epoxide reductase. Nature. 2010 Jan 28;463(7280):507-12. PubMed PMID: 20110994.


Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ. Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA. Cell Stem Cell. 2010 Sep 29. [Epub ahead of print] PMID: 20888316


Erwin JA, Lee JT. Characterization of X-chromosome inactivation status in human pluripotent stem cells. Curr Protoc Stem Cell Biol. 2010 Feb;Chapter 1:Unit 1B.6. PubMed PMID: 20127856.


Yang W, Cai Q, Lui VW, Everley PA, Kim J, Bhola N, Quesnelle KM, Zetter BR, Steen H, Freeman MR, Grandis JR. Quantitative proteomics analysis reveals molecular networks regulated by epidermal growth factor receptor level in head and neck cancer. J Proteome Res. 2010 Jun 4;9(6):3073-82. doi: 10.1021/pr901211j. PMID: 20426488 PMCID: PMC3149825 read article


Chiang CW, Gajdos ZK, Korn JM, Kuruvilla FG, Butler JL, Hackett R, Guiducci C, Nguyen TT, Wilks R, Forrester T, Haiman CA, Henderson KD, Le Marchand L, Henderson BE, Palmert MR, McKenzie CA, Lyon HN, Cooper RS, Zhu X, Hirschhorn JN. Rapid assessment of genetic ancestry in populations of unknown origin by genome-wide genotyping of pooled samples. PLoS Genet. 2010 Mar 5;6(3):e1000866. PubMed PMID: 20221249; PubMed Central PMCID: PMC2832667.


Gajdos ZK, Henderson KD, Hirschhorn JN, Palmert MR. Genetic determinants of pubertal timing in the general population. Mol Cell Endocrinol. 2010 Feb 6. [Epub ahead of print] PubMed PMID: 20144687.


Kharas MG, Okabe R, Ganis JJ, Gozo M, Khandan T, Paktinat M, Gilliland DG,Gritsman K. Constitutively active AKT depletes hematopoietic stem cells andinduces leukemia in mice. Blood. 2010 Feb 18;115(7):1406-15. Epub 2009 Dec 14. PubMed PMID: 20008787; PubMed Central PMCID: PMC2826762. read article


Gao D, Wan L, Inuzuka H, Berg AH, Tseng A, Zhai B, Shaik S, Bennett E, Tron AE, Gasser JA, Lau A, Gygi SP, Harper JW, DeCaprio JA, Toker A, Wei W. Rictor forms a complex with Cullin-1 to promote SGK1 ubiquitination and destruction. Mol Cell. 2010 Sep 10;39(5):797-808. doi: 10.1016/j.molcel.2010.08.016. PMID: 20832730 PMCID: PMC2939073 read article


Laurent G, German N, Haigis M. SIRT4 enzymatic activity and biological functions. Review. Experimental Medicine. December 2010. (Invited Review Article - Not a peer reviewed article.)


Grassian AR, Schafer ZT, Brugge JS. ErbB2 stabilizes epidermal growth factor receptor (EGFR) expression via Erk and Sprouty2 in extracellular matrix-detached cells. J Biol Chem. 2011 Jan 7;286(1):79-90. Epub 2010 Oct 18. PubMed PMID: 20956544; PubMed Central PMCID: PMC3013038.


Hall JA, Ribich S, Christoffolete MA, Simovic G, Correa-Medina M, Patti ME, Bianco AC. Absence of thyroid hormone activation during development underlies a permanent defect in adaptive thermogenesis. Endocrinology. 2010 Sep;151(9):4573-82. doi: 10.1210/en.2010-0511. Epub 2010 Jul 21. PMID: 20660060 PMCID: PMC2940501 read article


Gladden AB, Hebert AM, Schneeberger EE, McClatchey AI. The NF2 tumor suppressor, Merlin, regulates epidermal development through the establishment of a junctional polarity complex. Dev Cell. 2010 Nov 16;19(5):727-39. doi: 10.1016/j.devcel.2010.10.008. PMID: 21074722 PMCID: PMC3033574 read article


Rajamani S, Ichida JK, Antal T, Treco DA, Leu K, Nowak MA, Szostak JW, Chen IA. Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication. J Am Chem Soc. 2010 Apr 28;132(16):5880-5. PubMed PMID: 20359213; PubMed Central PMCID: PMC2857888.


Jensen DK, Lal A. Micromanaging senescence. Aging (Albany NY). 2010 Jun;2(6):322-3. PMID: 20603523 PMCID: PMC2919248 read article


Thiery J, Walch M, Jensen DK, Martinvalet D, Lieberman J. Isolation of cytotoxic T cell and NK granules and purification of their effector proteins. Curr Protoc Cell Biol. 2010 Jun;Chapter 3:Unit3.37. doi: 10.1002/0471143030.cb0337s47. PMID: 20521234


Wiig H, Keskin D, Kalluri R. Interaction between the extracellular matrix and lymphatics: consequences for lymphangiogenesis and lymphatic function. Matrix Biol. 2010 Oct;29(8):645-56. doi: 10.1016/j.matbio.2010.08.001. Epub 2010 Aug 18. PMID: 20727409 PMCID: PMC3992865 read article


Keskin D, Kalluri R. NF-kappaB-induced chromatin remodeling regulates angiogenesis.Blood. 2010 Jul 22;116(3):312-3. doi: 10.1182/blood-2010-03-274316. PMID: 20651081


Keebler ME, Deo RC, Surti A, Konieczkowski D, Guiducci C, Burtt N, Buxbaum SG, Sarpong DF, Steffes MW, Wilson JG, Taylor HA, Kathiresan S. Fine-mapping in African Americans of 8 recently discovered genetic loci for plasma lipids: the Jackson Heart Study. Circ Cardiovasc Genet. 2010 Aug;3(4):358-64. doi: 10.1161/CIRCGENETICS.109.914267. Epub 2010 Jun 22. PMID: 20570916 PMCID: PMC3074173
 read article


Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell. 2010 Dec 22;40(6):939-53. doi: 10.1016/j.molcel.2010.12.011. PMID: 21172659 PMCID: PMC3021903.  read article


Bradner JE, Mak R, Tanguturi SK, Mazitschek R, Haggarty SJ, Ross K, Chang CY, Bosco J, West N, Morse E, Lin K, Shen JP, Kwiatkowski NP, Gheldof N, Dekker J, DeAngelo DJ, Carr SA, Schreiber SL, Golub TR, Ebert BL. Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease. Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12617-22. doi: 10.1073/pnas.1006774107. Epub 2010 Jun 28. PMID: 20616024 PMCID: PMC2906581 read article


Kwiatkowski N, Jelluma N, Filippakopoulos P, Soundararajan M, Manak MS, Kwon M, Choi HG, Sim T, Deveraux QL, Rottmann S, Pellman D, Shah JV, Kops GJ, Knapp S, Gray NS. Small-molecule kinase inhibitors provide insight into Mps1 cell cycle function. Nat Chem Biol. 2010 May;6(5):359-68. doi: 10.1038/nchembio.345. Epub 2010 Apr 11. PMID: 20383151 PMCID: PMC2857554 read article


Jelluma N, Dansen TB, Sliedrecht T, Kwiatkowski NP, Kops GJ. Release of Mps1 from kinetochores is crucial for timely anaphase onset. J Cell Biol. 2010 Oct 18;191(2):281-90. doi: 10.1083/jcb.201003038. Epub 2010 Oct 11. PMID: 20937696 PMCID: PMC2958484 read article


Curtis SJ, Sinkevicius KW, Li D, Lau AN, Roach RR, Zamponi R, Woolfenden AE, Kirsch DG, Wong KK, Kim CF. Primary tumor genotype is an important determinant in identification of lung cancer propagating cells. Cell Stem Cell. 2010 Jul 2;7(1):127-33. doi: 10.1016/j.stem.2010.05.021. PMID: 20621056 PMCID: PMC2908996  read article


Liu JJ, Fisher DE. Lighting a path to pigmentation: mechanisms of MITF induction by UV. Pigment Cell Melanoma Res. 2010 Dec;23(6):741-5. doi: 10.1111/j.1755-148X.2010.00775.x. PMID: 20973930


Diebold ML, Koch M, Loeliger E, Cura V, Winston F, Cavarelli J, Romier C. The structure of an Iws1/Spt6 complex reveals an interaction domain conserved in TFIIS, Elongin A and Med26. EMBO J. 2010 Dec 1;29(23):3979-91. doi: 10.1038/emboj.2010.272. Epub 2010 Nov 5. PMID: 21057455 PMCID: PMC3020637 read article


Diebold ML, Loeliger E, Koch M, Winston F, Cavarelli J, Romier C. Noncanonical tandem SH2 enables interaction of elongation factor Spt6 with RNA polymerase II. J Biol Chem. 2010 Dec 3;285(49):38389-98. doi: 10.1074/jbc.M110.146696. Epub 2010 Oct 6. PMID: 20926373 PMCID: PMC2992272 read article


Leisner M, Bleris L, Lohmueller J, Xie Z, Benenson Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nat Nanotechnol. 2010 Sep;5(9):666-70. doi: 10.1038/nnano.2010.135. Epub 2010 Jul 11. PMID: 20622866 PMCID: PMC2934882 read article


Tukachinsky H, Lopez LV, Salic A. A mechanism for vertebrate Hedgehog signaling: recruitment to cilia and dissociation of SuFu-Gli protein complexes. J Cell Biol. 2010 Oct 18;191(2):415-28. doi: 10.1083/jcb.201004108. PMID: 20956384 PMCID: PMC2958481 read article


Mullally A, Lane SW, Ball B, Megerdichian C, Okabe R, Al-Shahrour F, Paktinat M, Haydu JE, Housman E, Lord AM, Wernig G, Kharas MG, Mercher T, Kutok JL, Gilliland DG, Ebert BL. Physiological Jak2V617F expression causes a lethal myeloproliferative neoplasm with differential effects on hematopoietic stem and progenitor cells. Cancer Cell. 2010 Jun 15;17(6):584-96. doi: 10.1016/j.ccr.2010.05.015. PMID: 20541703 PMCID: PMC2909585
 read article


Paradis-Bleau C, Markovski M, Uehara T, Lupoli TJ, Walker S, Kahne DE, Bernhardt TG. Lipoprotein cofactors located in the outer membrane activate bacterial cell wall polymerases. Cell. 2010 Dec 23;143(7):1110-20. PubMed PMID: 21183074; PubMed Central PMCID: PMC3085243.


LeBleu V, Sund M, Sugimoto H, Birrane G, Kanasaki K, Finan E, Miller CA,Gattone VH 2nd, McLaughlin H, Shield CF 3rd, Kalluri R. Identification of the NC1 domain of {alpha}3 chain as critical for {alpha}3{alpha}4{alpha}5 type IVcollagen network assembly. J Biol Chem. 2010 Dec 31;285(53):41874-85. Epub 2010 Sep 16. PubMed PMID: 20847057; PubMed Central PMCID: PMC3009915.


Min J, Zaslavsky A, Fedele G, McLaughlin SK, Reczek EE, De Raedt T, Guney I, Strochlic DE, Macconaill LE, Beroukhim R, Bronson RT, Ryeom S, Hahn WC, Loda M, Cichowski K. An oncogene-tumor suppressor cascade drives metastatic prostate cancer by coordinately activating Ras and nuclear factor-kappaB. Nat Med. 2010 Mar;16(3):286-94. doi: 10.1038/nm.2100. Epub 2010 Feb 14. PMID: 20154697 PMCID: PMC2903662 read article


Hellman NE, Liu Y, Merkel E, Austin C, Le Corre S, Beier DR, Sun Z, Sharma N, Yoder BK, Drummond IA. The zebrafish foxj1a transcription factor regulates cilia function in response to injury and epithelial stretch. Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18499-504. doi: 10.1073/pnas.1005998107. Epub 2010 Oct 11. PMID: 20937855 PMCID: PMC2972951 read article


Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, Cepko CL, Gygi SP, Sicinski P. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 2010 Jan 21;463(7279):374-8. doi: 10.1038/nature08684. PMID: 20090754 PMCID: PMC2943587 read article


Zhu H, Shah S, Shyh-Chang N, Shinoda G, Einhorn WS, Viswanathan SR, Takeuchi A, Grasemann C, Rinn JL, Lopez MF, Hirschhorn JN, Palmert MR, Daley GQ. Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies. Nat Genet. 2010 Jul;42(7):626-30. doi: 10.1038/ng.593. Epub 2010 May 30. PMID: 20512147 PMCID: PMC3069638 read article


Nielsen CM, Dymecki SM. Sonic hedgehog is required for vascular outgrowth in the hindbrain choroid plexus. Dev Biol. 2010 Apr 15;340(2):430-7. Epub 2010 Feb 1. PubMed PMID: 20123094.


Paik EJ, Zon LI. Hematopoietic development in the zebrafish. Int J Dev Biol. 2010;54(6-7):1127-37. doi: 10.1387/ijdb.093042ep. PMID: 20711990


Paik EJ, de Jong JL, Pugach E, Opara P, Zon LI. A chemical genetic screen in zebrafish for pathways interacting with cdx4 in primitive hematopoiesis. Zebrafish. 2010 Mar;7(1):61-8. doi: 10.1089/zeb.2009.0643. PMID: 20415644 PMCID: PMC2897134 read article


Puram SV, Kim AH, Bonni A. An old dog learns new tricks: a novel function for Cdc20-APC in dendrite morphogenesis in neurons. Cell Cycle. 2010 Feb 1;9(3):482-5. PMID: 20195072 PMCID: PMC2853878 read article


Levy C, Khaled M, Robinson KC, Veguilla RA, Chen PH, Yokoyama S, Makino E, Lu J, Larue L, Beermann F, Chin L, Bosenberg M, Song JS, Fisher DE. Lineage-specific transcriptional regulation of DICER by MITF in melanocytes. Cell. 2010 Jun 11;141(6):994-1005. doi: 10.1016/j.cell.2010.05.004. PMID: 20550935 PMCID: PMC2897150 read article


Cao S, Ross L, Tamayo G, Clardy J. Asterogynins: secondary metabolites from a Costa Rican endophytic fungus. Org Lett. 2010 Oct 15;12(20):4661-3. doi: 10.1021/ol101972g. PMID: 20839869 PMCID: PMC2951720 read article


Schlabach MR, Hu JK, Li M, Elledge SJ. Synthetic design of strong promoters. Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2538-43. Epub 2010 Jan 21. PubMed PMID: 20133776; PubMed Central PMCID: PMC2823900.


Turke AB, Zejnullahu K, Wu YL, Song Y, Dias-Santagata D, Lifshits E, Toschi L, Rogers A, Mok T, Sequist L, Lindeman NI, Murphy C, Akhavanfard S, Yeap BY, Xiao Y, Capelletti M, Iafrate AJ, Lee C, Christensen JG, Engelman JA, Jänne PA. Preexistence and clonal selection of MET amplification in EGFR mutant NSCLC. Cancer Cell. 2010 Jan 19;17(1):77-88. doi: 10.1016/j.ccr.2009.11.022. PMID: 20129249 PMCID: PMC2980857 read article


Turke AB, Engelman JA. PIKing the right patient. Clin Cancer Res. 2010 Jul 15;16(14):3523-5. doi: 10.1158/1078-0432.CCR-10-1201. Epub 2010 Jun 10. PMID: 20538763


Schulman S, Wang B, Li W, Rapoport TA. Vitamin K epoxide reductase prefers ER membrane-anchored thioredoxin-like redox partners. Proc Natl Acad Sci U S A. 2010 Aug 24;107(34):15027-32. doi: 10.1073/pnas.1009972107. Epub 2010 Aug 9. PMID: 20696932 PMCID: PMC2930587 read article


Li W, Schulman S, Dutton RJ, Boyd D, Beckwith J, Rapoport TA. Structure of a bacterial homologue of vitamin K epoxide reductase. Nature. 2010 Jan 28;463(7280):507-12. doi: 10.1038/nature08720. PMID: 20110994 PMCID: PMC2919313 read article


Millet YA, Danna CH, Clay NK, Songnuan W, Simon MD, Werck-Reichhart D, Ausubel FM. Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns. Plant Cell. 2010 Mar;22(3):973-90. Epub 2010 Mar 26. PubMed PMID: 20348432; PubMed Central PMCID: PMC2861455.


Smith AC, Raimondi AR, Salthouse CD, Ignatius MS, Blackburn JS, Mizgirev IV, Storer NY, de Jong JL, Chen AT, Zhou Y, Revskoy S, Zon LI, Langenau DM. High-throughput cell transplantation establishes that tumor-initiating cells are abundant in zebrafish T-cell acute lymphoblastic leukemia. Blood. 2010 Apr 22;115(16):3296-303. doi: 10.1182/blood-2009-10-246488. Epub 2010 Jan 7. PMID: 20056790 PMCID: PMC2858492 read article


Kulczyk AW, Tanner NA, Loparo JJ, Richardson CC, van Oijen AM. Direct observation of enzymes replicating DNA using a single-molecule DNA stretching assay. J Vis Exp. 2010 Mar 23;(37). pii: 1689. doi: 10.3791/1689. PMID: 20332766 PMCID: PMC2913797 read article


Tanner NA, van Oijen AM. Visualizing DNA replication at the single-molecule level. Methods Enzymol. 2010;475:259-78. doi: 10.1016/S0076-6879(10)75011-4. PMID: 20627161


Thomas M, Lieberman J, Lal A. Desperately seeking microRNA targets. Nat Struct Mol Biol. 2010 Oct;17(10):1169-74. doi: 10.1038/nsmb.1921. PMID: 20924405


Cronican JJ, Thompson DB, Beier KT, McNaughton BR, Cepko CL, Liu DR. Potent delivery of functional proteins into Mammalian cells in vitro and in vivo using a supercharged protein. ACS Chem Biol. 2010 Aug 20;5(8):747-52. doi: 10.1021/cb1001153. PMID: 20545362 PMCID: PMC2924640 read article


Tukachinsky H, Lopez LV, Salic A. A mechanism for vertebrate Hedgehog signaling: recruitment to cilia and dissociation of SuFu-Gli protein complexes. J Cell Biol. 2010 Oct 18;191(2):415-28. doi: 10.1083/jcb.201004108. PMID: 20956384 PMCID: PMC2958481 read article


Vo TT, Letai A. BH3-only proteins and their effects on cancer. Adv Exp Med Biol. 2010;687:49-63. PMID: 20919637 PMCID: PMC3733261 read article


Black JC, Allen A, Van Rechem C, Forbes E, Longworth M, Tschöp K, Rinehart C, Quiton J, Walsh R, Smallwood A, Dyson NJ, Whetstine JR. Conserved antagonism between JMJD2A/KDM4A and HP1γ during cell cycle progression. Mol Cell. 2010 Dec 10;40(5):736-48. doi: 10.1016/j.molcel.2010.11.008. PMID: 21145482


Walsh RM, Hochedlinger K. Modeling Rett syndrome with stem cells. Cell. 2010 Nov 12;143(4):499-500. doi: 10.1016/j.cell.2010.10.037. PMID: 21074040 PMCID: PMC3538362  read article


Birk E, Har-Zahav A, Manzini CM, Pasmanik-Chor M, Kornreich L, Walsh CA, Noben-Trauth K, Albin A, Simon AJ, Colleaux L, Morad Y, Rainshtein L, Tischfield DJ, Wang P, Magal N, Maya I, Shoshani N, Rechavi G, Gothelf D, Maydan G, Shohat M, Basel-Vanagaite L. SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system. Am J Hum Genet. 2010 Nov 12;87(5):694-700. Epub 2010 Oct 28. PMID: 21035105 PMCID: PMC2978971  read article


de Jong JL, Davidson AJ, Wang Y, Palis J, Opara P, Pugach E, Daley GQ, Zon LI. Interaction of retinoic acid and scl controls primitive blood development. Blood. 2010 Jul 15;116(2):201-9. doi: 10.1182/blood-2009-10-249557. Epub 2010 Apr 21. PMID: 20410509 PMCID: PMC2910607 read article


Wang Y, Krivtsov AV, Sinha AU, North TE, Goessling W, Feng Z, Zon LI, Armstrong SA. The Wnt/beta-catenin pathway is required for the development of leukemia stem cells in AML. Science. 2010 Mar 26;327(5973):1650-3. doi: 10.1126/science.1186624. PMID: 20339075 PMCID: PMC3084586 read article


Sakuma M, Morooka T, Wang Y, Shi C, Croce K, Gao H, Strainic M, Medof ME, Simon DI. The Intrinsic Complement Regulator Decay-Accelerating Factor Modulates the Biological Response to Vascular Injury. Arterioscler Thromb Vasc Biol. 2010 Jun;30(6):1196-202. doi: 10.1161/ATVBAHA.110.205559. Epub 2010 Mar 18. PMID: 20299685 PMCID: PMC2903214 read article


Nozari A, Dilekoz E, Sukhotinsky I, Stein T, Eikermann-Haerter K, Liu C, Wang Y, Frosch MP, Waeber C, Ayata C, Moskowitz MA. Microemboli may link spreading depression, migraine aura, and patent foramen ovale. Ann Neurol. 2010 Feb;67(2):221-9. doi: 10.1002/ana.21871. PMID: 20225282 PMCID: PMC2921919 read article


Wang H, Wu X, Wang Y, Oldenborg PA, Yang YG. CD47 is required for suppression of allograft rejection by donor-specific transfusion. J Immunol. 2010 Apr 1;184(7):3401-7. doi: 10.4049/jimmunol.0901550. Epub 2010 Mar 5. PMID: 20208011 PMCID: PMC3670954 read article


Tung N, Wang Y, Collins LC, Kaplan J, Li H, Gelman R, Comander AH, Gallagher B, Fetten K, Krag K, Stoeckert KA, Legare RD, Sgroi D, Ryan PD, Garber JE, Schnitt SJ. Estrogen receptor positive breast cancers in BRCA1 mutation carriers: clinical risk factors and pathologic features. Breast Cancer Res. 2010;12(1):R12. doi: 10.1186/bcr2478. Epub 2010 Feb 11. PMID: 20149218 PMCID: PMC2880433


Xu X, Yang Z, Liu Q, Wang Y. In vivo fluorescence imaging of muscle cell regeneration by transplanted EGFP-labeled myoblasts. Mol Ther. 2010 Apr;18(4):835-42. Epub 2010 Feb 2. PubMed PMID: 20125125. read article


Simunovic F, Yi M, Wang Y, Stephens R, Sonntag KC. Evidence for gender-specific transcriptional profiles of nigral dopamine neurons in Parkinson disease. PLoS One. 2010 Jan 25;5(1):e8856. doi: 10.1371/journal.pone.0008856. PMID: 20111594 PMCID: PMC2810324 read article


Hartwig S, Ho J, Pandey P, Macisaac K, Taglienti M, Xiang M, Alterovitz G, Ramoni M, Fraenkel E, Kreidberg JA. Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development. Development. 2010 Apr;137(7):1189-203. doi: 10.1242/dev.045732. PMID: 20215353 PMCID: PMC2835332 read article


Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. Ontology engineering. Nat Biotechnol. 2010 Feb;28(2):128-30. doi: 10.1038/nbt0210-128. PMID: 20139945


Xu C, Lo A, Yammanuru A, Tallarico AS, Brady K, Murakami A, Barteneva N, Zhu Q, Marasco WA. Unique biological properties of catalytic domain directed human anti-CAIX antibodies discovered through phage-display technology. PLoS One. 2010 Mar 10;5(3):e9625. PubMed PMID: 20224781; PubMed Central PMCID: PMC2835754.


Vandorpe DH, Xu C, Shmukler BE, Otterbein LE, Trudel M, Sachs F, Gottlieb PA, Brugnara C, Alper SL. Hypoxia activates a Ca2+-permeable cation conductance sensitive to carbon monoxide and to GsMTx-4 in human and mouse sickle erythrocytes. PLoS One. 2010 Jan 15;5(1):e8732. PubMed PMID: 20090940; PubMed Central PMCID: PMC2806905.


Huang M, Kim JM, Shiotani B, Yang K, Zou L, D'Andrea AD. The FANCM/FAAP24 complex is required for the DNA interstrand crosslink-induced checkpoint response. Mol Cell. 2010 Jul 30;39(2):259-68. PubMed PMID: 20670894; PubMed Central PMCID: PMC2928996.


Zeng X, Sigoillot F, Gaur S, Choi S, Pfaff KL, Oh DC, Hathaway N, Dimova N, Cuny GD, King RW. Pharmacologic inhibition of the anaphase-promoting complex induces a spindle checkpoint-dependent mitotic arrest in the absence of spindle damage. Cancer Cell. 2010 Oct 19;18(4):382-95. PubMed PMID: 20951947; PubMed Central PMCID: PMC2957475.


Lipinski MM, Hoffman G, Ng A, Zhou W, Py BF, Hsu E, Liu X, Eisenberg J, Liu J, Blenis J, Xavier RJ, Yuan J. A genome-wide siRNA screen reveals multiple mTORC1 independent signaling pathways regulating autophagy under normal nutritional conditions. Dev Cell. 2010 Jun 15;18(6):1041-52. doi: 10.1016/j.devcel.2010.05.005. PMID: 20627085 PMCID: PMC2935848 read article


top

2009


Agapakis CM, Silver PA. Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks. Mol Biosyst. 2009 Jul;5(7):704-13. doi: 10.1039/b901484e. Epub 2009 May 14. PMID: 19562109


Zhang L, Agosto MA, Ivanovic T, King DS, Nibert ML, Harrison SC. Requirements for the formation of membrane pores by the reovirus myristoylated micro1N peptide. J Virol. 2009 Jul;83(14):7004-14. doi: 10.1128/JVI.00377-09. Epub 2009 May 13. PMID: 19439475 PMCID: PMC2704788 read article


Armour SM, Baur JA, Hsieh SN, Land-Bracha A, Thomas SM, Sinclair DA. Inhibition of mammalian S6 kinase by resveratrol suppresses autophagy. Aging (Albany NY). 2009 Jun 3;1(6):515-28. PMID: 20157535 PMCID: PMC2806030 read article


Schrum JP, Ricardo A, Krishnamurthy M, Blain JC, Szostak JW. Efficient and rapid template-directed nucleic acid copying using 2'-amino-2',3'-dideoxyribonucleoside-5'-phosphorimidazolide monomers. J Am Chem Soc. 2009 Oct 14;131(40):14560-70. PubMed PMID: 19757789; PubMed Central PMCID: PMC2759813.


Py BF, Boyce M, Yuan J. A critical role of eEF-2K in mediating autophagy in response to multiple cellular stresses. Autophagy. 2009 Apr;5(3):393-6. Epub 2009 Apr 6. PMID: 19221463 PMCID: PMC2756538 read article


Boyle PM, Silver PA. Harnessing nature's toolbox: regulatory elements for synthetic biology. J R Soc Interface. 2009 Aug 6;6 Suppl 4:S535-46. doi: 10.1098/rsif.2008.0521.focus. Epub 2009 Mar 4. PMID: 19324675 PMCID: PMC2843961 read article


Kennedy CJ, Boyle PM, Waks Z, Silver PA. Systems-level engineering of nonfermentative metabolism in yeast. Genetics. 2009 Sep;183(1):385-97. doi: 10.1534/genetics.109.105254. Epub 2009 Jun 29. PMID: 19564482 PMCID: PMC2746161


Brown KM, Depristo MA, Weinreich DM, Hartl DL. Temporal constraints on the incorporation of regulatory mutants in evolutionary pathways. Mol Biol Evol. 2009 Nov;26(11):2455-62. Epub 2009 Jul 14. PubMed PMID: 19602543.


Lozovsky ER, Chookajorn T, Brown KM, Imwong M, Shaw PJ, Kamchonwongpaisan S, Neafsey DE, Weinreich DM, Hartl DL. Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):12025-30. Epub 2009 Jul 8. PubMed PMID: 19587242; PubMed Central PMCID: PMC2715478.


Bruckner RJ, Mansy SS, Ricardo A, Mahadevan L, Szostak JW. Flip-flop-induced relaxation of bending energy: implications for membrane remodeling. Biophys J. 2009 Dec 16;97(12):3113-22. PubMed PMID: 20006948; PubMed Central PMCID: PMC2793357.


Budin I, Bruckner RJ, Szostak JW. Formation of protocell-like vesicles in a thermal diffusion column. J Am Chem Soc. 2009 Jul 22;131(28):9628-9. PubMed PMID: 19601679; PubMed Central PMCID: PMC2710859.


Blachon S, Cai X, Roberts KA, Yang K, Polyanovsky A, Church A, Avidor-Reiss T. A proximal centriole-like structure is present in Drosophila spermatids and can serve as a model to study centriole duplication. Genetics. 2009 May;182(1):133-44. doi: 10.1534/genetics.109.101709. Epub 2009 Mar 16. PMID: 19293139 PMCID: PMC2674812 read article


MacConaill LE, Campbell CD, Kehoe SM, Bass AJ, Hatton C, Niu L, Davis M, Yao K, Hanna M, Mondal C, Luongo L, Emery CM, Baker AC, Philips J, Goff DJ, Fiorentino M, Rubin MA, Polyak K, Chan J, Wang Y, Fletcher JA, Santagata S, Corso G, Roviello F, Shivdasani R, Kieran MW, Ligon KL, Stiles CD, Hahn WC, Meyerson ML, Garraway LA. Profiling critical cancer gene mutations in clinical tumor samples. PLoS One. 2009 Nov 18;4(11):e7887. PubMed PMID: 19924296; PubMed Central PMCID: PMC2774511.


Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP. Next generation software for functional trend analysis. Bioinformatics. 2009 Nov 15;25(22):3043-4. Epub 2009 Aug 28. PubMed PMID: 19717575; PubMed Central PMCID: PMC2800365.


Qiao L, Choi S, Case A, Gainer TG, Seyb K, Glicksman MA, Lo DC, Stein RL, Cuny GD. Structure-activity relationship study of EphB3 receptor tyrosine kinase inhibitors. Bioorg Med Chem Lett. 2009 Nov 1;19(21):6122-6. Epub 2009 Sep 9. PubMed PMID: 19783434; PubMed Central PMCID: PMC2785710.


Hwang DY, Hong S, Jeong JW, Choi S, Kim H, Kim J, Kim KS. Vesicular monoamine transporter 2 and dopamine transporter are molecular targets of Pitx3 in the ventral midbrain dopamine neurons. J Neurochem. 2009 Dec;111(5):1202-12. Epub 2009 Sep 24. PubMed PMID: 19780901.


Schwartz D, Chou MF, Church GM. Predicting protein post-translational modifications using meta-analysis of proteome scale data sets. Mol Cell Proteomics. 2009 Feb;8(2):365-79. Epub 2008 Oct 28. PubMed PMID: 18974045; PubMed Central PMCID: PMC2634583.


Mahoney SJ, Dempsey JM, Blenis J. Cell signaling in protein synthesis ribosome biogenesis and translation initiation and elongation. Prog Mol Biol Transl Sci. 2009;90:53-107. doi: 10.1016/S1877-1173(09)90002-3. Epub 2009 Oct 27. PMID: 20374739


Dovey MC, Zon LI. Defining cancer stem cells by xenotransplantation in zebrafish. Methods Mol Biol. 2009;568:1-5. doi: 10.1007/978-1-59745-280-9_1. PMID: 19582417


Dovey M, Patton EE, Bowman T, North T, Goessling W, Zhou Y, Zon LI. Topoisomerase II alpha is required for embryonic development and liver regeneration in zebrafish. Mol Cell Biol. 2009 Jul;29(13):3746-53. doi: 10.1128/MCB.01684-08. Epub 2009 Apr 20. PMID: 19380487PMCID: PMC2698760 read article


Dovey M, White RM, Zon LI. Oncogenic NRAS cooperates with p53 loss to generate melanoma in zebrafish. Zebrafish. 2009 Dec;6(4):397-404. doi: 10.1089/zeb.2009.0606. PMID: 19954345 PMCID: PMC2943216 read article


Dutton RJ, Wayman A, Wei JR, Rubin EJ, Beckwith J, Boyd D. Inhibition of bacterial disulfide bond formation by the anticoagulant warfarin. Proc Natl Acad Sci USA. 2010 Jan 5;107(1):297-301. Epub 2009 Dec 15. PubMed PMID: 20018758; PubMed Central PMCID: PMC2806739.


Ebina W, Rowat AC, Weitz DA. Electrodes on a budget: Micropatterned electrode fabrication by wet chemical deposition. Electrodes on a budget: Micropatterned electrode fabrication by wet chemical deposition. Biomicrofluidics. 2009 Sep 8;3(3):34104. PMID: 20216960 PMCID: PMC2835278 read article


Liu Z, Meray RK, Grammatopoulos TN, Fredenburg RA, Cookson MR, Liu Y, Logan T, Lansbury PT Jr. Membrane-associated farnesylated UCH-L1 promotes alpha-synuclein neurotoxicity and is a therapeutic target for Parkinson's disease. Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4635-40. doi: 10.1073/pnas.0806474106. Epub 2009 Mar 4. PMID: 19261853 PMCID: PMC2651203 read article


Egyud MR, Gajdos ZK, Butler JL, Tischfield S, Le Marchand L, Kolonel LN, Haiman CA, Henderson BE, Hirschhorn JN. Use of weighted reference panels based on empirical estimates of ancestry for capturing untyped variation. Hum Genet. 2009 Apr;125(3):295-303. Epub 2009 Jan 28. PubMed PMID: 19184111.


Gajdos ZK, Hirschhorn JN, Palmert MR. What controls the timing of puberty? An update on progress from genetic investigation. Curr Opin Endocrinol Diabetes Obes. 2009 Feb;16(1):16-24. Review. PubMed PMID: 19104234.


Ganis JJ, Hsia N, Trompouki E, de Jong JL, DiBiase A, Lambert JS, Jia Z, Sabo PJ, Weaver M, Sandstrom R, Stamatoyannopoulos JA, Zhou Y, Zon LI. Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR. Dev Biol. 2012 Jun 15;366(2):185-94. Epub 2012 Apr 19. PubMed PMID: 22537494; PubMed Central PMCID: PMC3378398.  read article


Goldman JA, Garlick JD, Kingston RE. Chromatin remodeling by imitation switch (ISWI) class ATP-dependent remodelers is stimulated by histone variant H2A.Z. J Biol Chem. 2010 Feb 12;285(7):4645-51. Epub 2009 Nov 25. PubMed PMID: 19940112; PubMed Central PMCID: PMC2836070.


Tolstorukov MY, Kharchenko PV, Goldman JA, Kingston RE, Park PJ. Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes. Genome Res. 2009 Jun;19(6):967-77. Epub 2009 Feb 26. PubMed PMID: 19246569; PubMed Central PMCID: PMC2694475.


Schafer ZT, Grassian AR, Song L, Jiang Z, Gerhart-Hines Z, Irie HY, Gao S, Puigserver P, Brugge JS. Antioxidant and oncogene rescue of metabolic defects caused by loss of matrix attachment. Nature. 2009 Sep 3;461(7260):109-13. Epub 2009 Aug 19. PubMed PMID: 19693011; PubMed Central PMCID: PMC2931797.


Hall JA, Bianco AC. Triumphs of the thyroid despite lesser conversion. Endocrinology. 2009 Jun;150(6):2502-4. doi: 10.1210/en.2009-0347. PMID: 19458245


Huynh MA, Stegmüller J, Litterman N, Bonni A. Regulation of Cdh1-APC function in axon growth by Cdh1 phosphorylation. J Neurosci. 2009 Apr 1;29(13):4322-7. doi: 10.1523/JNEUROSCI.5329-08.2009. PMID: 19339626 PMCID: PMC2839872 read article


Ikeuchi Y, Stegmüller J, Netherton S, Huynh MA, Masu M, Frank D, Bonni S, Bonni A. A SnoN-Ccd1 pathway promotes axonal morphogenesis in the mammalian brain. J Neurosci. 2009 Apr 1;29(13):4312-21. doi: 10.1523/JNEUROSCI.0126-09.2009. PMID: 19339625 PMCID: PMC2853192 read article


Ichida JK, Blanchard J, Lam K, Son EY, Chung JE, Egli D, Loh KM, Carter AC, Di Giorgio FP, Koszka K, Huangfu D, Akutsu H, Liu DR, Rubin LL, Eggan K. A small-molecule inhibitor of tgf-Beta signaling replaces sox2 in reprogramming by inducing nanog. Cell Stem Cell. 2009 Nov 6;5(5):491-503. Epub 2009 Oct 8. PubMed PMID: 19818703.


Jadhav AP, Roesch K, Cepko CL. Development and neurogenic potential of Müller glial cells in the vertebrate retina. Prog Retin Eye Res. 2009 Jul;28(4):249-62. doi: 10.1016/j.preteyeres.2009.05.002. Epub 2009 May 22. PMID: 19465144 PMCID: PMC3233204 read article


Soukas AA, Kane EA, Carr CE, Melo JA, Ruvkun G. Rictor/TORC2 regulates fat metabolism, feeding, growth, and life span in Caenorhabditis elegans. Genes Dev. 2009 Feb 15;23(4):496-511. doi: 10.1101/gad.1775409. PMID: 19240135 PMCID: PMC2648650 read article


Vasudevan KM, Barbie DA, Davies MA, Rabinovsky R, McNear CJ, Kim JJ, Hennessy BT, Tseng H, Pochanard P, Kim SY, Dunn IF, Schinzel AC, Sandy P, Hoersch S, Sheng Q, Gupta PB, Boehm JS, Reiling JH, Silver S, Lu Y, Stemke-Hale K, Dutta B, Joy C, Sahin AA, Gonzalez-Angulo AM, Lluch A, Rameh LE, Jacks T, Root DE, Lander ES, Mills GB, Hahn WC, Sellers WR, Garraway LA. AKT-independent signaling downstream of oncogenic PIK3CA mutations in human cancer. Cancer Cell. 2009 Jul 7;16(1):21-32. doi: 10.1016/j.ccr.2009.04.012. PMID: 19573809 PMCID: PMC2752826 read article


Emery CM, Vijayendran KG, Zipser MC, Sawyer AM, Niu L, Kim JJ, Hatton C, Chopra R, Oberholzer PA, Karpova MB, MacConaill LE, Zhang J, Gray NS, Sellers WR, Dummer R, Garraway LA. MEK1 mutations confer resistance to MEK and B-RAF inhibition. Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20411-6. doi: 10.1073/pnas.0905833106. Epub 2009 Nov 13. PMID: 19915144 PMCID: PMC2777185 read article


Schweitzer MH, Zheng W, Organ CL, Avci R, Suo Z, Freimark LM, Lebleu VS, Duncan MB, Vander Heiden MG, Neveu JM, Lane WS, Cottrell JS, Horner JR, Cantley LC, Kalluri R, Asara JM. Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis. Science. 2009 May 1;324(5927):626-31. PubMed PMID: 19407199.


Tzur A, Kafri R, LeBleu VS, Lahav G, Kirschner MW. Cell growth and size homeostasis in proliferating animal cells. Science. 2009 Jul 10;325(5937):167-71. PubMed PMID: 19589995; PubMed Central PMCID: PMC2905160.


Shen X, Kim W, Fujiwara Y, Simon MD, Liu Y, Mysliwiec MR, Yuan GC, Lee Y, Orkin SH. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell. 2009 Dec 24;139(7):1303-14. PubMed PMID: 20064376; PubMed Central PMCID: PMC2810107.


Dominy JE Jr, Lee Y, Gerhart-Hines Z, Puigserver P. Nutrient-dependent regulation of PGC-1alpha's acetylation state and metabolic function through the enzymatic activities of Sirt1/GCN5. Biochim Biophys Acta. 2009 Dec 11. [Epub ahead of print] PubMed PMID: 20005308.


Chien K, Cai T, Hsu H, Su T, Chang W, Chen M, Lee Y, Hu FB. A prediction model for type 2 diabetes risk among Chinese people. Diabetologia. 2009 Mar;52(3):443-50. Epub 2008 Dec 5. PubMed PMID: 19057891.


Frueh DP, Leed A, Arthanari H, Koglin A, Walsh CT, Wagner G. Time-shared HSQC-NOESY for accurate distance constraints measured at high-field in (15)N-(13)C-ILV methyl labeled proteins. J Biomol NMR. 2009 Nov;45(3):311-8. doi: 10.1007/s10858-009-9372-5. PMID: 19728110 PMCID: PMC2778061 read article


Clatworthy AE, Lee JS, Leibman M, Kostun Z, Davidson AJ, Hung DT. Pseudomonas aeruginosa infection of zebrafish involves both host and pathogen determinants. Infect Immun. 2009 Apr;77(4):1293-303. doi: 10.1128/IAI.01181-08. Epub 2009 Jan 21. PMID: 19168742 PMCID: PMC2663173 read article


Johnson A, Li G, Sikorski TW, Buratowski S, Woodcock CL, Moazed D*. Reconstitution of heterochromatin-dependent transcriptional gene silencing. Mol Cell. 2009 Sep 24;35(6):769-81. PubMed PMID: 19782027; PubMed Central PMCID: PMC2842978.


Naylor ML, Li JM, Osborn AJ, Elledge SJ. Mrc1 phosphorylation in response to DNA replication stress is required for Mec1 accumulation at the stalled fork. Proc Natl Acad Sci USA. 2009 Aug 4;106(31):12765-70. Epub 2009 Jun 10. PubMed PMID: 19515819; PubMed Central PMCID: PMC2722297.


Li VC, Davis JC, Lenkov K, Bolival B, Fuller MT, Petrov DA. Molecular evolution of the testis TAFs of Drosophila. Mol Biol Evol. 2009 May;26(5):1103-16. doi: 10.1093/molbev/msp030. Epub 2009 Feb 25. PMID: 19244474 PMCID: PMC2727373 read article


Gordon WR, Vardar-Ulu D, L'Heureux S, Ashworth T, Malecki MJ, Sanchez-Irizarry C, McArthur DG, Histen G, Mitchell JL, Aster JC, Blacklow SC. Effects of S1 cleavage on the structure, surface export, and signaling activity of human Notch1 and Notch2. PLoS One. 2009 Aug 24;4(8):e6613. doi: 10.1371/journal.pone.0006613. PMID: 19701457 PMCID: PMC2726630 read article


Brencic A, McFarland KA, McManus HR, Castang S, Mogno I, Dove SL, Lory S. The GacS/GacA signal transduction system of Pseudomonas aeruginosa acts exclusively through its control over the transcription of the RsmY and RsmZ regulatory small RNAs. Mol Microbiol. 2009 Aug;73(3):434-45. doi: 10.1111/j.1365-2958.2009.06782.x. Epub 2009 Jul 9. PMID: 19602144 PMCID: PMC2761719 read article


Mitra D, Fisher DE. Transcriptional regulation in melanoma. Hematol Oncol Clin North Am. 2009 Jun;23(3):447-65, viii. doi: 10.1016/j.hoc.2009.03.003. PMID: 19464596


Morris ZS, McClatchey AI. The neurofibroma cell of origin: SKPs expand the playing field. Cell Stem Cell. 2009 May 8;4(5):371-2. doi: 10.1016/j.stem.2009.04.010. PMID: 19427284


Morris ZS, McClatchey AI. Aberrant epithelial morphology and persistent epidermal growth factor receptor signaling in a mouse model of renal carcinoma. Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9767-72. doi: 10.1073/pnas.0902031106. Epub 2009 Jun 1. PMID: 19487675 PMCID: PMC2700996
 read article


Naylor ML, Li JM, Osborn AJ, Elledge SJ. Mrc1 phosphorylation in response to DNA replication stress is required for Mec1 accumulation at the stalled fork. Proc Natl Acad Sci USA. 2009 Aug 4;106(31):12765-70. Epub 2009 Jun 10. PubMed PMID: 19515819; PubMed Central PMCID: PMC2722297.


Ng MR, Brugge JS. A stiff blow from the stroma: collagen crosslinking drives tumor progression. Cancer Cell. 2009 Dec 8;16(6):455-7. doi: 10.1016/j.ccr.2009.11.013. PMID: 19962663


Burns CE, Galloway JL, Smith AC, Keefe MD, Cashman TJ, Paik EJ, Mayhall EA, Amsterdam AH, Zon LI. A genetic screen in zebrafish defines a hierarchical network of pathways required for hematopoietic stem cell emergence. Blood. 2009 Jun 4;113(23):5776-82. doi: 10.1182/blood-2008-12-193607. Epub 2009 Mar 30. PMID: 19332767 PMCID: PMC2700318 read article


Hagan JP, Piskounova E, Gregory RI. Lin28 recruits the TUTase Zcchc11 to inhibit let-7 maturation in mouse embryonic stem cells. Nat Struct Mol Biol. 2009 Oct;16(10):1021-5. Epub 2009 Aug 27. PubMed PMID: 19713958; PubMed Central PMCID: PMC2758923.


de la Iglesia N, Puram SV, Bonni A. STAT3 regulation of glioblastoma pathogenesis. Curr Mol Med. 2009 Jun;9(5):580-90. PMID: 19601808 PMCID: PMC2712135 read article


Kim AH, Puram SV, Bilimoria PM, Ikeuchi Y, Keough S, Wong M, Rowitch D, Bonni A. A centrosomal Cdc20-APC pathway controls dendrite morphogenesis in postmitotic neurons. Cell. 2009 Jan 23;136(2):322-36. doi: 10.1016/j.cell.2008.11.050. PMID: 19167333 PMCID: PMC2707082 read article


Raiser DM, Kim CF. Commentary: Sca-1 and Cells of the Lung: A matter of Different Sorts. Stem Cells. 2009 Mar;27(3):606-11. doi: 10.1002/stem.10. PMID: 19259938 PMCID: PMC3408081 read article


Chan EM, Ratanasirintrawoot S, Park IH, Manos PD, Loh YH, Huo H, Miller JD, Hartung O, Rho J, Ince TA, Daley GQ, Schlaeger TM. Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. Nat Biotechnol. 2009 Nov;27(11):1033-7. doi: 10.1038/nbt.1580. Epub 2009 Oct 11. PMID: 19826408


Rhee DY, Zhao XQ, Francis RJ, Huang GY, Mably JD, Lo CW. Connexin 43 regulates epicardial cell polarity and migration in coronary vascular development. Development. 2009 Sep;136(18):3185-93. doi: 10.1242/dev.032334. PMID: 19700622 PMCID: PMC2730372 read article


Robinson KC, Fisher DE. Specification and loss of melanocyte stem cells. Semin Cell Dev Biol. 2009 Feb;20(1):111-6. doi: 10.1016/j.semcdb.2008.11.016. Epub 2008 Dec 13. PMID: 19124082


Rosen JN, Sweeney MF, Mably JD. Microinjection of zebrafish embryos to analyze gene function. J Vis Exp. 2009 Mar 9;(25). pii: 1115. doi: 10.3791/1115. PubMed PMID: 19274045.


Luo J, Emanuele MJ, Li D, Creighton CJ, Schlabach MR, Westbrook TF, Wong KK, Elledge SJ. A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene. Cell. 2009 May 29;137(5):835-48. PubMed PMID: 19490893; PubMed Central PMCID: PMC2768667.


Xu Q, Schlabach MR, Hannon GJ, Elledge SJ. Design of 240,000 orthogonal 25mer DNA barcode probes. Proc Natl Acad Sci U S A. 2009 Feb 17;106(7):2289-94. Epub 2009 Jan 26. PubMed PMID: 19171886; PubMed Central PMCID: PMC2631075.


Schneiderman JI, Sakai A, Goldstein S, Ahmad K*. The XNP remodeler targets dynamic chromatin in Drosophila. Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14472-7. Epub 2009 Aug 11. PubMed PMID: 19706533; PubMed Central PMCID: PMC2725014.


Sikorski TW, Buratowski S. The basal initiation machinery: beyond the general transcription factors. Curr Opin Cell Biol. 2009 Jun;21(3):344-51. doi: 10.1016/j.ceb.2009.03.006. Epub 2009 May 4. PMID: 19411170 PMCID: PMC2692371 read article


Johnson A, Li G, Sikorski TW, Buratowski S, Woodcock CL, Moazed D. Reconstitution of heterochromatin-dependent transcriptional gene silencing. Mol Cell. 2009 Sep 24;35(6):769-81. doi: 10.1016/j.molcel.2009.07.030. PMID: 19782027 PMCID: PMC2842978 read article


Sims JS, Militello KT, Sims PA, Patel VP, Kasper JM, Wirth DF. Patterns of gene-specific and total transcriptional activity during the Plasmodium falciparum intraerythrocytic developmental cycle. Eukaryot Cell. 2009 Mar;8(3):327-38. doi: 10.1128/EC.00340-08. Epub 2009 Jan 16. PMID: 19151330 PMCID: PMC2653245 read article


Tanner NA, Loparo JJ, van Oijen AM. Visualizing Single-molecule DNA Replication with Fluorescence Microscopy. J Vis Exp. 2009 Oct 9;(32). pii: 1529. doi: 10.3791/1529. PMID: 19820685 PMCID: PMC3142874 read article


Tanner NA, van Oijen AM. Single-molecule observation of prokaryotic DNA replication. Methods Mol Biol. 2009;521:397-410. doi: 10.1007/978-1-60327-815-7_22. PMID: 19563119 PMCID: PMC2943766 read article


Tanner NA, Loparo JJ, Hamdan SM, Jergic S, Dixon NE, van Oijen AM. Real-time single-molecule observation of rolling-circle DNA replication. Nucleic Acids Res. 2009 Mar;37(4):e27. doi: 10.1093/nar/gkp006. Epub 2009 Jan 20. PMID: 19155275 PMCID: PMC2651787 read article


McNaughton BR, Cronican JJ, Thompson DB, Liu DR. Mammalian cell penetration, siRNA transfection, and DNA transfection by supercharged proteins. Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6111-6. doi: 10.1073/pnas.0807883106. Epub 2009 Mar 23. PMID: 19307578 PMCID: PMC2659711 read article


Utikal J, Polo JM, Stadtfeld M, Maherali N, Kulalert W, Walsh RM, Khalil A, Rheinwald JG, Hochedlinger K. Immortalization eliminates a roadblock during cellular reprogramming into iPS cells. Nature. 2009 Aug 27;460(7259):1145-8. doi: 10.1038/nature08285. Epub 2009 Aug 9. PMID: 19668190 PMCID: PMC3987892 read article


Zhang X, Rice K, Wang Y, Chen W, Zhong Y, Nakayama Y, Zhou Y, Klibanski A. Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions. Endocrinology. 2010 Mar;151(3):939-47. doi: 10.1210/en.2009-0657. Epub 2009 Dec 23. PMID: 20032057 PMCID: PMC2840681 read article


Fraenkel PG, Gibert Y, Holzheimer JL, Lattanzi VJ, Burnett SF, Dooley KA, Wingert RA, Zon LI. Transferrin-a modulates hepcidin expression in zebrafish embryos. Blood. 2009 Mar 19;113(12):2843-50. doi: 10.1182/blood-2008-06-165340. Epub 2008 Dec 1. PMID: 19047682 PMCID: PMC2661867 read article


top

2008


Agosto MA, Myers KS, Ivanovic T, Nibert ML. A positive-feedback mechanism promotes reovirus particle conversion to the intermediate associated with membrane penetration. Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10571-6. doi: 10.1073/pnas.0802039105. Epub 2008 Jul 24. PMID: 18653761 PMCID: PMC2492467 read article


Ivanovic T, Agosto MA, Zhang L, Chandran K, Harrison SC, Nibert ML. Peptides released from reovirus outer capsid form membrane pores that recruit virus particles. EMBO J. 2008 Apr 23;27(8):1289-98. doi: 10.1038/emboj.2008.60. Epub 2008 Mar 27. PMID: 18369316 PMCID: PMC2367403 read article


Anderson SB, Goldberg AL, Whitman M. Identification of a novel pool of extracellular pro-myostatin in skeletal muscle. J Biol Chem. 2008 Mar 14;283(11):7027-35. doi: 10.1074/jbc.M706678200. Epub 2008 Jan 6. PMID: 18175804


Atkins BD, Yoshida S, Pellman D. Symmetry breaking: scaffold plays matchmaker for polarity signaling proteins. Curr Biol. 2008 Dec 23;18(24):R1130-2. doi: 10.1016/j.cub.2008.11.005. PMID: 19108767


Balibar CJ, Walsh CT. From thioesters to amides and back: condensation domain reversibility in the biosynthesis of vibriobactin. Chembiochem. 2008 Jan 4;9(1):42-5. PMID: 18022888


Ryan KS, Balibar CJ, Turo KE, Walsh CT, Drennan CL. The violacein biosynthetic enzyme VioE shares a fold with lipoprotein transporter proteins. J Biol Chem. 2008 Mar 7;283(10):6467-75. doi: 10.1074/jbc.M708573200. Epub 2008 Jan 2. PMID: 18171675


Villén J, Beausoleil SA, Gygi SP. Evaluation of the utility of neutral-loss-dependent MS3 strategies in large-scale phosphorylation analysis. Proteomics. 2008 Nov;8(21):4444-52. doi: 10.1002/pmic.200800283. PMID: 18972524 PMCID: PMC2745099
 read article


Dephoure N, Zhou C, Villén J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP. A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi: 10.1073/pnas.0805139105. Epub 2008 Jul 31. PMID: 18669648 PMCID: PMC2504835
 read article


Zhai B, Villén J, Beausoleil SA, Mintseris J, Gygi SP. Phosphoproteome analysis of Drosophila melanogaster embryos. J Proteome Res. 2008 Apr;7(4):1675-82. doi: 10.1021/pr700696a. Epub 2008 Mar 8. PMID: 18327897 PMCID: PMC3063950 read article


Boyce M, Py BF, Ryazanov AG, Minden JS, Long K, Ma D, Yuan J. A pharmacoproteomic approach implicates eukaryotic elongation factor 2 kinase in ER stress-induced cell death. Cell Death Differ. 2008 Mar;15(3):589-99. doi: 10.1038/sj.cdd.4402296. Epub 2008 Jan 11. PMID: 18188169


Bryant KF, Macari ER, Malik N, Boyce M, Yuan J, Coen DM. ICP34.5-dependent and -independent activities of salubrinal in herpes simplex virus-1 infected cells. Virology. 2008 Sep 30;379(2):197-204. doi: 10.1016/j.virol.2008.06.028. Epub 2008 Aug 6. PMID: 18684481 PMCID: PMC2665023 read article


Brown KM, Landry CR, Hartl DL, Cavalieri D. Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae. Mol Ecol. 2008 Jun;17(12):2985-97. Epub 2008 Apr 18. PubMed PMID: 18422925.


Burrows AE, Elledge SJ. How ATR turns on: TopBP1 goes on ATRIP with ATR. Genes Dev. 2008 Jun 1;22(11):1416-21. doi: 10.1101/gad.1685108. PMID: 18519633 PMCID: PMC2732414 read article


Hett EC, Chao MC, Deng LL, Rubin EJ. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008 Feb 29;4(2):e1000001. PubMed PMID: 18463693; PubMed Central PMCID: PMC2262848.


Young-Pearse TL, Chen AC, Chang R, Marquez C, Selkoe DJ. Secreted APP regulates the function of full-length APP in neurite outgrowth through interaction with integrin beta1. Neural Dev. 2008 Jun 23;3:15. PubMed PMID: 18573216; PubMed Central PMCID: PMC2442059.


Cheung V, Chua G, Batada NN, Landry CR, Michnick SW, Hughes TR, Winston F. Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. PLoS Biol. 2008 Nov 11;6(11):e277. PubMed PMID: 18998772; PubMed Central PMCID: PMC2581627.


Chiang CW, Derti A, Schwartz D, Chou MF, Hirschhorn JN, Wu CT. Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries. Genetics. 2008 Dec;180(4):2277-93. Epub 2008 Oct 28. PubMed PMID: 18957701; PubMed Central PMCID: PMC2600958.


Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SF, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, Derohannessian S, de Bakker PI, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CW, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, Fitzgerald GA. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One. 2008;3(10):e3583. Epub 2008 Oct 31. PubMed PMID: 18974833; PubMed Central PMCID: PMC2571995.


Cutler C, Stevenson K, Kim HT, Richardson P, Ho VT, Linden E, Revta C, Ebert R, Warren D, Choi S, Koreth J, Armand P, Alyea E, Carter S, Horowitz M, Antin JH, Soiffer R. Sirolimus is associated with veno-occlusive disease of the liver after myeloablative allogeneic stem cell transplantation. Blood. 2008 Dec 1;112(12):4425-31. Epub 2008 Sep 5. PubMed PMID: 18776081; PubMed Central PMCID: PMC2597119.


Mitnick CD, Shin SS, Seung KJ, Rich ML, Atwood SS, Furin JJ, Fitzmaurice GM, Alcantara Viru FA, Appleton SC, Bayona JN, Bonilla CA, Chalco K, Choi S, Franke MF, Fraser HS, Guerra D, Hurtado RM, Jazayeri D, Joseph K, Llaro K, Mestanza L, Mukherjee JS, Muñoz M, Palacios E, Sanchez E, Sloutsky A, Becerra MC. Comprehensive treatment of extensively drug-resistant tuberculosis. N Engl J Med. 2008 Aug 7;359(6):563-74. PubMed PMID: 18687637; PubMed Central PMCID: PMC2673722.


Liu M, Choi S, Cuny GD, Ding K, Dobson BC, Glicksman MA, Auerbach K, Stein RL. Kinetic studies of Cdk5/p25 kinase: phosphorylation of tau and complex inhibition by two prototype inhibitors. Biochemistry. 2008 Aug 12;47(32):8367-77. Epub 2008 Jul 18. PubMed PMID: 18636751.


Chiang CW, Derti A, Schwartz D, Chou MF, Hirschhorn JN, Wu CT. Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries. Genetics. 2008 Dec;180(4):2277-93. Epub 2008 Oct 28. PubMed PMID: 18957701; PubMed Central PMCID: PMC2600958.


Hitomi J, Christofferson DE, Ng A, Yao J, Degterev A, Xavier RJ, Yuan J. Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway. Cell. 2008 Dec 26;135(7):1311-23. doi: 10.1016/j.cell.2008.10.044. PMID: 19109899 PMCID: PMC2621059 read article


Chun DK, McEwen JM, Burbea M, Kaplan JM. UNC-108/Rab2 regulates postendocytic trafficking in Caenorhabditis elegans. Mol Biol Cell. 2008 Jul;19(7):2682-95. doi: 10.1091/mbc.E07-11-1120. Epub 2008 Apr 23. PMID: 18434599 PMCID: PMC2441656 read article


Raiser DM, Zacharek SJ, Roach RR, Curtis SJ, Sinkevicius KW, Gludish DW, Kim CF. Stem cell biology in the lung and lung cancers: using pulmonary context and classic approaches. Cold Spring Harb Symp Quant Biol. 2008;73:479-90. Epub 2008 Nov 21. Review. PubMed PMID: 19028984.


White RM, Sessa A, Burke C, Bowman T, LeBlanc J, Ceol C, Bourque C, Dovey M, Goessling W, Burns CE, Zon LI. Transparent adult zebrafish as a tool for in vivo transplantation analysis. Cell Stem Cell. 2008 Feb 7;2(2):183-9. doi: 10.1016/j.stem.2007.11.002. PMID: 18371439 PMCID: PMC2292119 read article


Dallabrida SM, Ismail NS, Pravda EA, Parodi EM, Dickie R, Durand EM, Lai J,Cassiola F, Rogers RA, Rupnick MA. Integrin binding angiopoietin-1 monomers reduce cardiac hypertrophy. FASEB J. 2008 Aug;22(8):3010-23. Epub 2008 May 23. PubMed PMID: 18502941; PubMed Central PMCID: PMC2493452.


Dutton RJ, Boyd D, Berkmen M, Beckwith J. Bacterial species exhibit diversity in their mechanisms and capacity for protein disulfide bond formation. Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11933-8. Epub 2008 Aug 11. PubMed PMID: 18695247; PubMed Central PMCID: PMC2575290.


Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science. 2008 Oct 31;322(5902):750-6. PubMed PMID: 18974356; PubMed Central PMCID: PMC2748911.


Erwin JA, Lee JT. New twists in X-chromosome inactivation. Curr Opin Cell Biol. 2008 Jun;20(3):349-55. Epub 2008 May 26. Review. PubMed PMID: 18508252; PubMed Central PMCID: PMC2491718.


Bakalarski CE, Elias JE, Villén J, Haas W, Gerber SA, Everley PA, Gygi SP. The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses. J Proteome Res. 2008 Nov;7(11):4756-65. doi: 10.1021/pr800333e. Epub 2008 Sep 18. PMID: 18798661 PMCID: PMC2746028


Paleologou KE, Schmid AW, Rospigliosi CC, Kim HY, Lamberto GR, Fredenburg RA, Lansbury PT Jr, Fernandez CO, Eliezer D, Zweckstetter M, Lashuel HA. Phosphorylation at Ser-129 but not the phosphomimics S129E/D inhibits the fibrillation of alpha-synuclein. J Biol Chem. 2008 Jun 13;283(24):16895-905. doi: 10.1074/jbc.M800747200. Epub 2008 Mar 14. PMID: 18343814 PMCID: PMC2423264 read article


Gabel HW, Ruvkun G. The exonuclease ERI-1 has a conserved dual role in 5.8S rRNA processing and RNAi. Nat Struct Mol Biol. 2008 May;15(5):531-3. Epub 2008 Apr 27. PubMed PMID: 18438419.


Pierce ML, Weston MD, Fritzsch B, Gabel HW, Ruvkun G, Soukup GA. MicroRNA-183 family conservation and ciliated neurosensory organ expression. Evol Dev. 2008 Jan-Feb;10(1):106-13. PubMed PMID: 18184361; PubMed Central PMCID: PMC2637451.


Gajdos ZK, Butler JL, Henderson KD, He C, Supelak PJ, Egyud M, Price A, Reich D, Clayton PE, Le Marchand L, Hunter DJ, Henderson BE, Palmert MR, Hirschhorn JN Association studies of common variants in 10 hypogonadotropic hypogonadism genes with age at menarche. J Clin Endocrinol Metab. 2008 Nov;93(11):4290-8. Epub 2008 Aug 26. PubMed PMID: 18728166; PubMed Central PMCID: PMC2582573.


Wilson-Grady JT, Villén J, Gygi SP. Phosphoproteome analysis of fission yeast. J Proteome Res. 2008 Mar;7(3):1088-97. doi: 10.1021/pr7006335. Epub 2008 Feb 8. PMID: 18257517


Yuan AH, Gregory BD, Sharp JS, McCleary KD, Dove SL, Hochschild A. Rsd family proteins make simultaneous interactions with regions 2 and 4 of the primary sigma factor. Mol Microbiol. 2008 Dec;70(5):1136-51. doi: 10.1111/j.1365-2958.2008.06462.x. Epub 2008 Sep 30. PMID: 18826409 PMCID: PMC2581641 read article


Kim JM, Kee Y, Gurtan A, D'Andrea AD. Cell cycle-dependent chromatin loading of the Fanconi anemia core complex by FANCM/FAAP24. Blood. 2008 May 15;111(10):5215-22. doi: 10.1182/blood-2007-09-113092. Epub 2008 Jan 3. PMID: 18174376 PMCID: PMC2384144 read article


Yoshida T, Hazan I, Zhang J, Ng SY, Naito T, Snippert HJ, Heller EJ, Qi X, Lawton LN, Williams CJ, Georgopoulos K. The role of the chromatin remodeler Mi-2beta in hematopoietic stem cell self-renewal and multilineage differentiation. Genes Dev. 2008 May 1;22(9):1174-89. doi: 10.1101/gad.1642808. PMID: 18451107 PMCID: PMC2335314 read article


Hill SJ, Berkowitz R, Granter SR, Hirsch MS. Pagetoid lesions of the vulva: a collision between malignant melanoma and extramammary Paget disease.Int J Gynecol Pathol. 2008 Apr;27(2):292-6. PMID: 18317209


Stegmüller J, Huynh MA, Yuan Z, Konishi Y, Bonni A. TGFbeta-Smad2 signaling regulates the Cdh1-APC/SnoN pathway of axonal morphogenesis. J Neurosci. 2008 Feb 20;28(8):1961-9. doi: 10.1523/JNEUROSCI.3061-07.2008. PMID: 18287512


Sarker KP, Kataoka H, Chan A, Netherton SJ, Pot I, Huynh MA, Feng X, Bonni A, Riabowol K, Bonni S. ING2 as a novel mediator of transforming growth factor-beta-dependent responses in epithelial cells. J Biol Chem. 2008 May 9;283(19):13269-79. doi: 10.1074/jbc.M708834200. Epub 2008 Mar 11. PMID: 18334480 PMCID: PMC2442333 read article


Sullivan S, Ichida JK, Umezawa A, Akutsu H. Elucidating nuclear reprogramming mechanisms: taking a synergistic approach. Reprod Biomed Online. 2008 Jan;16(1):41-50. Review. PubMed PMID: 18252046.


Roesch K, Jadhav AP, Trimarchi JM, Stadler MB, Roska B, Sun BB, Cepko CL. The transcriptome of retinal Müller glial cells. J Comp Neurol. 2008 Jul 10;509(2):225-38. doi: 10.1002/cne.21730. PMID: 18465787 PMCID: PMC2665263 read article


Damiani D, Alexander JJ, O'Rourke JR, McManus M, Jadhav AP, Cepko CL, Hauswirth WW, Harfe BD, Strettoi E. Dicer inactivation leads to progressive functional and structural degeneration of the mouse retina. J Neurosci. 2008 May 7;28(19):4878-87. doi: 10.1523/JNEUROSCI.0828-08.2008. PMID: 18463241 PMCID: PMC3325486 read article


Courtois-Cox S, Jones SL, Cichowski K. Many roads lead to oncogene-induced senescence. Oncogene. 2008 May 1;27(20):2801-9. doi: 10.1038/sj.onc.1210950. Epub 2008 Jan 14. PMID: 18193093


Andersen CB, Wan Y, Chang JW, Riggs B, Lee C, Liu Y, Sessa F, Villa F, Kwiatkowski N, Suzuki M, Nallan L, Heald R, Musacchio A, Gray NS. Discovery of selective aminothiazole aurora kinase inhibitors. ACS Chem Biol. 2008 Mar 20;3(3):180-92. doi: 10.1021/cb700200w. Epub 2008 Feb 29. PMID: 18307303


Estiu G, Greenberg E, Harrison CB, Kwiatkowski NP, Mazitschek R, Bradner JE, Wiest O. Structural origin of selectivity in class II-selective histone deacetylase inhibitors. J Med Chem. 2008 May 22;51(10):2898-906. doi: 10.1021/jm7015254. Epub 2008 Apr 16. PMID: 18412327


LeBleu VS, Kalluri R. Stem cell-based therapy for glomerular diseases: an evolving concept. J Am Soc Nephrol. 2008 Sep;19(9):1621-3. Epub 2008 Aug 13. PubMed PMID: 18701605.


Lebleu VS, Sugimoto H, Miller CA, Gattone VH 2nd, Kalluri R. Lymphocytes are dispensable for glomerulonephritis but required for renal interstitial fibrosis in matrix defect-induced Alport renal disease. Lab Invest. 2008 Mar;88(3):284-92. Epub 2008 Jan 7. PubMed PMID: 18180701.


Deighan P, Diez CM, Leibman M, Hochschild A, Nickels BE. The bacteriophage lambda Q antiterminator protein contacts the beta-flap domain of RNA polymerase. Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15305-10. doi: 10.1073/pnas.0805757105. Epub 2008 Oct 1. PMID: 18832144 PMCID: PMC2563111 read article


Buchberger JR, Onishi M, Li G, Seebacher J, Rudner AD, Gygi SP, Moazed D*. Sir3-nucleosome interactions in spreading of silent chromatin in Saccharomyces cerevisiae. Mol Cell Biol. 2008 Nov;28(22):6903-18. Epub 2008 Sep 15. PubMed PMID: 18794362; PubMed Central PMCID: PMC2573294.


Li JM, Tetzlaff MT, Elledge SJ. Identification of MSA1, a cell cycle-regulated, dosage suppressor of drc1/sld2 and dpb11 mutants. Cell Cycle. 2008 Nov 1;7(21):3388-98. Epub 2008 Nov 5. PubMed PMID: 18948746.


Li JM. Pain management in the hospitalized patient. Med Clin North Am. 2008 Mar;92(2):371-85, ix. Review. PubMed PMID: 18298984.


Liddle FJ, Frank DA. STAT1 expression is not required for polyp formation in Min mice. Mol Carcinog. 2008 Feb;47(2):75-9. PMID: 17683066


Denoux C, Galletti R, Mammarella N, Gopalan S, Werck D, De Lorenzo G, Ferrari S, Ausubel FM, Dewdney J. Activation of defense response pathways by OGs and Flg22 elicitors in Arabidopsis seedlings. Mol Plant. 2008 May;1(3):423-45. Epub 2008 May 22. Review. Erratum in: Mol Plant. 2009 Jul;2(4):838. PubMed PMID: 19825551.


McEwen JM, Kaplan JM. UNC-18 promotes both the anterograde trafficking and synaptic function of syntaxin. Mol Biol Cell. 2008 Sep;19(9):3836-46. Epub 2008 Jul 2. PubMed PMID: 18596236; PubMed Central PMCID: PMC2526711.


Chun DK, McEwen JM, Burbea M, Kaplan JM. UNC-108/Rab2 regulates postendocytic trafficking in Caenorhabditis elegans. Mol Biol Cell. 2008 Jul;19(7):2682-95. Epub 2008 Apr 23. PubMed PMID: 18434599; PubMed Central PMCID: PMC2441656.


Zhu BM, McLaughlin SK, Na R, Liu J, Cui Y, Martin C, Kimura A, Robinson GW, Andrews NC, Hennighausen L. Hematopoietic-specific Stat5-null mice display microcytic hypochromic anemia associated with reduced transferrin receptor gene expression. Blood. 2008 Sep 1;112(5):2071-80. doi: 10.1182/blood-2007-12-127480. Epub 2008 Jun 13. PMID: 18552213 PMCID: PMC2518907 read article


Castang S, McManus HR, Turner KH, Dove SL. H-NS family members function coordinately in an opportunistic pathogen. Proc Natl Acad Sci U S A. 2008 Dec 2;105(48):18947-52. doi: 10.1073/pnas.0808215105. Epub 2008 Nov 21. PMID: 19028873 PMCID: PMC2596223 read article


Sato-Jin K, Nishimura EK, Akasaka E, Huber W, Nakano H, Miller A, Du J, Wu M, Hanada K, Sawamura D, Fisher DE, Imokawa G. Epistatic connections between microphthalmia-associated transcription factor and endothelin signaling in Waardenburg syndrome and other pigmentary disorders. FASEB J. 2008 Apr;22(4):1155-68. Epub 2007 Nov 26. PMID: 18039926


Bracken CM, Mizeracka K, McLaughlin KA. Patterning the embryonic kidney: BMP signaling mediates the differentiation of the pronephric tubules and duct in Xenopus laevis. Dev Dyn. 2008 Jan;237(1):132-44. PMID: 18069689


Perlis RH, Moorjani P, Fagerness J, Purcell S, Trivedi MH, Fava M, Rush AJ, Smoller JW. Pharmacogenetic analysis of genes implicated in rodent models of antidepressant response: association of TREK1 and treatment resistance in the STAR(*)D study. Neuropsychopharmacology. 2008 Nov;33(12):2810-9. Epub 2008 Feb 20. PubMed PMID: 18288090.


Naxerova K, Bult CJ, Peaston A, Fancher K, Knowles BB, Kasif S, Kohane IS. Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biol. 2008;9(7):R108. Epub 2008 Jul 8. PubMed PMID: 18611264; PubMed Central PMCID: PMC2530866.


Lan F, Nottke AC, Shi Y. Mechanisms involved in the regulation of histone lysine demethylases. Curr Opin Cell Biol. 2008 Jun;20(3):316-25. Epub 2008 Apr 25. Review. PubMed PMID: 18440794; PubMed Central PMCID: PMC2674377.


Westbrook TF, Hu G, Ang XL, Mulligan P, Pavlova NN, Liang A, Leng Y, Maehr R, Shi Y, Harper JW, Elledge SJ. SCFbeta-TRCP controls oncogenic transformation and neural differentiation through REST degradation. Nature. 2008 Mar 20;452(7185):370-4. doi: 10.1038/nature06780. PMID: 18354483 PMCID: PMC2688689 read article


Piskounova E, Viswanathan SR, Janas M, LaPierre RJ, Daley GQ, Sliz P, Gregory RI. Determinants of microRNA processing inhibition by the developmentally regulated RNA-binding protein Lin28. J Biol Chem. 2008 Aug 1;283(31):21310-4. Epub 2008 Jun 12. PubMed PMID: 18550544.


Xie L, Palmsten K, MacDonald B, Kieran MW, Potenta S, Vong S, Kalluri R. Basement membrane derived fibulin-1 and fibulin-5 function as angiogenesis inhibitors and suppress tumor growth. Exp Biol Med (Maywood). 2008 Feb;233(2):155-62. doi: 10.3181/0706-RM-167. PMID: 18222970


Potenta S, Zeisberg E, Kalluri R. The role of endothelial-to-mesenchymal transition in cancer progression. Br J Cancer. 2008 Nov 4;99(9):1375-9. doi: 10.1038/sj.bjc.6604662. Epub 2008 Sep 16. PMID: 18797460 PMCID: PMC2579683 read article


Zeisberg EM, Potenta SE, Sugimoto H, Zeisberg M, Kalluri R. Fibroblasts in kidney fibrosis emerge via endothelial-to-mesenchymal transition. J Am Soc Nephrol. 2008 Dec;19(12):2282-7. doi: 10.1681/ASN.2008050513. Epub 2008 Nov 5. PMID: 18987304 PMCID: PMC2588112 read article


de la Iglesia N, Konopka G, Puram SV, Chan JA, Bachoo RM, You MJ, Levy DE, Depinho RA, Bonni A. Identification of a PTEN-regulated STAT3 brain tumor suppressor pathway. Genes Dev. 2008 Feb 15;22(4):449-62. doi: 10.1101/gad.1606508. Epub 2008 Feb 7. PMID: 18258752 PMCID: PMC2238667 read article


Raiser DM, Zacharek SJ, Roach RR, Curtis SJ, Sinkevicius KW, Gludish DW, Kim CF. Stem cell biology in the lung and lung cancers: using pulmonary context and classic approaches. Cold Spring Harb Symp Quant Biol. 2008;73:479-90. doi: 10.1101/sqb.2008.73.036. Epub 2008 Nov 21. PMID: 19028984


Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T, Voytas DF, Joung JK. Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods. 2008 May;5(5):374-5. Erratum in: Nat Methods. 2008 Jun;5(6):575. PubMed PMID: 18446154.


Mahrour N, Redwine WB, Florens L, Swanson SK, Martin-Brown S, Bradford WD, Staehling-Hampton K, Washburn MP, Conaway RC, Conaway JW. Characterization of Cullin-box sequences that direct recruitment of Cul2-Rbx1 and Cul5-Rbx2 modules to Elongin BC-based ubiquitin ligases. J Biol Chem. 2008 Mar 21;283(12):8005-13. doi: 10.1074/jbc.M706987200. Epub 2008 Jan 10. PMID: 18187417


Zhou B, von Gise A, Ma Q, Rivera-Feliciano J, Pu WT. Nkx2-5- and Isl1-expressing cardiac progenitors contribute to proepicardium. Biochem Biophys Res Commun. 2008 Oct 24;375(3):450-3. doi: 10.1016/j.bbrc.2008.08.044. Epub 2008 Aug 21. PMID: 18722343 PMCID: PMC2610421 read article


Zhou B, Ma Q, Rajagopal S, Wu SM, Domian I, Rivera-Feliciano J, Jiang D, von Gise A, Ikeda S, Chien KR, Pu WT. Epicardial progenitors contribute to the cardiomyocyte lineage in the developing heart. Nature. 2008 Jul 3;454(7200):109-13. doi: 10.1038/nature07060. Epub 2008 Jun 22. PMID: 18568026 PMCID: PMC2574791 read article


Patel V, Booker M, Kramer M, Ross L, Celatka CA, Kennedy LM, Dvorin JD, Duraisingh MT, Sliz P, Wirth DF, Clardy J. Identification and characterization of small molecule inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase. J Biol Chem. 2008 Dec 12;283(50):35078-85. doi: 10.1074/jbc.M804990200. Epub 2008 Oct 8. PMID: 18842591 PMCID: PMC2596402 read article


Runner VM, Podolny V, Buratowski S. The Rpb4 subunit of RNA polymerase II contributes to cotranscriptional recruitment of 3' processing factors. Mol Cell Biol. 2008 Mar;28(6):1883-91. doi: 10.1128/MCB.01714-07. Epub 2008 Jan 14. PMID: 18195044 PMCID: PMC2268395 read article


Schlabach MR, Luo J, Solimini NL, Hu G, Xu Q, Li MZ, Zhao Z, Smogorzewska A, Sowa ME, Ang XL, Westbrook TF, Liang AC, Chang K, Hackett JA, Harper JW, Hannon GJ, Elledge SJ. Cancer proliferation gene discovery through functional genomics. Science. 2008 Feb 1;319(5863):620-4. Erratum in: Science.2008 Apr 18;320(5874):316. PubMed PMID: 18239126.


Bentley AM, Artavanis-Tsakonas S, Stanford JS. Nanocourses: a short course format as an educational tool in a biological sciences graduate curriculum. CBE Life Sci Educ. 2008 Summer;7(2):175-83. doi: 10.1187/cbe.07-07-0049. PMID: 18519608 PMCID: PMC2424306 read article


Langenau DM, Keefe MD, Storer NY, Jette CA, Smith AC, Ceol CJ, Bourque C, Look AT, Zon LI. Co-injection strategies to modify radiation sensitivity and tumor initiation in transgenic Zebrafish. Oncogene. 2008 Jul 10;27(30):4242-8. doi: 10.1038/onc.2008.56. Epub 2008 Mar 17. PMID: 18345029 PMCID: PMC2680704 read article


Sural TH, Peng S, Li B, Workman JL, Park PJ, Kuroda MI. The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome. Nat Struct Mol Biol. 2008 Dec;15(12):1318-25. Epub 2008 Nov 23. PubMed PMID: 19029895; PubMed Central PMCID: PMC2636508.


Swinburne IA, Miguez DG, Landgraf D, Silver PA. Intron length increases oscillatory periods of gene expression in animal cells. Genes Dev. 2008 Sep 1;22(17):2342-6. doi: 10.1101/gad.1696108. Epub 2008 Aug 14. PMID: 18703678 PMCID: PMC2532923 read article


Swinburne IA, Silver PA. Intron delays and transcriptional timing during development. Dev Cell. 2008 Mar;14(3):324-30. doi: 10.1016/j.devcel.2008.02.002. PMID: 18331713 PMCID: PMC2825037 read article


Cironi P, Swinburne IA, Silver PA. Enhancement of cell type specificity by quantitative modulation of a chimeric ligand. PMID: 18230610 PMCID: PMC2417160 read article


Tanner NA, Hamdan SM, Jergic S, Loscha KV, Schaeffer PM, Dixon NE, van Oijen AM. Single-molecule studies of fork dynamics in Escherichia coli DNA replication. Nat Struct Mol Biol. 2008 Feb;15(2):170-6. doi: 10.1038/nsmb.1381. Epub 2008 Jan 27. PMID: 18223657 PMCID: PMC2651573 read article


Vashlishan AB, Madison JM, Dybbs M, Bai J, Sieburth D, Ch'ng Q, Tavazoie M, Kaplan JM. An RNAi screen identifies genes that regulate GABA synapses. Neuron. 2008 May 8;58(3):346-61. PubMed PMID: 18466746.


Xie L, Palmsten K, MacDonald B, Kieran MW, Potenta S, Vong S, Kalluri R. Basement membrane derived fibulin-1 and fibulin-5 function as angiogenesis inhibitors and suppress tumor growth. Exp Biol Med (Maywood). 2008 Feb;233(2):155-62. doi: 10.3181/0706-RM-167. PMID: 18222970


Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MI. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell. 2008 Aug 22;134(4):599-609. PubMed PMID: 18724933; PubMed Central PMCID: PMC2613042.


Dooley KA, Fraenkel PG, Langer NB, Schmid B, Davidson AJ, Weber G, Chiang K, Foott H, Dwyer C, Wingert RA, Zhou Y, Paw BH, Zon LI; Tübingen 2000 Screen Consortium. montalcino, A zebrafish model for variegate porphyria. Exp Hematol. 2008 Sep;36(9):1132-42. doi: 10.1016/j.exphem.2008.04.008. Epub 2008 Jun 11. PMID: 18550261 PMCID: PMC2630115 read article


Choi MY, Romer AI, Wang Y, Wu MP, Ito S, Leiter AB, Shivdasani RA. Requirement of the tissue-restricted homeodomain transcription factor Nkx6.3 in differentiation of gastrin-producing G cells in the stomach antrum. Mol Cell Biol. 2008 May;28(10):3208-18. doi: 10.1128/MCB.01737-07. Epub 2008 Mar 17. PMID: 18347062 PMCID: PMC2423174
 read article


Wang B, Yanez A, Novina CD. MicroRNA-repressed mRNAs contain 40S but not 60S components. Proc Natl Acad Sci U S A. 2008 Apr 8;105(14):5343-8. doi: 10.1073/pnas.0801102105. Epub 2008 Apr 4. PMID: 18390669 PMCID: PMC2291078 read article


top

2007


Agosto MA, Middleton JK, Freimont EC, Yin J, Nibert ML. Thermolabilizing pseudoreversions in reovirus outer-capsid protein micro 1 rescue the entry defect conferred by a thermostabilizing mutation. J Virol. 2007 Jul;81(14):7400-9. Epub 2007 May 16. PMID: 17507494 PMCID: PMC1933377 read article


Ivanovic T, Agosto MA, Chandran K, Nibert ML. A role for molecular chaperone Hsc70 in reovirus outer capsid disassembly. J Biol Chem. 2007 Apr 20;282(16):12210-9. Epub 2007 Feb 6. PMID: 17284448


Middleton JK, Agosto MA, Severson TF, Yin J, Nibert ML. Thermostabilizing mutations in reovirus outer-capsid protein mu1 selected by heat inactivation of infectious subvirion particles. Virology. 2007 May 10;361(2):412-25. Epub 2007 Jan 17. PMID: 17208266 PMCID: PMC1913285 read article


Kim D, Nguyen MD, Dobbin MM, Fischer A, Sananbenesi F, Rodgers JT, Delalle I, Baur JA, Sui G, Armour SM, Puigserver P, Sinclair DA, Tsai LH. SIRT1 deacetylase protects against neurodegeneration in models for Alzheimer's disease and amyotrophic lateral sclerosis. EMBO J. 2007 Jul 11;26(13):3169-79. Epub 2007 Jun 21. PMID: 17581637 PMCID: PMC1914106 read article


Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S. Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol. 2007 Dec;3(12):e254. doi: 10.1371/journal.pcbi.0030254. Epub 2007 Nov 14. PMID: 18166073 PMCID: PMC2230682 read article


Asthana S, Noble WS, Kryukov G, Grant CE, Sunyaev S, Stamatoyannopoulos JA. Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12410-5. Epub 2007 Jul 17. PMID: 17640883 PMCID: PMC1941483 read article


Balibar CJ, Garneau-Tsodikova S, Walsh CT. Covalent CouN7 enzyme intermediate for acyl group shuttling in aminocoumarin biosynthesis. Chem Biol. 2007 Jun;14(6):679-90. PMID: 17584615


Fridman M, Balibar CJ, Lupoli T, Kahne D, Walsh CT, Garneau-Tsodikova S. Chemoenzymatic formation of novel aminocoumarin antibiotics by the enzymes CouN1 and CouN7. Biochemistry. 2007 Jul 17;46(28):8462-71. Epub 2007 Jun 20. PMID: 17580964


Balibar CJ, Howard-Jones AR, Walsh CT. Terrequinone A biosynthesis through L-tryptophan oxidation, dimerization and bisprenylation. Nat Chem Biol. 2007 Sep;3(9):584-92. Epub 2007 Aug 12. PMID: 17704773


Stokes MP, Rush J, Macneill J, Ren JM, Sprott K, Nardone J, Yang V, Beausoleil SA, Gygi SP, Livingstone M, Zhang H, Polakiewicz RD, Comb MJ. Profiling of UV-induced ATM/ATR signaling pathways. Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):19855-60. Epub 2007 Dec 6. PMID: 18077418 PMCID: PMC2148387 read article


Li X, Gerber SA, Rudner AD, Beausoleil SA, Haas W, Villén J, Elias JE, Gygi SP. Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae. J Proteome Res. 2007 Mar;6(3):1190-7. PMID: 17330950


Villén J, Beausoleil SA, Gerber SA, Gygi SP. Large-scale phosphorylation analysis of mouse liver. Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1488-93. Epub 2007 Jan 22. PMID: 17242355 PMCID: PMC1785252 read article


Yi CH, Sogah DK, Boyce M, Degterev A, Christofferson DE, Yuan J. A genome-wide RNAi screen reveals multiple regulators of caspase activation. J Cell Biol. 2007 Nov 19;179(4):619-26. Epub 2007 Nov 12. PMID: 17998402 PMCID: PMC2080898 read article


Cnop M, Ladriere L, Hekerman P, Ortis F, Cardozo AK, Dogusan Z, Flamez D, Boyce M, Yuan J, Eizirik DL. Selective inhibition of eukaryotic translation initiation factor 2 alpha dephosphorylation potentiates fatty acid-induced endoplasmic reticulum stress and causes pancreatic beta-cell dysfunction and apoptosis. J Biol Chem. 2007 Feb 9;282(6):3989-97. Epub 2006 Dec 8. PMID: 17158450


Kiel DP, Magaziner J, Zimmerman S, Ball L, Barton BA, Brown KM, Stone JP, Dewkett D, Birge SJ. Efficacy of a hip protector to prevent hip fracture in nursing home residents: the HIP PRO randomized controlled trial. JAMA. 2007 Jul 25;298(4):413-22. PubMed PMID: 17652295.


Colmenares SU, Buker SM, Buhler M, Dlakić M, Moazed D. Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi. Mol Cell. 2007 Aug 3;27(3):449-61. Epub 2007 Jul 19. PubMed PMID: 17658285.


Buker SM, Iida T, Bühler M, Villén J, Gygi SP, Nakayama J, Moazed D. Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast. Nat Struct Mol Biol. 2007 Mar;14(3):200-7. Epub 2007 Feb 25. PubMed PMID: 17310250.


Hett EC, Chao MC, Steyn AJ, Fortune SM, Deng LL, Rubin EJ. A partner for the resuscitation-promoting factors of Mycobacterium tuberculosis. Mol Microbiol. 2007 Nov;66(3):658-68. Epub 2007 Oct 4. PubMed PMID: 17919286.


Chen AC, Selkoe DJ. Response to: Pardossi-Piquard et al., "Presenilin-Dependent Transcriptional Control of the Abeta-Degrading Enzyme Neprilysin by Intracellular Domains of betaAPP and APLP." Neuron 46, 541-554. Neuron. 2007 Feb 15;53(4):479-83. PubMed PMID: 17296549.


Yang H, Baur JA, Chen A, Miller C, Adams JK, Kisielewski A, Howitz KT, Zipkin RE, Sinclair DA. Design and synthesis of compounds that extend yeast replicative lifespan. Aging Cell. 2007 Feb;6(1):35-43. Epub 2006 Dec 5. Erratum in: Aging Cell. 2007 Aug;6(4):593. Adams, Jeffrey K [added]; Kisielewski, Anne [added]; Howitz, Konrad T [added]; Zipkin, Robert E [added]. PubMed PMID: 17156081.


Yi CH, Sogah DK, Boyce M, Degterev A, Christofferson DE, Yuan J. A genome-wide RNAi screen reveals multiple regulators of caspase activation. J Cell Biol. 2007 Nov 19;179(4):619-26. Epub 2007 Nov 12. PMID: 17998402 PMCID: PMC2080898 read article


Colmenares SU, Buker SM, Buhler M, Dlakić M, Moazed D. Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi. Mol Cell. 2007 Aug 3;27(3):449-61. Epub 2007 Jul 19. PubMed PMID: 17658285.


Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA, Cavanaugh CM. The Calyptogena magnifica chemoautotrophic symbiont genome.Science. 2007 Feb 16;315(5814):998-1000. PubMed PMID: 17303757.


Cohen DE, Davidow LS, Erwin JA, Xu N, Warshawsky D, Lee JT. The DXPas34 repeat regulates random and imprinted X inactivation. Dev Cell. 2007 Jan;12(1):57-71. PubMed PMID: 17199041.


Lu HA, Sun TX, Matsuzaki T, Yi XH, Eswara J, Bouley R, McKee M, Brown D. Heat shock protein 70 interacts with aquaporin-2 and regulates its trafficking. J Biol Chem. 2007 Sep 28;282(39):28721-32. Epub 2007 Jul 18. PMID: 17636261


Everley PA, Gartner CA, Haas W, Saghatelian A, Elias JE, Cravatt BF, Zetter BR, Gygi SP. Assessing enzyme activities using stable isotope labeling and mass spectrometry. Mol Cell Proteomics. 2007 Oct;6(10):1771-7. Epub 2007 Jul 11. PMID: 17627935


Fredenburg RA, Rospigliosi C, Meray RK, Kessler JC, Lashuel HA, Eliezer D, Lansbury PT Jr. The impact of the E46K mutation on the properties of alpha-synuclein in its monomeric and oligomeric states. Biochemistry. 2007 Jun 19;46(24):7107-18. Epub 2007 May 26. PMID: 17530780


Dapprich J, Witter K, Gabel HW, Murphy NB, Albert ED. Identification of a new HLA-B allele (B*1576) by haplotype specific extraction. Hum Immunol. 2007 May;68(5):418-21. Epub 2007 Feb 15. PubMed PMID: 17462508; PubMed Central PMCID: PMC1945813.


Mougous JD, Gifford CA, Ramsdell TL, Mekalanos JJ. Threonine phosphorylation post-translationally regulates protein secretion in Pseudomonas aeruginosa. Nat Cell Biol. 2007 Jul;9(7):797-803. Epub 2007 Jun 10. PMID: 17558395


Giraud J, Haas M, Feener EP, Copps KD, Dong X, Dunn SL, White MF. Phosphorylation of Irs1 at SER-522 inhibits insulin signaling. Mol Endocrinol. 2007 Sep;21(9):2294-302. Epub 2007 Jun 19. PMID: 17579213


Zhang Z, Fan HY, Goldman JA, Kingston RE. Homology-driven chromatin remodeling by human RAD54. Nat Struct Mol Biol. 2007 May;14(5):397-405. Epub 2007 Apr 8. PubMed PMID: 17417655.


Kowal P, Gurtan AM, Stuckert P, D'Andrea AD, Ellenberger T. Structural determinants of human FANCF protein that function in the assembly of a DNA damage signaling complex. J Biol Chem. 2007 Jan 19;282(3):2047-55. Epub 2006 Nov 1. PMID: 17082180


Mukherjee S, Robinson CA, Howe AG, Mazor T, Wood PA, Urgaonkar S, Hebert AM, Raychaudhuri D, Shaw JT. N-Benzyl-3-sulfonamidopyrrolidines as novel inhibitors of cell division in E. coli. Bioorg Med Chem Lett. 2007 Dec 1;17(23):6651-5. Epub 2007 Sep 7. PMID: 17923406 PMCID: PMC3335298 read article


Corbo JC, Myers CA, Lawrence KA, Jadhav AP, Cepko CL. A typology of photoreceptor gene expression patterns in the mouse. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12069-74. Epub 2007 Jul 9. PMID: 17620597 PMCID: PMC1913549 read article


Fredenburg RA, Rospigliosi C, Meray RK, Kessler JC, Lashuel HA, Eliezer D, Lansbury PT Jr. The impact of the E46K mutation on the properties of alpha-synuclein in its monomeric and oligomeric states. Biochemistry. 2007 Jun 19;46(24):7107-18. Epub 2007 May 26. PMID: 17530780


Kowalski MP, Dubouix-Bourandy A, Bajmoczi M, Golan DE, Zaidi T, Coutinho-Sledge YS, Gygi MP, Gygi SP, Wiemer EA, Pier GB. Host resistance to lung infection mediated by major vault protein in epithelial cells. Science. 2007 Jul 6;317(5834):130-2. PMID: 17615361 PMCID: PMC3685177 read article


Landis MW, Brown NE, Baker GL, Shifrin A, Das M, Geng Y, Sicinski P, Hinds PW. The LxCxE pRb interaction domain of cyclin D1 is dispensable for murine development. Cancer Res. 2007 Aug 15;67(16):7613-20. PMID: 17699765


Kanasaki K, Kanda Y, Palmsten K, Tanjore H, Lee SB, Lebleu VS, Gattone VH Jr, Kalluri R. Integrin beta1-mediated matrix assembly and signaling are critical for the normal development and function of the kidney glomerulus. Dev Biol. 2008 Jan 15;313(2):584-93. Epub 2007 Nov 12. PubMed PMID: 18082680.


LeBleu VS, Macdonald B, Kalluri R. Structure and function of basement membranes. Exp Biol Med (Maywood). 2007 Oct;232(9):1121-9. Review. PubMed PMID: 17895520.


Sugimoto H, Yang C, LeBleu VS, Soubasakos MA, Giraldo M, Zeisberg M, Kalluri R. BMP-7 functions as a novel hormone to facilitate liver regeneration. FASEB J. 2007 Jan;21(1):256-64. Epub 2006 Nov 20. PubMed PMID: 17116741.


Salahuddin S, Lee Y, Vadnais M, Sachs BP, Karumanchi SA, Lim KH. Diagnostic utility of soluble fms-like tyrosine kinase 1 and soluble endoglin in hypertensive diseases of pregnancy. Am J Obstet Gynecol. 2007 Jul;197(1):28.e1-6. PubMed PMID: 17618745.


Leibman M, Hochschild A. A sigma-core interaction of the RNA polymerase holoenzyme that enhances promoter escape. EMBO J. 2007 Mar 21;26(6):1579-90. Epub 2007 Mar 1. PMID: 17332752 PMCID: PMC1829379 read article


Sabeti PC1, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES; International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, Zhao H, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao Z, Huang W, Chu X, He Y, Jin L, Liu Y, Shen Y, Sun W, Wang H, Wang Y, Wang Y, Xiong X, Xu L, Waye MM, Tsui SK, Xue H, Wong JT, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallée C, Verner A, Hudson TJ, Kwok PY, Cai D, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PK, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, de Bakker PI, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan W, Li Y, Munro HM, Qin ZS, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Johnson TA, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang H, Zeng C, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CD, Leppert MF, Dixon M, Peiffer A, Qiu R, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archevêque P, Bellemare G, Saeki K, Wang H, An D, Fu H, Li Q, Wang Z, Wang R, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18;449(7164):913-8. PMID: 17943131 PMCID: PMC2687721 read article


McKee AE, Neretti N, Carvalho LE, Meyer CA, Fox EA, Brodsky AS, Silver PA. Exon expression profiling reveals stimulus-mediated exon use in neural cells. Genome Biol. 2007;8(8):R159. PMID: 17683528 PMCID: PMC2374990 read article


McKee AE, Silver PA. Systems perspectives on mRNA processing. Cell Res. 2007 Jul;17(7):581-90. PMID: 17621309


Crowson AN, Magro C, Miller A, Mihm MC Jr. The molecular basis of melanomagenesis and the metastatic phenotype. Semin Oncol. 2007 Dec;34(6):476-90. PMID: 18083371


Catic A, Misaghi S, Korbel GA, Ploegh HL. ElaD, a Deubiquitinating protease expressed by E. coli. PLoS One. 2007 Apr 18;2(4):e381. PMID: 17440617 PMCID: PMC1847702 read article


Catic A, Sun ZY, Ratner DM, Misaghi S, Spooner E, Samuelson J, Wagner G, Ploegh HL. Sequence and structure evolved separately in a ribosomal ubiquitin variant. EMBO J. 2007 Jul 25;26(14):3474-83. Epub 2007 Jun 28. PMID: 17599068 PMCID: PMC1933403 read article


Moerke NJ, Aktas H, Chen H, Cantel S, Reibarkh MY, Fahmy A, Gross JD, Degterev A, Yuan J, Chorev M, Halperin JA, Wagner G. Small-molecule inhibition of the interaction between the translation initiation factors eIF4E and eIF4G. Cell. 2007 Jan 26;128(2):257-67. PMID: 17254965


Rickmyre JL, Dasgupta S, Ooi DL, Keel J, Lee E, Kirschner MW, Waddell S, Lee LA. The Drosophila homolog of MCPH1, a human microcephaly gene, is required for genomic stability in the early embryo. J Cell Sci. 2007 Oct 15;120(Pt 20):3565-77. Epub 2007 Sep 25. PMID: 17895362


Pacholec M, Sello JK, Walsh CT, Thomas MG. Formation of an aminoacyl-S-enzyme intermediate is a key step in the biosynthesis of chloramphenicol. Org Biomol Chem. 2007 Jun 7;5(11):1692-4. Epub 2007 Apr 26. PMID: 17520135


Cinar B, Fang PK, Lutchman M, Di Vizio D, Adam RM, Pavlova N, Rubin MA, Yelick PC, Freeman MR. The pro-apoptotic kinase Mst1 and its caspase cleavage products are direct inhibitors of Akt1. EMBO J. 2007 Oct 31;26(21):4523-34. Epub 2007 Oct 11. PMID: 17932490 PMCID: PMC2063482 read article


Storch KF, Paz C, Signorovitch J, Raviola E, Pawlyk B, Li T, Weitz CJ. Intrinsic circadian clock of the mammalian retina: importance for retinal processing of visual information. Cell. 2007 Aug 24;130(4):730-41. PMID: 17719549 PMCID: PMC2040024 read article


Storch KF, Paz C, Signorovitch J, Raviola E, Pawlyk B, Li T, Weitz CJ. Physiological importance of a circadian clock outside the suprachiasmatic nucleus. Cold Spring Harb Symp Quant Biol. 2007;72:307-18. doi: 10.1101/sqb.2007.72.053. PMID: 18419288


Pesola JM, Coen DM. In vivo fitness and virulence of a drug-resistant herpes simplex virus 1 mutant. J Gen Virol. 2007 May;88(Pt 5):1410-4. PMID: 17412967


Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, Silver PA. Rational design of memory in eukaryotic cells. Genes Dev. 2007 Sep 15;21(18):2271-6.PMID: 17875664 PMCID: PMC1973140  read article


Zeisberg EM, Potenta S, Xie L, Zeisberg M, Kalluri R. Discovery of endothelial to mesenchymal transition as a source for carcinoma-associated fibroblasts. Cancer Res. 2007 Nov 1;67(21):10123-8. PMID: 17974953


Seale P, Kajimura S, Yang W, Chin S, Rohas LM, Uldry M, Tavernier G, Langin D, Spiegelman BM. Transcriptional control of brown fat determination by PRDM16. Cell Metab. 2007 Jul;6(1):38-54. PMID: 17618855 PMCID: PMC2564846 read article


Rohas LM, St-Pierre J, Uldry M, Jäger S, Handschin C, Spiegelman BM. A fundamental system of cellular energy homeostasis regulated by PGC-1alpha. Proc Natl Acad Sci U S A. 2007 May 8;104(19):7933-8. Epub 2007 Apr 30. PMID: 17470778 PMCID: PMC1876550 read article


Saparov SM, Erlandson K, Cannon K, Schaletzky J, Schulman S, Rapoport TA, Pohl P. Determining the conductance of the SecY protein translocation channel for small molecules. Mol Cell. 2007 May 25;26(4):501-9. PMID: 17531809


Li W, Schulman S, Boyd D, Erlandson K, Beckwith J, Rapoport TA. The plug domain of the SecY protein stabilizes the closed state of the translocation channel and maintains a membrane seal. Mol Cell. 2007 May 25;26(4):511-21. PMID: 17531810


Schwabish MA, Struhl K. The Swi/Snf complex is important for histone eviction during transcriptional activation and RNA polymerase II elongation in vivo. Mol Cell Biol. 2007 Oct;27(20):6987-95. Epub 2007 Aug 20. PMID: 17709398 PMCID: PMC2168902 read article


Gunasekera AM, Myrick A, Militello KT, Sims JS, Dong CK, Gierahn T, Le Roch K, Winzeler E, Wirth DF. Regulatory motifs uncovered among gene expression clusters in Plasmodium falciparum. Mol Biochem Parasitol. 2007 May;153(1):19-30. Epub 2007 Jan 18. PMID: 17307259


Deitsch K, Duraisingh M, Dzikowski R, Gunasekera A, Khan S, Le Roch K, Llinás M, Mair G, McGovern V, Roos D, Shock J, Sims J, Wiegand R, Winzeler E.


Yi CH, Sogah DK, Boyce M, Degterev A, Christofferson DE, Yuan J. A genome-wide RNAi screen reveals multiple regulators of caspase activation. J Cell Biol. 2007 Nov 19;179(4):619-26. Epub 2007 Nov 12. PMID: 17998402 PMCID: PMC2080898 read article


Langenau DM, Keefe MD, Storer NY, Guyon JR, Kutok JL, Le X, Goessling W, Neuberg DS, Kunkel LM, Zon LI. Effects of RAS on the genesis of embryonal rhabdomyosarcoma. Genes Dev. 2007 Jun 1;21(11):1382-95. Epub 2007 May 17. PMID: 17510286 PMCID: PMC1877750 read article


Hamdan SM, Johnson DE, Tanner NA, Lee JB, Qimron U, Tabor S, van Oijen AM, Richardson CC. Dynamic DNA helicase-DNA polymerase interactions assure processive replication fork movement. Mol Cell. 2007 Aug 17;27(4):539-49. PMID: 17707227


Tse JC, Kalluri R. Mechanisms of metastasis: epithelial-to-mesenchymal transition and contribution of tumor microenvironment. J Cell Biochem. 2007 Jul 1;101(4):816-29. PMID: 17243120


Ulm JW, Perron M, Sodroski J, C Mulligan R. Complex determinants within the Moloney murine leukemia virus capsid modulate susceptibility of the virus to Fv1 and Ref1-mediated restriction. Virology. 2007 Jul 5;363(2):245-55. Epub 2007 Mar 6. PMID: 17343889


Yoon S, Molloy MJ, Wu MP, Cowan DB, Gussoni E. C6ORF32 is upregulated during muscle cell differentiation and induces the formation of cellular filopodia. Dev Biol. 2007 Jan 1;301(1):70-81. Epub 2006 Nov 7. PMID: 17150207 PMCID: PMC1779902 read article


top

2006


Agosto MA, Ivanovic T, Nibert ML. Mammalian reovirus, a nonfusogenic nonenveloped virus, forms size-selective pores in a model membrane. Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16496-501. Epub 2006 Oct 19. PMID: 17053074 PMCID: PMC1637610 read article


Alvarez JV, Greulich H, Sellers WR, Meyerson M, Frank DA. Signal transducer and activator of transcription 3 is required for the oncogenic effects of non-small-cell lung cancer-associated mutations of the epidermal growth factor receptor. Cancer Res. 2006 Mar 15;66(6):3162-8. PMID: 16540667


Liddle FJ, Alvarez JV, Poli V, Frank DA. Tyrosine phosphorylation is required for functional activation of disulfide-containing constitutively active STAT mutants. Biochemistry. 2006 May 2;45(17):5599-605. PMID: 16634641


Balibar CJ, Walsh CT. GliP, a multimodular nonribosomal peptide synthetase in Aspergillus fumigatus, makes the diketopiperazine scaffold of gliotoxin. Biochemistry. 2006 Dec 19;45(50):15029-38. PMID: 17154540


Balibar CJ, Walsh CT. In vitro biosynthesis of violacein from L-tryptophan by the enzymes VioA-E from Chromobacterium violaceum. Biochemistry. 2006 Dec 26;45(51):15444-57. Epub 2006 Dec 19. PMID: 17176066


Beausoleil SA, Villén J, Gerber SA, Rush J, Gygi SP. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nat Biotechnol. 2006 Oct;24(10):1285-92. Epub 2006 Sep 10. PMID: 16964243


Everley PA, Bakalarski CE, Elias JE, Waghorne CG, Beausoleil SA, Gerber SA, Faherty BK, Zetter BR, Gygi SP. Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. J Proteome Res. 2006 May;5(5):1224-31. PMID: 16674112


Haas W, Faherty BK, Gerber SA, Elias JE, Beausoleil SA, Bakalarski CE, Li X, Villén J, Gygi SP. Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Mol Cell Proteomics. 2006 Jul;5(7):1326-37. Epub 2006 Apr 23. PMID: 16635985


Boyce M, Yuan J. Cellular response to endoplasmic reticulum stress: a matter of life or death. Cell Death Differ. 2006 Mar;13(3):363-73. PMID: 16397583


Boyce M, Scott F, Guogas LM, Gehrke L. Base-pairing potential identified by in vitro selection predicts the kinked RNA backbone observed in the crystal structure of the alfalfa mosaic virus RNA-coat protein complex. J Mol Recognit. 2006 Jan-Feb;19(1):68-78. PMID: 16312015


Moazed D, Bühler M, Buker SM, Colmenares SU, Gerace EL, Gerber SA, Hong EJ, Motamedi MR, Verdel A, Villén J, Gygi SP. Studies on the mechanism of RNAi-dependent heterochromatin assembly. Cold Spring Harb Symp Quant Biol. 2006;71:461-71. Review. PubMed PMID: 17381328.


Moazed D, Bühler M, Buker SM, Colmenares SU, Gerace EL, Gerber SA, Hong EJ, Motamedi MR, Verdel A, Villén J, Gygi SP. Studies on the mechanism of RNAi-dependent heterochromatin assembly. Cold Spring Harb Symp Quant Biol. 2006;71:461-71. Review. PubMed PMID: 17381328.


Davis IJ, Kim JJ, Ozsolak F, Widlund HR, Rozenblatt-Rosen O, Granter SR, Du J, Fletcher JA, Denny CT, Lessnick SL, Linehan WM, Kung AL, Fisher DE. Oncogenic MITF dysregulation in clear cell sarcoma: defining the MiT family of human cancers. Cancer Cell. 2006 Jun;9(6):473-84. PMID: 16766266


Cheng H, Dufu K, Lee CS, Hsu JL, Dias A, Reed R. Human mRNA export machinery recruited to the 5' end of mRNA. Cell. 2006 Dec 29;127(7):1389-400. PMID: 17190602


Das R, Dufu K, Romney B, Feldt M, Elenko M, Reed R. Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev. 2006 May 1;20(9):1100-9. PMID: 16651655 PMCID: PMC1472470 read article


Everley PA, Bakalarski CE, Elias JE, Waghorne CG, Beausoleil SA, Gerber SA, Faherty BK, Zetter BR, Gygi SP. Enhanced analysis of metastatic prostate cancer using stable isotopes and high mass accuracy instrumentation. J Proteome Res. 2006 May;5(5):1224-31. PMID: 16674112


Selenko P, Serber Z, Gadea B, Ruderman J, Wagner G. Quantitative NMR analysis of the protein G B1 domain in Xenopus laevis egg extracts and intact oocytes. Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11904-9. Epub 2006 Jul 27. PMID: 16873549 PMCID: PMC1523310 read article


Gadea BB, Ruderman JV. Aurora B is required for mitotic chromatin-induced phosphorylation of Op18/Stathmin. Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4493-8. Epub 2006 Mar 14. PMID: 16537398 PMCID: PMC1401233 read article


Moazed D, Bühler M, Buker SM, Colmenares SU, Gerace EL, Gerber SA, Hong EJ, Motamedi MR, Verdel A, Villén J, Gygi SP. Studies on the mechanism of RNAi-dependent heterochromatin assembly. Cold Spring Harb Symp Quant Biol. 2006;71:461-71. Review. PubMed PMID: 17381328.


Gurtan AM, Stuckert P, D'Andrea AD. The WD40 repeats of FANCL are required for Fanconi anemia core complex assembly. J Biol Chem. 2006 Apr 21;281(16):10896-905. Epub 2006 Feb 10. PMID: 16474167


Gurtan AM, D'Andrea AD. Dedicated to the core: understanding the Fanconi anemia complex. DNA Repair (Amst). 2006 Sep 8;5(9-10):1119-25. Epub 2006 Jun 19. PMID: 16784902


Machida YJ, Machida Y, Chen Y, Gurtan AM, Kupfer GM, D'Andrea AD, Dutta A. UBE2T is the E2 in the Fanconi anemia pathway and undergoes negative autoregulation.Mol Cell. 2006 Aug;23(4):589-96. PMID: 16916645


Hayes GD, Frand AR, Ruvkun G. The mir-84 and let-7 paralogous microRNA genes of Caenorhabditis elegans direct the cessation of molting via the conserved nuclear hormone receptors NHR-23 and NHR-25. Development. 2006 Dec;133(23):4631-41. Epub 2006 Oct 25. PMID: 17065234


Hayes GD, Ruvkun G. Misexpression of the Caenorhabditis elegans miRNA let-7 is sufficient to drive developmental programs. Cold Spring Harb Symp Quant Biol. 2006;71:21-7. PMID: 17381276


Stegmüller J, Konishi Y, Huynh MA, Yuan Z, Dibacco S, Bonni A. Cell-intrinsic regulation of axonal morphogenesis by the Cdh1-APC target SnoN. Neuron. 2006 May 4;50(3):389-400. PMID: 16675394


Jadhav AP, Cho SH, Cepko CL. Notch activity permits retinal cells to progress through multiple progenitor states and acquire a stem cell property. Proc Natl Acad Sci U S A. 2006 Dec 12;103(50):18998-9003. Epub 2006 Dec 5. PMID: 17148603 PMCID: PMC1682012 read article


Jadhav AP, Mason HA, Cepko CL. Notch 1 inhibits photoreceptor production in the developing mammalian retina. Development. 2006 Mar;133(5):913-23. Epub 2006 Feb 1. PMID: 16452096


James RG, Kamei CN, Wang Q, Jiang R, Schultheiss TM. Odd-skipped related 1 is required for development of the metanephric kidney and regulates formation and differentiation of kidney precursor cells. Development. 2006 Aug;133(15):2995-3004. Epub 2006 Jun 21. PubMed PMID: 16790474.


Lee AM, Wu CT. Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions. Genetics. 2006 Dec;174(4):1867-80. Epub 2006 Oct 22. PubMed PMID: 17057235; PubMed Central PMCID: PMC1698615.


Bateman JR, Lee AM, Wu CT. Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange. Genetics. 2006 Jun;173(2):769-77. Epub 2006 Mar 17. PubMed PMID: 16547094; PubMed Central PMCID: PMC1526508.


Landis MW, Pawlyk BS, Li T, Sicinski P, Hinds PW. Cyclin D1-dependent kinase activity in murine development and mammary tumorigenesis. Cancer Cell. 2006 Jan;9(1):13-22. PMID: 16413468


Liddle FJ, Alvarez JV, Poli V, Frank DA. Tyrosine phosphorylation is required for functional activation of disulfide-containing constitutively active STAT mutants. Biochemistry. 2006 May 2;45(17):5599-605. PMID: 16634641


Malecki MJ, Sanchez-Irizarry C, Mitchell JL, Histen G, Xu ML, Aster JC, Blacklow SC. Leukemia-associated mutations within the NOTCH1 heterodimerization domain fall into at least two distinct mechanistic classes. Mol Cell Biol. 2006 Jun;26(12):4642-51. PMID: 16738328 PMCID: PMC1489116 read article


McKee AE, Silver PA. Systems biology of gene regulation fulfills its promise. Genome Biol. 2006;7(5):316. Epub 2006 May 22. PMID: 16719937


Miller AJ, Mihm MC Jr. Melanoma. N Engl J Med. 2006 Jul 6;355(1):51-65. PMID: 16822996


Misaghi S, Korbel GA, Kessler B, Spooner E, Ploegh HL. z-VAD-fmk inhibits peptide:N-glycanase and may result in ER stress. Cell Death Differ. 2006 Jan;13(1):163-5. PMID: 16003388


Misaghi S, Balsara ZR, Catic A, Spooner E, Ploegh HL, Starnbach MN. Chlamydia trachomatis-derived deubiquitinating enzymes in mammalian cells during infection. Mol Microbiol. 2006 Jul;61(1):142-50. PMID: 16824101


Artavanis-Tsakonas K, Misaghi S, Comeaux CA, Catic A, Spooner E, Duraisingh MT, Ploegh HL. Identification by functional proteomics of a deubiquitinating/deNeddylating enzyme in Plasmodium falciparum. Mol Microbiol. 2006 Sep;61(5):1187-95. PMID: 16925553


Balsara ZR, Misaghi S, Lafave JN, Starnbach MN. Chlamydia trachomatis infection induces cleavage of the mitotic cyclin B1. Infect Immun. 2006 Oct;74(10):5602-8. PMID: 16988235 PMCID: PMC1594933 read article


von der Haar T, Oku Y, Ptushkina M, Moerke N, Wagner G, Gross JD, McCarthy JE. Folding transitions during assembly of the eukaryotic mRNA cap-binding complex. J Mol Biol. 2006 Mar 3;356(4):982-92. Epub 2005 Dec 27. PMID: 16405910


Rivera-Feliciano J, Lee KH, Kong SW, Rajagopal S, Ma Q, Springer Z, Izumo S, Tabin CJ, Pu WT. Development of heart valves requires Gata4 expression in endothelial-derived cells. Development. 2006 Sep;133(18):3607-18. Epub 2006 Aug 16. PMID: 16914500 PMCID: PMC2735081 read article


Rivera-Feliciano J, Tabin CJ*. Bmp2 instructs cardiac progenitors to form the heart-valve-inducing field. Dev Biol. 2006 Jul 15;295(2):580-8. Epub 2006 Apr 4. PMID: 16730346 PMCID: PMC2680002 read article


Cooper MP, Qu L, Rohas LM, Lin J, Yang W, Erdjument-Bromage H, Tempst P, Spiegelman BM. Defects in energy homeostasis in Leigh syndrome French Canadian variant through PGC-1alpha/LRP130 complex. Genes Dev. 2006 Nov 1;20(21):2996-3009. Epub 2006 Oct 18. PMID: 17050673 PMCID: PMC1620022 read article


Voynov V, Verstrepen KJ, Jansen A, Runner VM, Buratowski S, Fink GR. Genes with internal repeats require the THO complex for transcription. Proc Natl Acad Sci U S A. 2006 Sep 26;103(39):14423-8. Epub 2006 Sep 18. PMID: 16983072 PMCID: PMC1599979 read article


Schwabish MA, Struhl K. Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II. Mol Cell. 2006 May 5;22(3):415-22. PMID:
16678113


Swinburne IA, Meyer CA, Liu XS, Silver PA, Brodsky AS. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res. 2006 Jul;16(7):912-21. Epub 2006 Jun 12. PMID: 16769980 PMCID: PMC1484458 read article


Shaw GC, Cope JJ, Li L, Corson K, Hersey C, Ackermann GE, Gwynn B, Lambert AJ, Wingert RA, Traver D, Trede NS, Barut BA, Zhou Y, Minet E, Donovan A, Brownlie A, Balzan R, Weiss MJ, Peters LL, Kaplan J, Zon LI, Paw BH. Mitoferrin is essential for erythroid iron assimilation. Nature. 2006 Mar 2;440(7080):96-100. PMID: 16511496


top

2005


Nibert ML, Odegard AL, Agosto MA, Chandran K, Schiff LA. Putative autocleavage of reovirus mu1 protein in concert with outer-capsid disassembly and activation for membrane permeabilization. J Mol Biol. 2005 Jan 21;345(3):461-74. PMID: 15581891


Alvarez JV, Febbo PG, Ramaswamy S, Loda M, Richardson A, Frank DA. Identification of a genetic signature of activated signal transducer and activator of transcription 3 in human tumors. Cancer Res. 2005 Jun 15;65(12):5054-62. PMID: 15958548


Greulich H, Chen TH, Feng W, Jänne PA, Alvarez JV, Zappaterra M, Bulmer SE, Frank DA, Hahn WC, Sellers WR, Meyerson M. Oncogenic transformation by inhibitor-sensitive and -resistant EGFR mutants. PLoS Med. 2005 Nov;2(11):e313. Epub 2005 Oct 4. PMID: 16187797 PMCID: PMC1240052 read article


Selak MA, Armour SM, MacKenzie ED, Boulahbel H, Watson DG, Mansfield KD, Pan Y, Simon MC, Thompson CB, Gottlieb E. Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-alpha prolyl hydroxylase. Cancer Cell. 2005 Jan;7(1):77-85. PMID: 15652751


Asthana S, Schmidt S, Sunyaev S. A limited role for balancing selection. Trends Genet. 2005 Jan;21(1):30-2. PMID: 15680511


Balibar CJ, Vaillancourt FH, Walsh CT. Generation of D amino acid residues in assembly of arthrofactin by dual condensation/epimerization domains. Chem Biol. 2005 Nov;12(11):1189-200. PMID: 16298298


Dieguez-Acuna FJ, Gerber SA, Kodama S, Elias JE, Beausoleil SA, Faustman D, Gygi SP. Characterization of mouse spleen cells by subtractive proteomics. Mol Cell Proteomics. 2005 Oct;4(10):1459-70. Epub 2005 Jul 21. PMID: 16037072


Boyce M, Bryant KF, Jousse C, Long K, Harding HP, Scheuner D, Kaufman RJ, Ma D, Coen DM, Ron D, Yuan J. A selective inhibitor of eIF2alpha dephosphorylation protects cells from ER stress. Science. 2005 Feb 11;307(5711):935-9. PMID: 15705855


Degterev A, Huang Z, Boyce M, Li Y, Jagtap P, Mizushima N, Cuny GD, Mitchison TJ, Moskowitz MA, Yuan J. Chemical inhibitor of nonapoptotic cell death with therapeutic potential for ischemic brain injury. Nat Chem Biol. 2005 Jul;1(2):112-9. Epub 2005 May 29. PMID: 16408008


Chan B, Greenan G, McKeon F, Ellenberger T. Identification of a peptide fragment of DSCR1 that competitively inhibits calcineurin activity in vitro and in vivo. Proc Natl Acad Sci U S A. 2005 Sep 13;102(37):13075-80. Epub 2005 Aug 30. PMID: 16131541 PMCID: PMC1201586 read article


Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML, Fisher DE, Sellers WR. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature. 2005 Jul 7;436(7047):117-22. PMID: 16001072


Benes CH, Wu N, Elia AE, Dharia T, Cantley LC, Soltoff SP. The C2 domain of PKCdelta is a phosphotyrosine binding domain. Cell. 2005 Apr 22;121(2):271-80. PMID: 15851033


Everley PA, Zetter BR. Proteomics in tumor progression and metastasis. Ann N Y Acad Sci. 2005 Nov;1059:1-10. PMID: 16382037


Wang D, Kennedy S, Conte D Jr, Kim JK, Gabel HW, Kamath RS, Mello CC, Ruvkun G. Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Nature. 2005 Jul 28;436(7050):593-7. PubMed PMID: 16049496.


Kim JK, Gabel HW, Kamath RS, Tewari M, Pasquinelli A, Rual JF, Kennedy S, Dybbs M, Bertin N, Kaplan JM, Vidal M, Ruvkun G. Functional genomic analysis of RNA interference in C. elegans. Science. 2005 May 20;308(5725):1164-7. Epub 2005 Mar 24. PubMed PMID: 15790806.


Gadea BB, Ruderman JV. Aurora kinase inhibitor ZM447439 blocks chromosome-induced spindle assembly, the completion of chromosome condensation, and the establishment of the spindle integrity checkpoint in Xenopus egg extracts. Mol Biol Cell. 2005 Mar;16(3):1305-18. Epub 2004 Dec 22. PMID: 15616188 PMCID: PMC551494 read article


Hong EJ, Villén J, Gerace EL, Gygi SP, Moazed D. A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for RNAi-mediated heterochromatin formation. RNA Biol. 2005 Jul-Sep;2(3):106-11. Epub 2005 Jul 30. PubMed PMID: 17114925.


Gregory BD, Nickels BE, Darst SA, Hochschild A. An altered-specificity DNA-binding mutant of Escherichia coli sigma70 facilitates the analysis of sigma70 function in vivo. Mol Microbiol. 2005 Jun;56(5):1208-19. PMID: 15882415


Gregory BD, Deighan P, Hochschild A. An artificial activator that contacts a normally occluded surface of the RNA polymerase holoenzyme. J Mol Biol. 2005 Oct 28;353(3):497-506. Epub 2005 Sep 2. PMID: 16185714


Ichida JK, Horhota A, Zou K, McLaughlin LW, Szostak JW. High fidelity TNA synthesis by Therminator polymerase. Nucleic Acids Res. 2005 Sep 12;33(16):5219-25. Print 2005. PubMed PMID: 16157867; PubMed Central PMCID: PMC1214552.


Ichida JK, Zou K, Horhota A, Yu B, McLaughlin LW, Szostak JW. An in vitro selection system for TNA. J Am Chem Soc. 2005 Mar 9;127(9):2802-3. PubMed PMID: 15740086.


Sakata Y, Koibuchi N, Xiang F, Youngblood JM, Kamei CN, Chin MT. The spectrum of cardiovascular anomalies in CHF1/Hey2 deficient mice reveals roles in endocardial cushion, myocardial and vascular maturation. J Mol Cell Cardiol. 2006 Feb;40(2):267-73. Epub 2005 Oct 19. PubMed PMID: 16242143.


Field SJ, Madson N, Kerr ML, Galbraith KA, Kennedy CE, Tahiliani M, Wilkins A, Cantley LC. PtdIns(4,5)P2 functions at the cleavage furrow during cytokinesis. Curr Biol. 2005 Aug 9;15(15):1407-12. PMID: 16085494


Baker GL, Landis MW, Hinds PW. Multiple functions of D-type cyclins can antagonize pRb-mediated suppression of proliferation. Cell Cycle. 2005 Feb;4(2):330-8. Epub 2005 Feb 21. PMID: 15684604


Weingart SN, Pagovich O, Sands DZ, Li JM, Aronson MD, Davis RB, Phillips RS, Bates DW. Patient-reported service quality on a medicine unit. Int J Qual Health Care. 2006 Apr;18(2):95-101. Epub 2005 Nov 10. PubMed PMID: 16282334.


Weingart SN, Pagovich O, Sands DZ, Li JM, Aronson MD, Davis RB, Bates DW, Phillips RS. What can hospitalized patients tell us about adverse events? Learning from patient-reported incidents. J Gen Intern Med. 2005 Sep;20(9):830-6. PubMed PMID: 16117751; PubMed Central PMCID: PMC1490203.


Li JM, Li Y, Elledge SJ. Genetic analysis of the kinetochore DASH complex reveals an antagonistic relationship with the ras/protein kinase A pathway and a novel subunit required for Ask1 association. Mol Cell Biol. 2005 Jan;25(2):767-78. PubMed PMID: 15632076; PubMed Central PMCID: PMC543429.


McKee AE, Minet E, Stern C, Riahi S, Stiles CD, Silver PA. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. BMC Dev Biol. 2005 Jul 20;5:14. PMID: 16033648 PMCID: PMC1199591 read article


Miller AJ, Levy C, Davis IJ, Razin E, Fisher DE. Sumoylation of MITF and its related family members TFE3 and TFEB. J Biol Chem. 2005 Jan 7;280(1):146-55. Epub 2004 Oct 25. PMID: 15507434


Misaghi S, Galardy PJ, Meester WJ, Ovaa H, Ploegh HL, Gaudet R. Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate. J Biol Chem. 2005 Jan 14;280(2):1512-20. Epub 2004 Nov 5. PMID: 15531586


Ayad NG, Rankin S, Ooi D, Rape M, Kirschner MW. Identification of ubiquitin ligase substrates by in vitro expression cloning. Methods Enzymol. 2005;399:404-14. PMID: 16338372


Clarke AS, Tang TT, Ooi DL, Orr-Weaver TL. POLO kinase regulates the Drosophila centromere cohesion protein MEI-S332. Dev Cell. 2005 Jan;8(1):53-64. PMID: 15621529


Pacholec M, Freel Meyers CL, Oberthür M, Kahne D, Walsh CT. Characterization of the aminocoumarin ligase SimL from the simocyclinone pathway and tandem incubation with NovM,P,N from the novobiocin pathway. Biochemistry. 2005 Mar 29;44(12):4949-56. PMID: 15779922


Pacholec M, Hillson NJ, Walsh CT. NovJ/NovK catalyze benzylic oxidation of a beta-hydroxyl tyrosyl-S-pantetheinyl enzyme during aminocoumarin ring formation in novobiocin biosynthesis. Biochemistry. 2005 Sep 27;44(38):12819-26. PMID: 16171397


Pacholec M, Tao J, Walsh CT. CouO and NovO: C-methyltransferases for tailoring the aminocoumarin scaffold in coumermycin and novobiocin antibiotic biosynthesis. Biochemistry. 2005 Nov 15;44(45):14969-76. PMID: 16274243


Westbrook TF, Martin ES, Schlabach MR, Leng Y, Liang AC, Feng B, Zhao JJ, Roberts TM, Mandel G, Hannon GJ, Depinho RA, Chin L, Elledge SJ. A genetic screen for candidate tumor suppressors identifies REST. Cell. 2005 Jun 17;121(6):837-48. PubMed PMID: 15960972.


Stanford JS, Ruderman JV. Changes in regulatory phosphorylation of Cdc25C Ser287 and Wee1 Ser549 during normal cell cycle progression and checkpoint arrests. Mol Biol Cell. 2005 Dec;16(12):5749-60. Epub 2005 Sep 29. PMID: 16195348 PMCID: PMC1289418 read article


Stolt PC, Chen Y, Liu P, Bock HH, Blacklow SC, Herz J. Phosphoinositide binding by the disabled-1 PTB domain is necessary for membrane localization and Reelin signal transduction. J Biol Chem. 2005 Mar 11;280(10):9671-7. Epub 2005 Jan 4. PMID: 15632144


Brodsky AS, Meyer CA, Swinburne IA, Hall G, Keenan BJ, Liu XS, Fox EA, Silver PA. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. PMID: 16086846 PMCID: PMC1273631 read article


Zheng G, Patolsky F, Cui Y, Wang WU, Lieber CM. Multiplexed electrical detection of cancer markers with nanowire sensor arrays. Nat Biotechnol. 2005 Oct;23(10):1294-301. Epub 2005 Sep 18. PMID: 16170313


Wang WU, Chen C, Lin KH, Fang Y, Lieber CM. Label-free detection of small-molecule-protein interactions by using nanowire nanosensors. Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3208-12. Epub 2005 Feb 16. PMID: 15716362 PMCID: PMC548960 read article


Galloway JL, Wingert RA, Thisse C, Thisse B, Zon LI. Loss of gata1 but not gata2 converts erythropoiesis to myelopoiesis in zebrafish embryos. Dev Cell. 2005 Jan;8(1):109-16. PMID: 15621534


Wingert RA, Galloway JL, Barut B, Foott H, Fraenkel P, Axe JL, Weber GJ, Dooley K, Davidson AJ, Schmid B, Paw BH, Shaw GC, Kingsley P, Palis J, Schubert H, Chen O, Kaplan J, Zon LI; Tübingen 2000 Screen Consortium. Deficiency of glutaredoxin 5 reveals Fe-S clusters are required for vertebrate haem synthesis. Nature. 2005 Aug 18;436(7053):1035-39. PMID: 16110529


top

2004


Nelson EA, Walker SR, Alvarez JV, Frank DA. Isolation of unique STAT5 targets by chromatin immunoprecipitation-based gene identification. J Biol Chem. 2004 Dec 24;279(52):54724-30. Epub 2004 Oct 20. PMID: 15498775


Alvarez JV, Frank DA. Genome-wide analysis of STAT target genes: elucidating the mechanism of STAT-mediated oncogenesis. Cancer Biol Ther. 2004 Nov;3(11):1045-50. Epub 2004 Nov 22. PMID: 15539936


Asthana S, King OD, Gibbons FD, Roth FP. Predicting protein complex membership using probabilistic network reliability. Genome Res. 2004 Jun;14(6):1170-5. Epub 2004 May 12. PMID: 15140827 PMCID: PMC419795 read article


Hillson NJ, Balibar CJ, Walsh CT. Catalytically inactive condensation domain C1 is responsible for the dimerization of the VibF subunit of vibriobactin synthetase. Biochemistry. 2004 Sep 7;43(35):11344-51. PMID: 15366944


Ballif BA, Villén J, Beausoleil SA, Schwartz D, Gygi SP. Phosphoproteomic analysis of the developing mouse brain. Mol Cell Proteomics. 2004 Nov;3(11):1093-101. Epub 2004 Sep 2. PMID: 5345747


Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villén J, Li J, Cohn MA, Cantley LC, Gygi SP. Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12130-5. Epub 2004 Aug 9. PMID: 15302935 PMCID: PMC514446
 read article


Boyce M, Degterev A, Yuan J. Caspases: an ancient cellular sword of Damocles. Cell Death Differ. 2004 Jan;11(1):29-37. PMID: 14647235


Chen J, Wall NR, Kocher K, Duclos N, Fabbro D, Neuberg D, Griffin JD, Shi Y, Gilliland DG. Stable expression of small interfering RNA sensitizes TEL-PDGFbetaR to inhibition with imatinib or rapamycin. J Clin Invest. 2004 Jun;113(12):1784-91. PubMed PMID: 15199413; PubMed Central PMCID: PMC420507.


Hamar P, Song E, Kokeny G, Chen A, Ouyang N, Lieberman J. Small interfering RNA targeting Fas protects mice against renal ischemia-reperfusion injury. Proc Natl Acad Sci U S A. 2004 Oct 12;101(41):14883-8.


Takahashi TS, Yiu P, Chou MF, Gygi S, Walter JC. Recruitment of Xenopus Scc2 and cohesin to chromatin requires the pre-replication complex. Nat Cell Biol. 2004 Oct;6(10):991-6. Epub 2004 Sep 26. PubMed PMID: 15448702.


Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D*. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell. 2004 Dec 17;119(6):789-802. PubMed PMID: 15607976.


Miller AJ, Du J, Rowan S, Hershey CL, Widlund HR, Fisher DE. Transcriptional regulation of the melanoma prognostic marker melastatin (TRPM1) by MITF in melanocytes and melanoma. Cancer Res. 2004 Jan 15;64(2):509-16. PMID: 14744763


Vetrini F, Auricchio A, Du J, Angeletti B, Fisher DE, Ballabio A, Marigo V. The microphthalmia transcription factor (Mitf) controls expression of the ocular albinism type 1 gene: link between melanin synthesis and melanosome biogenesis. Mol Cell Biol. 2004 Aug;24(15):6550-9. PMID: 15254223 PMCID: PMC444869 read article


Du J, Widlund HR, Horstmann MA, Ramaswamy S, Ross K, Huber WE, Nishimura EK, Golub TR, Fisher DE. Critical role of CDK2 for melanoma growth linked to its melanocyte-specific transcriptional regulation by MITF. Cancer Cell. 2004 Dec;6(6):565-76. PMID: 15607961


Bentires-Alj M, Paez JG, David FS, Keilhack H, Halmos B, Naoki K, Maris JM, Richardson A, Bardelli A, Sugarbaker DJ, Richards WG, Du J, Girard L, Minna JD, Loh ML, Fisher DE, Velculescu VE, Vogelstein B, Meyerson M, Sellers WR, Neel BG. Activating mutations of the noonan syndrome-associated SHP2/PTPN11 gene in human solid tumors and adult acute myelogenous leukemia. Cancer Res. 2004 Dec 15;64(24):8816-20. PMID: 15604238


Everley PA, Krijgsveld J, Zetter BR, Gygi SP. Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research. Mol Cell Proteomics. 2004 Jul;3(7):729-35. Epub 2004 Apr 21. PMID: 15102926


Cuervo AM, Stefanis L, Fredenburg R, Lansbury PT, Sulzer D. Impaired degradation of mutant alpha-synuclein by chaperone-mediated autophagy. Science. 2004 Aug 27;305(5688):1292-5. PMID: 15333840


Li S, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JD, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, Van Den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M. A map of the interactome network of the metazoan C. elegans. Science. 2004 Jan 23;303(5657):540-3. Epub 2004 Jan 2. PubMed PMID: 14704431; PubMed Central PMCID: PMC1698949.


Crane R, Gadea B, Littlepage L, Wu H, Ruderman JV. Aurora A, meiosis and mitosis. Biol Cell. 2004 Apr;96(3):215-29. PMID: 15182704


Giraud J, Leshan R, Lee YH, White MF. Nutrient-dependent and insulin-stimulated phosphorylation of insulin receptor substrate-1 on serine 302 correlates with increased insulin signaling. J Biol Chem. 2004 Jan 30;279(5):3447-54. Epub 2003 Nov 17. PMID: 14623899


Gregory BD, Nickels BE, Garrity SJ, Severinova E, Minakhin L, Urbauer RJ, Urbauer JL, Heyduk T, Severinov K, Hochschild A. A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme. PMID: 15070756 PMCID: PMC384785 read article


Pineda M, Gregory BD, Szczypinski B, Baxter KR, Hochschild A, Miller ES, Hinton DM. A family of anti-sigma70 proteins in T4-type phages and bacteria that are similar to AsiA, a Transcription inhibitor and co-activator of bacteriophage T4. J Mol Biol. 2004 Dec 10;344(5):1183-97. PMID: 15561138


Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A. 2004 Jan 6;101(1):360-5. Epub 2003 Dec 22. PMID: 14691248 PMCID: PMC314190 read article


Sakata Y, Xiang F, Chen Z, Kiriyama Y, Kamei CN, Simon DI, Chin MT. Transcription factor CHF1/Hey2 regulates neointimal formation in vivo and vascular smooth muscle proliferation and migration in vitro. Arterioscler Thromb Vasc Biol. 2004 Nov;24(11):2069-74. Epub 2004 Sep 2. PubMed PMID: 15345511.


Morris JR, Petrov DA, Lee AM, Wu CT. Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter. Genetics. 2004 Aug;167(4):1739-47. PubMed PMID: 15342512; PubMed Central PMCID: PMC1471007.


Kowalski MP, Pier GB. Localization of cystic fibrosis transmembrane conductance regulator to lipid rafts of epithelial cells is required for Pseudomonas aeruginosa-induced cellular activation. J Immunol. 2004 Jan 1;172(1):418-25. PMID: 14688350


Yuan H, Liddle FJ, Mahajan S, Frank DA. IL-6-induced survival of colorectal carcinoma cells is inhibited by butyrate through down-regulation of the IL-6 receptor. Carcinogenesis. 2004 Nov;25(11):2247-55. Epub 2004 Jul 29. PMID: 15284182


McKee AE, Silver PA. REF-ereeing the cytoplasmic fate of mRNA via nuclear export. Dev Cell. 2004 Jun;6(6):740-2. PMID: 15177019


Misaghi S, Sun ZY, Stern P, Gaudet R, Wagner G, Ploegh H. Structural and functional analysis of human cytomegalovirus US3 protein. J Virol. 2004 Jan;78(1):413-23. PMID: 14671122 PMCID: PMC303419 read article


Hirsch C, Misaghi S, Blom D, Pacold ME, Ploegh HL. Yeast N-glycanase distinguishes between native and non-native glycoproteins. EMBO Rep. 2004 Feb;5(2):201-6. Epub 2004 Jan 9. PMID: 14726951 PMCID: PMC1298977 read article


Misaghi S, Pacold ME, Blom D, Ploegh HL, Korbel GA. Using a small molecule inhibitor of peptide: N-glycanase to probe its role in glycoprotein turnover. Chem Biol. 2004 Dec;11(12):1677-87. PMID: 15610852


Miyamoto DT, Perlman ZE, Burbank KS, Groen AC, Mitchison TJ. The kinesin Eg5 drives poleward microtubule flux in Xenopus laevis egg extract spindles. J Cell Biol. 2004 Dec 6;167(5):813-8. PMID: 15583027 PMCID: PMC2172449 read article


Groen AC, Cameron LA, Coughlin M, Miyamoto DT, Mitchison TJ, Ohi R. XRHAMM functions in ran-dependent microtubule nucleation and pole formation during anastral spindle assembly. Curr Biol. 2004 Oct 26;14(20):1801-11. PMID: 15498487


Natarajan A, Moerke N, Fan YH, Chen H, Christ WJ, Wagner G, Halperin JA. Synthesis of fluorescein labeled 7-methylguanosinemonophosphate. Bioorg Med Chem Lett. 2004 May 17;14(10):2657-60. PMID: 15109672


Pi N, Meyers CL, Pacholec M, Walsh CT, Leary JA. Mass spectrometric characterization of a three-enzyme tandem reaction for assembly and modification of the novobiocin skeleton. Proc Natl Acad Sci U S A. 2004 Jul 6;101(27):10036-41. Epub 2004 Jun 24. PMID: 15218104 PMCID: PMC454160 read article


Lin J, Wu PH, Tarr PT, Lindenberg KS, St-Pierre J, Zhang CY, Mootha VK, Jäger S, Vianna CR, Reznick RM, Cui L, Manieri M, Donovan MX, Wu Z, Cooper MP, Fan MC, Rohas LM, Zavacki AM, Cinti S, Shulman GI, Lowell BB, Krainc D, Spiegelman BM. Defects in adaptive energy metabolism with CNS-linked hyperactivity in PGC-1alpha null mice. Cell. 2004 Oct 1;119(1):121-35. PMID: 15454086


Schwabish MA, Struhl K. Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2004 Dec;24(23):10111-7. PMID: 15542822 PMCID: PMC529037 read article


Stolt PC, Vardar D, Blacklow SC. The dual-function disabled-1 PTB domain exhibits site independence in binding phosphoinositide and peptide ligands. Biochemistry. 2004 Aug 31;43(34):10979-87. PMID: 15323557


Lu Q, Sun EE, Flanagan JG. Analysis of PDZ-RGS3 function in ephrin-B reverse signaling. Methods Enzymol. 2004;390:120-8. PMID: 15488174


Tseng CC, McLoughlin SM, Kelleher NL, Walsh CT. Role of the active site cysteine of DpgA, a bacterial type III polyketide synthase. Biochemistry. 2004 Feb 3;43(4):970-80.


Tseng CC, Vaillancourt FH, Bruner SD, Walsh CT. DpgC is a metal- and cofactor-free 3,5-dihydroxyphenylacetyl-CoA 1,2-dioxygenase in the vancomycin biosynthetic pathway. Chem Biol. 2004 Sep;11(9):1195-203. PMID: 15380180


Perron MJ, Stremlau M, Song B, Ulm W, Mulligan RC, Sodroski J. TRIM5alpha mediates the postentry block to N-tropic murine leukemia viruses in human cells. Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11827-32. Epub 2004 Jul 27. PMID: 15280539 PMCID: PMC511059 read article


Wingert RA, Brownlie A, Galloway JL, Dooley K, Fraenkel P, Axe JL, Davidson AJ, Barut B, Noriega L, Sheng X, Zhou Y, Zon LI. The chianti zebrafish mutant provides a model for erythroid-specific disruption of transferrin receptor 1. Development. 2004 Dec;131(24):6225-35. PMID: 15563524


top

2003


Degterev A, Boyce M, Yuan J. A decade of caspases. Oncogene. 2003 Nov 24;22(53):8543-67. PMID: 14634618


Chan B, Lanyi A, Song HK, Griesbach J, Simarro-Grande M, Poy F, Howie D, Sumegi J, Terhorst C, Eck MJ. SAP couples Fyn to SLAM immune receptors. Nat Cell Biol. 2003 Feb;5(2):155-60. PMID: 12545174


Du J, Miller AJ, Widlund HR, Horstmann MA, Ramaswamy S, Fisher DE. MLANA/MART1 and SILV/PMEL17/GP100 are transcriptionally regulated by MITF in melanocytes and melanoma. Am J Pathol. 2003 Jul;163(1):333-43. PMID: 12819038 PMCID: PMC1868174 read article


Huber WE, Price ER, Widlund HR, Du J, Davis IJ, Wegner M, Fisher DE. A tissue-restricted cAMP transcriptional response: SOX10 modulates alpha-melanocyte-stimulating hormone-triggered expression of microphthalmia-associated transcription factor in melanocytes. J Biol Chem. 2003 Nov 14;278(46):45224-30. Epub 2003 Aug 27. PMID: 12944398


Elia AE, Rellos P, Haire LF, Chao JW, Ivins FJ, Hoepker K, Mohammad D, Cantley LC, Smerdon SJ, Yaffe MB. The molecular basis for phosphodependent substrate targeting and regulation of Plks by the Polo-box domain. Cell. 2003 Oct 3;115(1):83-95.PMID: 14532005


Elia AE, Cantley LC, Yaffe MB. Proteomic screen finds pSer/pThr-binding domain localizing Plk1 to mitotic substrates. Science. 2003 Feb 21;299(5610):1228-31. PMID: 12595692


Lee YH, Giraud J, Davis RJ, White MF. c-Jun N-terminal kinase (JNK) mediates feedback inhibition of the insulin signaling cascade. J Biol Chem. 2003 Jan 31;278(5):2896-902. Epub 2002 Nov 1. PMID: 12417588


Cruz JC, Tseng HC, Goldman JA, Shih H, Tsai LH. Aberrant Cdk5 activation by p25 triggers pathological events leading to neurodegeneration and neurofibrillary tangles. Neuron. 2003 Oct 30;40(3):471-83. PubMed PMID: 14642273.


Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J. Computational and experimental identification of C. elegans microRNAs. Mol Cell. 2003 May;11(5):1253-63. PMID: 12769849


Chaput JC, Ichida JK, Szostak JW. DNA polymerase-mediated DNA synthesis on a TNA template. J Am Chem Soc. 2003 Jan 29;125(4):856-7. PubMed PMID: 12537469.


Kessler JC, Rochet JC, Lansbury PT Jr. The N-terminal repeat domain of alpha-synuclein inhibits beta-sheet and amyloid fibril formation. Biochemistry. 2003 Jan 28;42(3):672-8. PMID: 12534279


Cannon CL, Kowalski MP, Stopak KS, Pier GB. Pseudomonas aeruginosa-induced apoptosis is defective in respiratory epithelial cells expressing mutant cystic fibrosis transmembrane conductance regulator. Am J Respir Cell Mol Biol. 2003 Aug;29(2):188-97. PMID: 12878584


Du J, Miller AJ, Widlund HR, Horstmann MA, Ramaswamy S, Fisher DE. MLANA/MART1 and SILV/PMEL17/GP100 are transcriptionally regulated by MITF in melanocytes and melanoma. Am J Pathol. 2003 Jul;163(1):333-43. PMID: 12819038 PMCID: PMC1868174 read article


Gupta A, Sanada K, Miyamoto DT, Rovelstad S, Nadarajah B, Pearlman AL, Brunstrom J, Tsai LH. Layering defect in p35 deficiency is linked to improper neuronal-glial interaction in radial migration. Nat Neurosci. 2003 Dec;6(12):1284-91. Epub 2003 Nov 9. PMID: 14608361


Miyamoto DT, Perlman ZE, Mitchison TJ, Shirasu-Hiza M. Dynamics of the mitotic spindle--potential therapeutic targets. Prog Cell Cycle Res. 2003;5:349-60. PMID: 14593729


Gross JD, Moerke NJ, von der Haar T, Lugovskoy AA, Sachs AB, McCarthy JE, Wagner G. Ribosome loading onto the mRNA cap is driven by conformational coupling between eIF4G and eIF4E. Cell. 2003 Dec 12;115(6):739-50. PMID: 14675538


Thayer SP, di Magliano MP, Heiser PW, Nielsen CM, Roberts DJ, Lauwers GY, Qi YP, Gysin S, Fernández-del Castillo C, Yajnik V, Antoniu B, McMahon M, Warshaw AL, Hebrok M. Hedgehog is an early and late mediator of pancreatic cancer tumorigenesis. Nature. 2003 Oct 23;425(6960):851-6. Epub 2003 Sep 14. PubMed PMID: 14520413.


Tao J, Hu S, Pacholec M, Walsh CT. Synthesis of proposed oxidation-cyclization-methylation intermediates of the coumarin antibiotic biosynthetic pathway. Org Lett. 2003 Sep 4;5(18):3233-6. PMID: 12943395


Stanford JS, Lieberman SL, Wong VL, Ruderman JV. Regulation of the G2/M transition in oocytes of xenopus tropicalis. Dev Biol. 2003 Aug 15;260(2):438-48. PMID: 12921744


Stolt PC, Jeon H, Song HK, Herz J, Eck MJ, Blacklow SC. Origins of peptide selectivity and phosphoinositide binding revealed by structures of disabled-1 PTB domain complexes. Structure. 2003 May;11(5):569-79. PMID: 2737822


McAlpine MC, Friedman RS, Jin S, Lin K, Wang WU, Lieber CM, High-Performance Nanowire Electronics and Photonics on Glass and Plastic Substrates. Nano Lett. 2003. 3, 1531-1535.


Cui Y, Zhong Z, Wang D, Wang WU, Lieber CM. High Performance Silicon Nanowire Field Effect Transistors. Nano Lett. 2003. 3, 149-152.


top

2002


Gozani O, Boyce M, Yoo L, Karuman P, Yuan J. Life and death in paradise. PMID: 12042835


Du J, Fisher DE. Identification of Aim-1 as the underwhite mouse mutant and its transcriptional regulation by MITF. J Biol Chem. 2002 Jan 4;277(1):402-6. Epub 2001 Nov 7. PMID: 11700328


McGill GG, Horstmann M, Widlund HR, Du J, Motyckova G, Nishimura EK, Lin YL, Ramaswamy S, Avery W, Ding HF, Jordan SA, Jackson IJ, Korsmeyer SJ, Golub TR, Fisher DE. Bcl2 regulation by the melanocyte master regulator Mitf modulates lineage survival and melanoma cell viability. Cell. 2002 Jun 14;109(6):707-18. PMID: 2086670


Baksh S, Widlund HR, Frazer-Abel AA, Du J, Fosmire S, Fisher DE, DeCaprio JA, Modiano JF, Burakoff SJ. NFATc2-mediated repression of cyclin-dependent kinase 4 expression. Mol Cell. 2002 Nov;10(5):1071-81. PMID: 12453415


Aguirre V, Werner ED, Giraud J, Lee YH, Shoelson SE, White MF. Phosphorylation of Ser307 in insulin receptor substrate-1 blocks interactions with the insulin receptor and inhibits insulin action. J Biol Chem. 2002 Jan 11;277(2):1531-7. Epub 2001 Oct 17. PMID: 11606564


Koipally J, Heller EJ, Seavitt JR, Georgopoulos K. Unconventional potentiation of gene expression by Ikaros. J Biol Chem. 2002 Apr 12;277(15):13007-15. Epub 2002 Jan 17. PMID: 11799125


Sakata Y, Kamei CN, Nakagami H, Bronson R, Liao JK, Chin MT. Ventricular septal defect and cardiomyopathy in mice lacking the transcription factor CHF1/Hey2. Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16197-202. Epub 2002 Nov 26. PubMed PMID: 12454287; PubMed Central PMCID: PMC138588.


McDonald WH, Ohi R, Miyamoto DT, Mitchison TJ, and Yates JR 3rd. Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: single-dimensional LC-MS/MS, 2-phase MudPIT, and 3-phase MudPIT. International Journal of Mass Spectrometry. 2002; 219, 245-251.


Duckworth BC, Weaver JS, Ruderman JV. G2 arrest in Xenopus oocytes depends on phosphorylation of cdc25 by protein kinase A. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16794-9. Epub 2002 Dec 11. PMID: 12477927 PMCID: PMC139223
 read article


Tseng CC, Bruner SD, Kohli RM, Marahiel MA, Walsh CT, Sieber SA. Characterization of the surfactin synthetase C-terminal thioesterase domain as a cyclic depsipeptide synthase. Biochemistry. 2002 Nov 12;41(45):13350-9. PMID: 12416979


top

2001


Degterev A, Boyce M, Yuan J. The channel of death. J Cell Biol. 2001 Nov 26;155(5):695-8. Epub 2001 Nov 26. PMID: 11724809 PMCID: PMC2150877 read article


Chiu HT, Hubbard BK, Shah AN, Eide J, Fredenburg RA, Walsh CT, Khosla C. Molecular cloning and sequence analysis of the complestatin biosynthetic gene cluster. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8548-53. Epub 2001 Jul 10. PMID: 11447274 PMCID: PMC37473 read article


Sun J, Kamei CN, Layne MD, Jain MK, Liao JK, Lee ME, Chin MT. Regulation of myogenic terminal differentiation by the hairy-related transcription factor CHF2. J Biol Chem. 2001 May 25;276(21):18591-6. Epub 2001 Feb 22. PubMed PMID: 11279181.


Volles MJ, Lee SJ, Rochet JC, Shtilerman MD, Ding TT, Kessler JC, Lansbury PT Jr. Vesicle permeabilization by protofibrillar alpha-synuclein: implications for the pathogenesis and treatment of Parkinson's disease. Biochemistry. 2001 Jul 3;40(26):7812-9. PMID: 11425308


Karuman P, Gozani O, Odze RD, Zhou XC, Zhu H, Shaw R, Brien TP, Bozzuto CD, Ooi D, Cantley LC, Yuan J. The Peutz-Jegher gene product LKB1 is a mediator of p53-dependent cell death. Mol Cell. 2001 Jun;7(6):1307-19. PMID: 11430832


Lu Q, Sun EE, Klein RS, Flanagan JG. Ephrin-B reverse signaling is mediated by a novel PDZ-RGS protein and selectively inhibits G protein-coupled chemoattraction. Cell. 2001 Apr 6;105(1):69-79. PMID: 11301003


Suo Z, Tseng CC, Walsh CT. Purification, priming, and catalytic acylation of carrier protein domains in the polyketide synthase and nonribosomal peptidyl synthetase modules of the HMWP1 subunit of yersiniabactin synthetase. Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):99-104. PMID: 11134531 PMCID: PMC14551 read article


Chen H, Tseng CC, Hubbard BK, Walsh CT. Glycopeptide antibiotic biosynthesis: enzymatic assembly of the dedicated amino acid monomer (S)-3,5-dihydroxyphenylglycine. Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14901-6. PMID: 11752437 PMCID: PMC64956 read article


top

2000


Haggarty SJ, Mayer TU, Miyamoto DT, Fathi R, King RW, Mitchison TJ, Schreiber SL. Dissecting cellular processes using small molecules: identification of colchicine-like, taxol-like and other small molecules that perturb mitosis. Chem Biol. 2000 Apr;7(4):275-86. PMID: 10780927


top

Student Body

2013-2014 Enrollment


 

Total Enrollment: 349

Average Size of Incoming Class: 60

Average Time to Degree:

Ph.D. Students: 6.06 years

M.D./Ph.D. Students: 4.56 years

 

Women: 185 (53%)

Men: 164 (47%)

 

Underrepresented Minority: 25 (7%)

 

Domestic: 264 (76%)

International: 85 (24%)

 

PhD: 318 (91%)

MD-PhD: 31 (9%)


© 2014 by the President and Fellows of Harvard College