Student Publications

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2019


Toepfer CN, Sharma A, Cicconet M, Garfinkel AC, Mücke M, Neyazi M, Willcox JA, Agarwal R, Schmid M, Rao J, Ewoldt JK, Pourquié O, Chopra A, Chen C, Seidman JG, Seidman CE. SarcTrack: An Adaptable Software Tool for Efficient Large-Scale Analysis of Sarcomere Function in hiPSC-Cardiomyocytes. Circ Res. 2019 Jan 31. doi: 10.1161/CIRCRESAHA.118.314505. PMID: 30700234  read article


Bagonis MM, Fusco L, Pertz O, Danuser G. Automated profiling of growth cone heterogeneity defines relations between morphology and motility. J Cell Biol. 2019 Jan 7;218(1):350-379. doi: 10.1083/jcb.201711023. Epub 2018 Dec 6. PMID: 30523041 PMCID: PMC6314545 [Available on 2019-07-07] read article


Bohrson CL, Barton AR, Lodato MA, Rodin RE, Luquette LJ, Viswanadham VV, Gulhan DC, Cortés-Ciriano I, Sherman MA, Kwon M, Coulter ME, Galor A, Walsh CA, Park PJ. Linked-read analysis identifies mutations in single-cell DNA-sequencing data. Nat Genet. 2019 Mar 18. doi: 10.1038/s41588-019-0366-2. [Epub ahead of print] PMID: 30886424 read article


Menotti M, Ambrogio C, Cheong TC, Pighi C, Mota I, Cassel SH, Compagno M, Wang Q, Dall'Olio R, Minero VG, Poggio T, Sharma GG, Patrucco E, Mastini C, Choudhari R, Pich A, Zamo A, Piva R, Giliani S, Mologni L, Collings CK, Kadoch C, Gambacorti-Passerini C, Notarangelo LD, Anton IM, Voena C, Chiarle R. Wiskott-Aldrich syndrome protein (WASP) is a tumor suppressor in T cell lymphoma. Nat Med. 2019 Jan;25(1):130-140. doi: 10.1038/s41591-018-0262-9. Epub 2018 Dec 3. PMID: 30510251 read article


Sohail M, Maier RM, Ganna A, Bloemendal A, Martin AR, Turchin MC, Chiang CW, Hirschhorn J, Daly MJ, Patterson N, Neale B, Mathieson I, Reich D, Sunyaev SR. Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies. Elife. 2019 Mar 21;8. pii: e39702. doi: 10.7554/eLife.39702. PMID: 30895926 PMCID: PMC6428571 read article


Colognori D, Sunwoo H, Kriz AJ, Wang CY, Lee JT. Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X. Mol Cell. 2019 Feb 28. pii: S1097-2765(19)30035-8. doi: 10.1016/j.molcel.2019.01.015. [Epub ahead of print] PMID: 30827740 read article


Tye BW, Commins N, Ryazanova LV, Wühr M, Springer M, Pincus D, Churchman LS. Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness. Elife. 2019 Mar 7;8. pii: e43002. doi: 10.7554/eLife.43002. [Epub ahead of print] PMID: 30843788 read article


Chen J, Swofford R, Johnson J, Cummings BB, Rogel N, Lindblad-Toh K, Haerty W, Palma FD, Regev A. A quantitative framework for characterizing the evolutionary history of mammalian gene expression. Genome Res. 2019 Jan;29(1):53-63. doi: 10.1101/gr.237636.118. Epub 2018 Dec 14. PMID: 30552105 PMCID: PMC6314168 [Available on 2019-07-01] read article


Bolduc V, Foley AR, Solomon-Degefa H, Sarathy A, Donkervoort S, Hu Y, Chen GS, Sizov K, Nalls M, Zhou H, Aguti S, Cummings BB, Lek M, Tukiainen T, Marshall JL, Regev O, Marek-Yagel D, Sarkozy A, Butterfield RJ, Jou C, Jimenez-Mallebrera C, Li Y, Gartioux C, Mamchaoui K, Allamand V, Gualandi F, Ferlini A, Hanssen E; COLA Intron Study Group, Wilton SD, Lamandé SR, MacArthur DG, Wagener R, Muntoni F, Bönnemann CG. A recurrent COL6A1 pseudoexon insertion causes muscular dystrophy and is effectively targeted by splice-correction therapies. JCI Insight. 2019 Mar 21;4(6). pii: 124403. doi: 10.1172/jci.insight.124403. eCollection 2019 Mar 21. PMID: 30895940 read article


Hubbard TP, D'Gama JD, Billings G, Davis BM, Waldor MK. Unsupervised Learning Approach for Comparing Multiple Transposon Insertion Sequencing Studies. mSphere. 2019 Feb 20;4(1). pii: e00031-19. doi: 10.1128/mSphere.00031-19. PMID: 30787116 PMCID: PMC6382967 read article


Ferguson FM, Doctor ZM, Ficarro SB, Browne CM, Marto JA, Johnson JL, Yaron TM, Cantley LC, Kim ND, Sim T, Berberich MJ, Kalocsay M, Sorger PK, Gray NS. Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. Cell Chem Biol. 2019 Mar 11. pii: S2451-9456(19)30070-4. doi: 10.1016/j.chembiol.2019.02.015. [Epub ahead of print] PMID: 30930164 read article


Justice AE, Karaderi T, Highland HM, Young KL, Graff M, Lu Y, Turcot V, Auer PL, Fine RS, Guo X, Schurmann C, Lempradl A, Marouli E, Mahajan A, Winkler TW, Locke AE, Medina-Gomez C Esko T, Vedantam S, Giri A, Lo KS Alfred T, Mudgal P, Ng MCY Heard-Costa NL, Feitosa MF, Manning AK, Willems SM, Sivapalaratnam S, Abecasis G, Alam DS, Allison M, Amouyel P, Arzumanyan Z, Balkau B, Bastarache L, Bergmann S, Bielak LF, Blüher M Boehnke M, Boeing H, Boerwinkle E Böger CA, Bork-Jensen J, Bottinger EP, Bowden DW, Brandslund I, Broer L, Burt AA, Butterworth AS, Caulfield MJ, Cesana G, Chambers JC, Chasman DI, Chen YI, Chowdhury R, Christensen C, Chu AY, Collins FS, Cook JP, Cox AJ, Crosslin DS, Danesh J, de Bakker PIW, Denus S, Mutsert R, Dedoussis G, Demerath EW, Dennis JG, Denny JC, Angelantonio ED, Dörr M, Drenos F, Dubé MP, Dunning AM, Easton DF Elliott P, Evangelou E Farmaki AE, Feng S, Ferrannini E Ferrieres J, Florez JC, Fornage M, Fox CS, Franks PW, Friedrich N, Gan W, Gandin I, Gasparini P, Giedraitis V, Girotto G Gorski M Grallert H, Grarup N, Grove ML, Gustafsson S, Haessler J, Hansen T, Hattersley AT, Hayward C, Heid IM Holmen OL, Hovingh GK, Howson JMM, Hu Y, Hung YJ Hveem K Ikram MA, Ingelsson E Jackson AU, Jarvik GP Jia Y, Jørgensen T, Jousilahti P, Justesen JM, Kahali B Karaleftheri M, Kardia SLR, Karpe F Kee F, Kitajima H, Komulainen P, Kooner JS Kovacs P, Krämer BK, Kuulasmaa K, Kuusisto J, Laakso M, Lakka TA, Lamparter D, Lange LA, Langenberg C, Larson EB, Lee NR Lee WJ Lehtimäki T Lewis CE, Li H, Li J, Li-Gao R, Lin LA, Lin X, Lind L, Lindström J, Linneberg A, Liu CT, Liu DJ, Luan J, Lyytikäinen LP, MacGregor S, Mägi R, Männistö S, Marenne G, Marten J, Masca NGD, McCarthy MI, Meidtner K, Mihailov E, Moilanen L, Moitry M, Mook-Kanamori DO, Morgan A, Morris AP, Müller-Nurasyid M, Munroe PB, Narisu N, Nelson CP, Neville M, Ntalla I, O'Connell JR, Owen KR Pedersen O, Peloso GM, Pennell CE Perola M Perry JA, Perry JRB, Pers TH, Ewing A, Polasek O Raitakari OT, Rasheed A, Raulerson CK, Rauramaa R, Reilly DF, Reiner AP Ridker PM, Rivas MA, Robertson NR Robino A, Rudan I, Ruth KS, Saleheen D, Salomaa V, Samani NJ, Schreiner PJ, Schulze MB Scott RA, Segura-Lepe M, Sim X, Slater AJ, Small KS, Smith BH, Smith JA, Southam L, Spector TD, Speliotes EK, Stefansson K, Steinthorsdottir V, Stirrups KE, Strauch K, Stringham HM, Stumvoll M, Sun L, Surendran P, Swart KMA, Tardif JC Taylor KD, Teumer A, Thompson DJ, Thorleifsson G, Thorsteinsdottir U, Thuesen BH, Tönjes A, Torres M, Tsafantakis E, Tuomilehto J, Uitterlinden AG, Uusitupa M, van Duijn CM, Vanhala M Varma R, Vermeulen SH, Vestergaard H Vitart V, Vogt TF, Vuckovic D, Wagenknecht LE, Walker M, Wallentin L, Wang F, Wang CA Wang S, Wareham NJ, Warren HR Waterworth DM, Wessel J, White HD, Willer CJ, Wilson JG, Wood AR, Wu Y, Yaghootkar H, Yao J, Yerges-Armstrong LM Young R Zeggini E, Zhan X, Zhang W Zhao JH, Zhao W, Zheng H, Zhou W Zillikens MC,; CHD Exome+ Consortium; Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium; EPIC-CVD Consortium; ExomeBP Consortium; Global Lipids Genetic Consortium; GoTD Genes Consortium; InterAct; ReproGen Consortium; TD-Genes Consortium; MAGIC Investigators, Rivadeneira F, Borecki IB, Pospisilik JA, Deloukas P, Frayling TM, Lettre G, Mohlke KL, Rotter JI, Kutalik Z, Hirschhorn JN, Cupples LA, Loos RJF, North KE, Lindgren CM. Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution. Nat Genet. 2019 Mar;51(3):452-469. doi: 10.1038/s41588-018-0334-2. Epub 2019 Feb 18. PMID: 30778226 read article


Howard TP, Arnoff TE, Song MR, Giacomelli AO, Wang X, Hong AL, Dharia NV, Wang S, Vazquez F, Pham MT, Morgan AM, Wachter F, Bird GH, Kugener G, Oberlick EM, Rees MG, Tiv HL, Hwang JH, Walsh KH, Cook A, Krill-Burger JM, Tsherniak A, Gokhale PC, Park PJ, Stegmaier K, Walensky LD, Hahn WC, Roberts CWM. MDM2 and MDM4 are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Res. 2019 Feb 12. pii: canres.3066.2018. doi: 10.1158/0008-5472.CAN-18-3066. [Epub ahead of print] PMID: 30755442 read article


Gopalakrishnan R, Marr SK, Kingston RE Winston F. A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation. Nucleic Acids Res. 2019 Feb 22. pii: gkz119. doi: 10.1093/nar/gkz119. [Epub ahead of print] PMID: 30793188  read article


Ulirsch JC, Lareau CA, Bao EL, Ludwig LS, Guo MH, Benner C, Satpathy AT, Kartha VK, Salem RM, Hirschhorn JN, Finucane HK, Aryee MJ, Buenrostro JD, Sankaran VG. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet. 2019 Apr;51(4):683-693. doi: 10.1038/s41588-019-0362-6. Epub 2019 Mar 11. PMID: 30858613 PMCID: PMC6441389 read article


Poulopoulos A, Murphy AJ, Ozkan A, Davis P, Hatch J, Kirchner R, Macklis JD. Subcellular transcriptomes and proteomes of developing axon projections in the cerebral cortex. Nature. 2019 Jan;565(7739):356-360. doi: 10.1038/s41586-018-0847-y. Epub 2019 Jan 9. PMID: 30626971 read article


Fleming E, Yuan AH, Heller DM, Hochschild A. A bacteria-based genetic assay detects prion formation. Proc Natl Acad Sci U S A. 2019 Feb 19. pii: 201817711. doi: 10.1073/pnas.1817711116. PMID: 30782808 PMCID: PMC6410773 [Available on 2019-09-05] read article


Horvat C, Johnson R, Lam L, Munro J, Mazzarotto F, Roberts AM, Herman DS, Parfenov M, Haghighi A, McDonough B, DePalma SR, Keogh AM, Macdonald PS, Hayward CS, Roberts A, Barton PJR, Felkin LE, Giannoulatou E, Cook SA, Seidman JG, Seidman CE, Fatkin D. A gene-centric strategy for identifying disease-causing rare variants in dilated cardiomyopathy. Genet Med. 2019 Jan;21(1):133-143. doi: 10.1038/s41436-018-0036-2. Epub 2018 Jun 11. PMID: 29892087 read article


Fagbami L, Deik AA, Singh K, Santos SA, Herman JD, Bopp SE, Lukens AK, Clish CB, Wirth DF, Mazitschek R. The Adaptive Proline Response in P. falciparum Is Independent of PfeIK1 and eIF2α Signaling. ACS Infect Dis. 2019 Feb 21. doi: 10.1021/acsinfecdis.8b00363. [Epub ahead of print] PMID: 30773881  read article


Hinshaw SM, Harrison SC. The structure of the Ctf19c/CCAN from budding yeast. Elife. 2019 Feb 14;8. pii: e44239. doi: 10.7554/eLife.44239. PMID: 30762520 PMCID: PMC6407923 read article


Hubbard TP, D'Gama JD, Billings G, Davis BM, Waldor MK. Unsupervised Learning Approach for Comparing Multiple Transposon Insertion Sequencing Studies. mSphere. 2019 Feb 20;4(1). pii: e00031-19. doi: 10.1128/mSphere.00031-19. PMID: 30787116 PMCID: PMC6382967 read article


Neinast MD, Jang C, Hui S, Murashige DS, Chu Q, Morscher RJ, Li X, Zhan L, White E, Anthony TG, Rabinowitz JD, Arany Z. Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids. Cell Metab. 2019 Feb 5;29(2):417-429.e4. doi: 10.1016/j.cmet.2018.10.013. Epub 2018 Nov 15. PMID: 30449684 PMCID: PMC6365191 [Available on 2020-02-05] read article


Hrvatin S, Tzeng CP, Nagy MA, Stroud H, Koutsioumpa C, Wilcox OF, Griffith EC, Greenberg ME. PESCA: A scalable platform for the development of cell-type-specific viral drivers. (March 08, 2019) doi: https://doi.org/10.1101/570895


Del Rosario BC, Kriz AJ, Del Rosario AM, Anselmo A, Fry CJ, White FM, Sadreyev RI, Lee JT. Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition. Elife. 2019 Jan 24;8. pii: e42341. doi: 10.7554/eLife.42341. PMID: 30676316 PMCID: PMC6361588  read article


Colognori D, Sunwoo H, Kriz AJ, Wang CY, Lee JT. Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X. Mol Cell. 2019 Apr 4;74(1):101-117.e10. doi: 10.1016/j.molcel.2019.01.015. Epub 2019 Feb 28. PMID: 30827740 read article


Maertens O, Kuzmickas R, Manchester HE, Emerson CE, Gavin AG, Guild CJ, Wong TC, De Raedt T, Bowman-Colin C, Hatchi E, Garraway LA, Flaherty KT, Pathania S, Elledge SJ, Cichowski K. MAPK Pathway Suppression Unmasks Latent DNA Repair Defects and Confers a Chemical Synthetic Vulnerability in BRAF-, NRAS-, and NF1-Mutant Melanomas. Cancer Discov. 2019 Feb 1. doi: 10.1158/2159-8290.CD-18-0879. [Epub ahead of print] PMID: 30709805 read article


Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C. Publisher Correction: N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol. 2019 May;15(5):549. doi: 10.1038/s41589-019-0233-6. PMID: 30737498 read article


Ulirsch JC, Lareau CA, Bao EL, Ludwig LS, Guo MH, Benner C, Satpathy AT, Kartha VK, Salem RM, Hirschhorn JN, Finucane HK, Aryee MJ, Buenrostro JD, Sankaran VG. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet. 2019 Mar 11. doi: 10.1038/s41588-019-0362-6. [Epub ahead of print] PMID: 30858613 read article


Ludwig LS, Lareau CA, Ulirsch JC, Christian E, Muus C, Li LH, Pelka K, Ge W, Oren Y, Brack A, Law T, Rodman C, Chen JH, Boland GM, Hacohen N, Rozenblatt-Rosen O, Aryee MJ, Buenrostro JD, Regev A, Sankaran VG. Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics. Cell. 2019 Mar 7;176(6):1325-1339.e22. doi: 10.1016/j.cell.2019.01.022. Epub 2019 Feb 28. PMID: 30827679 PMCID: PMC6408267 read article


Kousa YA, Zhu H, Fakhouri WD, Lei Y, Kinoshita A, Roushangar RR, Patel NK, Agopian AJ, Yang W, Leslie EJ, Busch TD, Mansour TA, Li X, Smith AL, Li EB, Sharma DB, Williams TJ, Chai Y, Amendt BA, Liao EC, Mitchell LE, Bassuk AG, Gregory S, Ashley-Koch A, Shaw GM, Finnell RH, Schutte BC. The TFAP2A-IRF6-GRHL3 genetic pathway is conserved in neurulation. Hum Mol Genet. 2019 Jan 25. doi: 10.1093/hmg/ddz010. [Epub ahead of print] PMID: 30689861 read article


Wu RA, Semlow DR, Kamimae-Lanning AN, Kochenova OV, Chistol G, Hodskinson MR, Amunugama R, Sparks JL, Wang M, Deng L, Mimoso CA, Low E, Patel KJ, Walter JC. TRAIP is a master regulator of DNA interstrand crosslink repair. Nature. 2019 Mar;567(7747):267-272. doi: 10.1038/s41586-019-1002-0. Epub 2019 Mar 6. PMID: 30842657 read article


Fagbami L, Deik AA, Singh K, Santos SA, Herman JD, Bopp SE, Lukens AK, Clish CB, Wirth DF, Mazitschek R. The Adaptive Proline Response in P. falciparum Is Independent of PfeIK1 and eIF2α Signaling. ACS Infect Dis. 2019 Apr 12;5(4):515-520. doi: 10.1021/acsinfecdis.8b00363. Epub 2019 Feb 21. PMID: 30773881 DOI: 10.1021/acsinfecdis.8b00363 read article


Hayes TK, Luo F, Cohen O, Goodale AB, Lee Y, Pantel S, Bagul M, Piccioni F, Root DE, Garraway LA, Meyerson M, Johannessen CM. A functional landscape of resistance to MEK1/2 and CDK4/6 inhibition in NRAS mutant melanoma. Cancer Res. 2019 Feb 28. pii: canres.2711.2018. doi: 10.1158/0008-5472.CAN-18-2711. PMID: 30819666 read article


Maertens O, Kuzmickas R, Manchester HE, Emerson CE, Gavin AG, Guild CJ, Wong TC, De Raedt T, Bowman-Colin C, Hatchi E, Garraway LA, Flaherty KT, Pathania S, Elledge SJ, Cichowski K. MAPK Pathway Suppression Unmasks Latent DNA Repair Defects and Confers a Chemical Synthetic Vulnerability in BRAF-, NRAS-, and NF1-Mutant Melanomas. Cancer Discov. 2019 Feb 1. doi: 10.1158/2159-8290.CD-18-0879. [Epub ahead of print] PMID: 30709805 read article


Ishizuka JJ, Manguso RT, Cheruiyot CK, Bi K, Panda A, Iracheta-Vellve A, Miller BC, Du PP, Yates KB, Dubrot J, Buchumenski I, Comstock DE, Brown FD, Ayer A, Kohnle IC, Pope HW, Zimmer MD, Sen DR, Lane-Reticker SK, Robitschek EJ, Griffin GK, Collins NB, Long AH, Doench JG, Kozono D, Levanon EY, Haining WN. Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade. Nature. 2019 Jan;565(7737):43-48. doi: 10.1038/s41586-018-0768-9. Epub 2018 Dec 17. PMID: 30559380 read article


Miller BC, Sen DR, Al Abosy R, Bi K, Virkud YV, LaFleur MW, Yates KB, Lako A, Felt K, Naik GS, Manos M, Gjini E, Kuchroo JR, Ishizuka JJ, Collier JL, Griffin GK, Maleri S, Comstock DE, Weiss SA, Brown FD, Panda A, Zimmer MD, Manguso RT, Hodi FS, Rodig SJ, Sharpe AH, Haining WN. Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade. Nat Immunol. 2019 Mar;20(3):326-336. doi: 10.1038/s41590-019-0312-6. Epub 2019 Feb 18. PMID: 30778252 read article


Mattioli K, Volders PJ, Gerhardinger C, Lee JC, Maass PG, Melé M, Rinn JL. High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity. Genome Res. 2019 Mar;29(3):344-355. doi: 10.1101/gr.242222.118. Epub 2019 Jan 25. PMID: 30683753 read article


Maurer AC, Cepeda Diaz AK, Vandenberghe LH. Residues on Adeno-associated Virus Capsid Lumen Dictate Interactions and Compatibility with the Assembly-Activating Protein. J Virol. 2019 Mar 21;93(7). pii: e02013-18. doi: 10.1128/JVI.02013-18. Print 2019 Apr 1. PMID: 30651367 read article


Galvin A, Weglarz M, Folz-Donahue K, Handley M, Baum M, Mazzola M, Litwa H, Scadden DT, Silberstein L. Cell Cycle Analysis of Hematopoietic Stem and Progenitor Cells by Multicolor Flow Cytometry. Curr Protoc Cytom. 2019 Jan;87(1):e50. doi: 10.1002/cpcy.50. Epub 2018 Oct 18. PMID: 30335223  read article


Chakraborty AA, Laukka T, Myllykoski M, Ringel AE, Booker MA, Tolstorukov MY, Meng YJ, Meier SR, Jennings RB, Creech AL, Herbert ZT, McBrayer SK, Olenchock BA, Jaffe JD, Haigis MC, Beroukhim R, Signoretti S, Koivunen P2, Kaelin WG Jr. Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate. Science. 2019 Mar 15;363(6432):1217-1222. doi: 10.1126/science.aaw1026. Epub 2019 Mar 14. PMID: 30872525 read article


Mengwasser KE, Adeyemi RO, Leng Y, Choi MY, Clairmont C, D'Andrea AD, Elledge SJ. Genetic Screens Reveal FEN1 and APEX2 as BRCA2 Synthetic Lethal Targets. Mol Cell. 2019 Mar 7;73(5):885-899.e6. doi: 10.1016/j.molcel.2018.12.008. Epub 2019 Jan 24. PMID: 30686591 read article


Whiffin N, Roberts AM, Minikel E, Zappala Z, Walsh R, O'Donnell-Luria AH, Karczewski KJ, Harrison SM, Thomson KL, Sage H, Ing AY, Barton PJR, Funke B, Cook SA, MacArthur DG, Ware JS. Using High-Resolution Variant Frequencies Empowers Clinical Genome Interpretation and Enables Investigation of Genetic Architecture. Am J Hum Genet. 2019 Jan 3;104(1):187-190. doi: 10.1016/j.ajhg.2018.11.012. PMID: 30609406 PMCID: PMC6323549 read article


Chauhan VP, Chen IX, Tong R, Ng MR, Martin JD, Naxerova K, Wu MW, Huang P, Boucher Y, Kohane DS, Langer R, Jain RK. Reprogramming the microenvironment with tumor-selective angiotensin blockers enhances cancer immunotherapy. Proc Natl Acad Sci U S A. 2019 Apr 30. pii: 201819889. doi: 10.1073/pnas.1819889116. [Epub ahead of print] PMID: 31040208 read article


Howard TP, Arnoff TE, Song MR, Giacomelli AO, Wang X, Hong AL, Dharia NV, Wang S, Vazquez F, Pham MT, Morgan AM, Wachter F, Bird GH, Kugener G, Oberlick EM, Rees MG, Tiv HL, Hwang JH, Walsh KH, Cook A, Krill-Burger JM, Tsherniak A, Gokhale PC, Park PJ, Stegmaier K, Walensky LD, Hahn WC, Roberts CWM. MDM2 and MDM4 are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Res. 2019 Feb 12. pii: canres.3066.2018. doi: 10.1158/0008-5472.CAN-18-3066. [Epub ahead of print] PMID: 30755442 read article


Pan J, McKenzie ZM, D'Avino AR, Mashtalir N, Lareau CA, St Pierre R, Wang L, Shilatifard A, Kadoch C. The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting. Nat Genet. 2019 Apr;51(4):618-626. doi: 10.1038/s41588-019-0363-5. Epub 2019 Mar 11. PMID: 30858614 read article


Yermalovich AV, Osborne JK, Sousa P, Han A, Kinney MA, Chen MJ, Robinton DA, Montie H, Pearson DS, Wilson SB, Combes AN, Little MH, Daley GQ. Lin28 and let-7 regulate the timing of cessation of murine nephrogenesis. Nat Commun. 2019 Jan 11;10(1):168. doi: 10.1038/s41467-018-08127-4. PMID: 30635573 PMCID: PMC6329821 read article


Roh JD, Hobson R, Chaudhari V, Quintero P, Yeri A, Benson M, Xiao C, Zlotoff D, Bezzerides V, Houstis N, Platt C, Damilano F, Lindman BR, Elmariah S, Biersmith M, Lee SJ, Seidman CE, Seidman JG, Gerszten RE, Lach-Trifilieff E, Glass DJ, Rosenzweig A. Activin type II receptor signaling in cardiac aging and heart failure. Sci Transl Med. 2019 Mar 6;11(482). pii: eaau8680. doi: 10.1126/scitranslmed.aau8680. PMID: 30842316 read article


Yermalovich AV, Osborne JK, Sousa P, Han A, Kinney MA, Chen MJ, Robinton DA, Montie H, Pearson DS, Wilson SB, Combes AN, Little MH, Daley GQ. Lin28 and let-7 regulate the timing of cessation of murine nephrogenesis. Nat Commun. 2019 Jan 11;10(1):168. doi: 10.1038/s41467-018-08127-4. PMID: 30635573 PMCID: PMC6329821 read article


Robinton DA, Chal J, Lummertz da Rocha E, Han A, Yermalovich AV, Oginuma M, Schlaeger TM, Sousa P, Rodriguez A, Urbach A, Pourquié O, Daley GQ. The Lin28/let-7 Pathway Regulates the Mammalian Caudal Body Axis Elongation Program. Dev Cell. 2019 Feb 11;48(3):396-405.e3. doi: 10.1016/j.devcel.2018.12.016. Epub 2019 Jan 17. PMID: 30661985 read article


Sharifnia T, Wawer MJ, Chen T, Huang QY, Weir BA, Sizemore A, Lawlor MA, Goodale A, Cowley GS, Vazquez F, Ott CJ, Francis JM, Sassi S, Cogswell P, Sheppard HE, Zhang T, Gray NS, Clarke PA, Blagg J, Workman P, Sommer J, Hornicek F, Root DE, Hahn WC, Bradner JE, Wong KK, Clemons PA, Lin CY, Kotz JD, Schreiber SL. Small-molecule targeting of brachyury transcription factor addiction in chordoma. Nat Med. 2019 Feb;25(2):292-300. doi: 10.1038/s41591-018-0312-3. Epub 2019 Jan 21. PMID: 30664779 read article


Sharma N, Pollina EA, Nagy MA, Yap EL, DiBiase FA, Hrvatin S, Hu L, Lin C, Greenberg ME. ARNT2 Tunes Activity-Dependent Gene Expression through NCoR2-Mediated Repression and NPAS4-Mediated Activation. Neuron. 2019 Mar 1. pii: S0896-6273(19)30116-3. doi: 10.1016/j.neuron.2019.02.007. [Epub ahead of print] PMID: 30846309 read article


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McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry R, Meyer I, Kellis M, Zinzen RP. A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs. Development. 2019 Mar 28;146(6). pii: dev175265. doi: 10.1242/dev.175265.
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Taguchi A, Welsh MA, Marmont LS, Lee W, Sjodt M, Kruse AC, Kahne D, Bernhardt TG, Walker S. FtsW is a peptidoglycan polymerase that is functional only in complex with its cognate penicillin-binding protein. Nat Microbiol. 2019 Apr;4(4):587-594. doi: 10.1038/s41564-018-0345-x. Epub 2019 Jan 28. PMID: 30692671 PMCID: PMC6430707 [Available on 2019-07-28] read article


Lakhani CM, Tierney BT, Manrai AK, Yang J, Visscher PM, Patel CJ. Author Correction: Repurposing large health insurance claims data to estimate genetic and environmental contributions in 560 phenotypes. Nat Genet. 2019 Feb 27. doi: 10.1038/s41588-019-0377-z. [Epub ahead of print] PMID: 30814726 read article


Ulirsch JC, Lareau CA, Bao EL, Ludwig LS, Guo MH, Benner C, Satpathy AT, Kartha VK, Salem RM, Hirschhorn JN, Finucane HK, Aryee MJ, Buenrostro JD1, Sankaran VG. Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nat Genet. 2019 Mar 11. doi: 10.1038/s41588-019-0362-6. [Epub ahead of print] PMID: 30858613 read article


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Walton T, Pazienza L, Szostak JW. Template-Directed Catalysis of a Multistep Reaction Pathway for Nonenzymatic RNA Primer Extension. Biochemistry. 2019 Feb 12;58(6):755-762. doi: 10.1021/acs.biochem.8b01156. Epub 2018 Dec 31. PMID: 30566332 read article


Warr AR, Klimova AN, Nwaobasi AN, Sandler SJ. Protease-deficient SOS constitutive cells have RecN-dependent cell division phenotypes. Mol Microbiol. 2019 Feb;111(2):405-422. doi: 10.1111/mmi.14162. Epub 2018 Dec 5. PMID: 30422330 PMCID: PMC6368896 [Available on 2020-02-01] read article


Rogers JM, Waters CT, Seegar TCM, Jarrett SM, Hallworth AN, Blacklow SC, Bulyk ML. Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes. Mol Cell. 2019 Feb 22. pii: S1097-2765(19)30039-5. doi: 10.1016/j.molcel.2019.01.019. PMID: 30826165 read article


Wu C, Watts ME, Rubin LL. MAP4K4 Activation Mediates Motor Neuron Degeneration in Amyotrophic Lateral Sclerosis. Cell Rep. 2019 Jan 29;26(5):1143-1156.e5. doi: 10.1016/j.celrep.2019.01.019. PMID: 30699345 read article


Low IIC, Williams CR, Chong MK, McLachlan IG, Wierbowski BM, Kolotuev I, Heiman MG. Morphogenesis of neurons and glia within an epithelium. Development. 2019 Feb 20;146(4). pii: dev171124. doi: 10.1242/dev.171124. PMID: 30683663 read article


Thams S, Lowry ER, Larraufie MH, Spiller KJ, Li H, Williams DJ, Hoang P, Jiang E, Williams LA, Sandoe J, Eggan K, Lieberam I, Kanning KC, Stockwell BR, Henderson CE, Wichterle H. A Stem Cell-Based Screening Platform Identifies Compounds that Desensitize Motor Neurons to Endoplasmic Reticulum Stress. Mol Ther. 2019 Jan 2;27(1):87-101. doi: 10.1016/j.ymthe.2018.10.010. Epub 2018 Oct 19. PMID: 30446391 PMCID: PMC6318783 [Available on 2020-01-02] read article


Klim JR, Williams LA, Limone F, Guerra San Juan I, Davis-Dusenbery BN, Mordes DA, Burberry A, Steinbaugh MJ, Gamage KK, Kirchner R, Moccia R, Cassel SH, Chen K, Wainger BJ, Woolf CJ, Eggan K. ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair. Nat Neurosci. 2019 Feb;22(2):167-179. doi: 10.1038/s41593-018-0300-4. Epub 2019 Jan 14. PMID: 30643292 read article


Witten LW, Cheng CJ, Slack FJ. miR-155 drives oncogenesis by promoting and cooperating with mutations in the c-Kit oncogene. Oncogene. 2019 Mar;38(12):2151-2161. doi: 10.1038/s41388-018-0571-y. Epub 2018 Nov 20. PMID: 30459357 read article


Maertens O, Kuzmickas R, Manchester HE, Emerson CE, Gavin AG, Guild CJ, Wong TC, De Raedt T, Bowman-Colin C, Hatchi E, Garraway LA, Flaherty KT, Pathania S, Elledge SJ, Cichowski K. MAPK Pathway Suppression Unmasks Latent DNA Repair Defects and Confers a Chemical Synthetic Vulnerability in BRAF-, NRAS-, and NF1-Mutant Melanomas. Cancer Discov. 2019 Apr;9(4):526-545. doi: 10.1158/2159-8290.CD-18-0879. Epub 2019 Feb 1. PMID: 30709805 read article


Xu C, Tang HW, Hung RJ, Hu Y, Ni X, Housden BE, Perrimon N. The Septate Junction Protein Tsp2A Restricts Intestinal Stem Cell Activity via Endocytic Regulation of aPKC and Hippo Signaling. Cell Rep. 2019 Jan 15;26(3):670-688.e6. doi: 10.1016/j.celrep.2018.12.079. PMID: 30650359 PMCID: PMC6394833 [Available on 2020-01-15] read article


Yuan J, Ma M, Guo Y, He B, Cai Z, Ye B, Xu L, Liu J, Ding J, Zheng Z, Duan J, Wang L. Delayed endoscopic removal of sharp foreign body in the esophagus increased clinical complications: An experience from multiple centers in China. Medicine (Baltimore). 2019 Jun;98(26):e16146. doi: 10.1097/MD.0000000000016146. PMID: 31261541  read article


Jégu T, Blum R, Cochrane JC, Yang L, Wang CY, Gilles ME, Colognori D, Szanto A, Marr SK, Kingston RE, Lee JT. Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome. Nat Struct Mol Biol. 2019 Feb;26(2):96-109. doi: 10.1038/s41594-018-0176-8. Epub 2019 Jan 21. PMID: 30664740 PMCID: PMC6421574 [Available on 2019-07-21] read article


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Blake KJ, Baral P, Voisin T, Lubkin A, Pinho-Ribeiro FA, Adams KL, Roberson DP, Ma YC, Otto M, Woolf CJ, Torres VJ, Chiu IM. Staphylococcus aureus produces pain through pore-forming toxins and neuronal TRPV1 that is silenced by QX-314. Nat Commun. 2018 Jan 2;9(1):37. doi: 10.1038/s41467-017-02448-6. PMID: 29295977 PMCID: PMC5750211 read article


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Zuo C, Wang L, Kamalesh RM, Bowen ME, Moore DC, Dooner MS, Reginato AM, Wu Q, Schorl C, Song Y, Warman ML, Neel BG, Ehrlich MG, Yang W. SHP2 regulates skeletal cell fate by modifying SOX9 expression and transcriptional activity. Bone Res. 2018 Apr 6;6:12. doi: 10.1038/s41413-018-0013-z. eCollection 2018. PMID: 29644115 PMCID: PMC5886981 read article


Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM. The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science. 2018 Jun 1;360(6392). pii: eaar5780. doi: 10.1126/science.aar5780. Epub 2018 Apr 26. PMID: 29700227 PMCID: PMC6038144 read article


Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science. 2018 Jun 1;360(6392):981-987. doi: 10.1126/science.aar4362. Epub 2018 Apr 26. PMID: 29700229 PMCID: PMC6083445 read article


Brown AS, Patel CJ. A review of validation strategies for computational drug repositioning. Brief Bioinform. 2018 Jan 1;19(1):174-177. doi: 10.1093/bib/bbw110. PMID: 27881429 PMCID: PMC5862266 read article


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Shannon ML, Fame RM, Chau KF, Dani N, Calicchio ML, Géléoc GS, Lidov HGW, Alexandrescu S, Lehtinen MK. Mice Expressing Myc in Neural Precursors Develop Choroid Plexus and Ciliary Body Tumors. Am J Pathol. 2018 Jun;188(6):1334-1344. doi: 10.1016/j.ajpath.2018.02.009. Epub 2018 Mar 13. PMID: 29545198 PMCID: PMC5971223 [Available on 2019-06-01]  read article


Lubner JM, Balsbaugh JL, Church GM, Chou MF, Schwartz D. Characterizing Protein Kinase Substrate Specificity Using the Proteomic Peptide Library (ProPeL) Approach. Curr Protoc Chem Biol. 2018 Jun;10(2):e38. doi: 10.1002/cpch.38. PMID: 29927115 PMCID: PMC6014603 [Available on 2019-06-01] read article


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Christov M, Clark AR, Corbin B, Hakroush S, Rhee EP, Saito H, Brooks D, Hesse E, Bouxsein M, Galjart N, Jung JY, Mundel P, Jüppner H, Weins A, Greka A. Inducible podocyte-specific deletion of CTCF drives progressive kidney disease and bone abnormalities. JCI Insight. 2018 Feb 22;3(4). pii: 95091. doi: 10.1172/jci.insight.95091. eCollection 2018 Feb 22. PMID: 29467330 PMCID: PMC5916242 read article


Sieber J, Wieder N, Clark A, Reitberger M, Matan S, Schoenfelder J, Zhang J, Mandinova A, Bittker JA, Gutierrez J, Aygün O, Udeshi N, Carr S, Mundel P, Jehle AW, Greka A. GDC-0879, a BRAFV600E Inhibitor, Protects Kidney Podocytes from Death. Cell Chem Biol. 2018 Feb 15;25(2):175-184.e4. doi: 10.1016/j.chembiol.2017.11.006. Epub 2017 Dec 14. PMID: 29249695 PMCID: PMC5819995  read article


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Ling AV, Gearing ME, Semova I, Shin DJ, Clements R, Lai ZW, Biddinger SB. FoxO1 Is Required for Most of the Metabolic and Hormonal Perturbations Produced by Hepatic Insulin Receptor Deletion in Male Mice.Endocrinology. 2018 Mar 1;159(3):1253-1263. doi: 10.1210/en.2017-00870. PMID: 29300910 PMCID: PMC5802805 read article


Zhou J, Li J, Serafim RB, Ketchum S, Ferreira CG, Liu JC, Coe KA, Price BD, Yusufzai T. Human CHD1 is required for early DNA-damage signaling and is uniquely regulated by its N terminus. Nucleic Acids Res. 2018 May 4;46(8):3891-3905. doi: 10.1093/nar/gky128. PMID: 29529298 PMCID: PMC5934646  read article


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Wagner DE, Weinreb C, Collins ZM, Briggs JA, Megason SG, Klein AM. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science. 2018 Jun 1;360(6392):981-987. doi: 10.1126/science.aar4362. Epub 2018 Apr 26. PMID: 29700229 PMCID: PMC6083445 read article


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Jiao AL, Foster DJ, Dixon J, Slack FJ. lin-4 and the NRDE pathway are required to activate a transgenic lin-4 reporter but not the endogenous lin-4 locus in C. elegans. PLoS One. 2018 Jan 11;13(1):e0190766. doi: 10.1371/journal.pone.0190766. eCollection 2018. PMID: 29324872 PMCID: PMC5764303 read article


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Hayden MA, Ordulu Z, Gallagher CS, Quade BJ, Anchan RM, Middleton NR, Srouji SS, Stewart EA, Morton CC. Clinical, pathologic, cytogenetic, and molecular profiling in self-identified black women with uterine leiomyomata. Cancer Genet. 2018 Apr;222-223:1-8. doi: 10.1016/j.cancergen.2018.01.001. Epub 2018 Feb 19. PMID: 29666002 PMCID: PMC5909837 read article


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Ling AV, Gearing ME, Semova I, Shin DJ, Clements R, Lai ZW, Biddinger SB. FoxO1 Is Required for Most of the Metabolic and Hormonal Perturbations Produced by Hepatic Insulin Receptor Deletion in Male Mice. Endocrinology. 2018 Mar 1;159(3):1253-1263. doi: 10.1210/en.2017-00870. PMID: 29300910 PMCID: PMC5802805 read article


Gechijian LN, Buckley DL, Lawlor MA, Reyes JM, Paulk J, Ott CJ, Winter GE, Erb MA, Scott TG, Xu M, Seo HS, Dhe-Paganon S, Kwiatkowski NP, Perry JA, Qi J, Gray NS, Bradner JE Functional TRIM24 degrader via conjugation of ineffectual bromodomain and VHL ligands. Nat Chem Biol. 2018 Apr;14(4):405-412. doi: 10.1038/s41589-018-0010-y. Epub 2018 Mar 5. PMID: 29507391 PMCID: PMC5866761 read article


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Hemming ML, Lawlor MA, Zeid R, Lesluyes T, Fletcher JA, Raut CP, Sicinska ET, Chibon F, Armstrong SA, Demetri GD, Bradner JE. Gastrointestinal stromal tumor enhancers support a transcription factor network predictive of clinical outcome. Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):E5746-E5755. doi: 10.1073/pnas.1802079115. Epub 2018 Jun 4. PMID: 29866822 PMCID: PMC6016782 read article


Kiskinis E, Kralj JM, Zou P Weinstein EN, Zhang H, Tsioras K, Wiskow O, Ortega JA, Eggan K, Cohen AE. All-Optical Electrophysiology for High-Throughput Functional Characterization of a Human iPSC-Derived Motor Neuron Model of ALS. Stem Cell Reports. 2018 Jun 5;10(6):1991-2004. doi: 10.1016/j.stemcr.2018.04.020. Epub 2018 May 17. PMID: 29779896 PMCID: PMC5993648 read article


Yuen KS, Wang ZM, Wong NM, Zhang ZQ, Cheng TF, Lui WY, Chan CP, Jin DY. Suppression of Epstein-Barr virus DNA load in latently infected nasopharyngeal carcinoma cells by CRISPR/Cas9. Virus Res. 2018 Jan 15;244:296-303. doi: 10.1016/j.virusres.2017.04.019. Epub 2017 Apr 27. PMID: 28456574  read article


Ziesack M, Rollins N, Shah A, Dusel B, Webster G, Silver PA, Way JC. Chimeric Fatty Acyl-Acyl Carrier Protein Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression. Appl Environ Microbiol. 2018 May 1;84(10). pii: e02868-17. doi: 10.1128/AEM.02868-17. Print 2018 May 15. PMID: 29549102 PMCID: PMC5930381 read article


Kim S, Kerns SJ, Ziesack M, Bry L, Gerber GK, Way JC, Silver PA. Quorum Sensing Can Be Repurposed To Promote Information Transfer between Bacteria in the Mammalian Gut. ACS Synth Biol. 2018 Sep 21;7(9):2270-2281. doi: 10.1021/acssynbio.8b00271. Epub 2018 Aug 31. PMID: 30125499 read article


Ziesack M, Karrenbelt MAP, Bues J, Schaefer E, Silver P, Way J. Escherichia coli NGF-1, a Genetically Tractable, Efficiently Colonizing Murine Gut Isolate. Microbiol Resour Announc. 2018 Dec 6;7(22). pii: e01416-18. doi: 10.1128/MRA.01416-18. eCollection 2018 Dec. PMID: 30533859 PMCID: PMC6284091 read article


Michel BC, D'Avino AR, Cassel SH, Mashtalir N, McKenzie ZM, McBride MJ, Valencia AM, Zhou Q, Bocker M, Soares LMM, Pan J, Remillard DI, Lareau CA, Zullow HJ, Fortoul N, Gray NS, Bradner JE, Chan HM, Kadoch C. A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nat Cell Biol. 2018 Dec;20(12):1410-1420. doi: 10.1038/s41556-018-0221-1. Epub 2018 Nov 5. PMID: 30397315
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Mashtalir N, D'Avino AR, Michel BC, Luo J, Pan J, Otto JE, Zullow HJ, McKenzie ZM, Kubiak RL, St Pierre R, Valencia AM, Poynter SJ, Cassel SH, Ranish JA, Kadoch C. Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes. Cell. 2018 Nov 15;175(5):1272-1288.e20. doi: 10.1016/j.cell.2018.09.032. Epub 2018 Oct 18. PMID: 30343899 read article


2017


Ponnuswamy N, Bastings MMC, Nathwani B, Ryu JH, Chou LYT, Vinther M, Li WA, Anastassacos FM, Mooney DJ, Shih WM. Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation. Nat Commun. 2017 May 31;8:15654. doi: 10.1038/ncomms15654. PMID: 28561045 PMCID: PMC5460023 read article


Arellano-Santoyo H, Geyer EA, Stokasimov E, Chen GY, Su X, Hancock W, Rice LM, Pellman D. A Tubulin Binding Switch Underlies Kip3/Kinesin-8 Depolymerase Activity. Dev Cell. 2017 Jul 10;42(1):37-51.e8. doi: 10.1016/j.devcel.2017.06.011. PMID: 28697331 PMCID: PMC5573156 read article


Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F. Erratum to: Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biol. 2017 May 2;18(1):80. doi: 10.1186/s13059-017-1183-5. PMID: 28464947 PMCID: PMC5412043 read article


Pease-Raissi SE, Pazyra-Murphy MF, Li Y, Wachter F, Fukuda Y, Fenstermacher SJ, Barclay LA, Bird GH, Walensky LD, Segal RA. Paclitaxel Reduces Axonal Bclw to Initiate IP3R1-Dependent Axon Degeneration. Neuron. 2017 Oct 11;96(2):373-386.e6. doi: 10.1016/j.neuron.2017.09.034. PMID: 29024661 PMCID: PMC5680044 read article


Everley RA, Huttlin EL, Erickson AR, Beausoleil SA, Gygi SP. Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags. J Proteome Res. 2017 Feb 3;16(2):1069-1076. doi: 10.1021/acs.jproteome.6b00487. Epub 2016 Dec 30. PMID: 27978624 PMCID: PMC5479408 read article


Possemato AP, Paulo JA, Mulhern D, Guo A, Gygi SP, Beausoleil SA. Multiplexed Phosphoproteomic Profiling Using Titanium Dioxide and Immunoaffinity Enrichments Reveals Complementary Phosphorylation Events. J Proteome Res. 2017 Apr 7;16(4):1506-1514. doi: 10.1021/acs.jproteome.6b00905. Epub 2017 Feb 24. PMID: 28171727 PMCID: PMC5538569 read article


Beliveau BJ, Boettiger AN, Nir G, Bintu B, Yin P, Zhuang X, Wu CT. In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT. Methods Mol Biol. 2017;1663:231-252. doi: 10.1007/978-1-4939-7265-4_19. PMID: 28924672 PMCID: PMC5919218 read article


Mercader JM, Liao RG, Bell AD, Dymek Z, Estrada K, Tukiainen T, Huerta-Chagoya A, Moreno-Macías H, Jablonski KA, Hanson RL, Walford GA, Moran I, Chen L, Agarwala V, Ordoñez-Sánchez ML, Rodríguez-Guillen R, Rodríguez-Torres M, Segura-Kato Y, García-Ortiz H, Centeno-Cruz F, Barajas-Olmos F, Caulkins L, Puppala S, Fontanillas P, Williams AL, Bonàs-Guarch S, Hartl C, Ripke S; Diabetes Prevention Program Research Group, Tooley K, Lane J, Zerrweck C, Martínez-Hernández A, Córdova EJ, Mendoza-Caamal E, Contreras-Cubas C, González-Villalpando ME, Cruz-Bautista I, Muñoz-Hernández L, Gómez-Velasco D, Alvirde U, Henderson BE, Wilkens LR, Le Marchand L, Arellano-Campos O, Riba L, Harden M; Broad Genomics Platform, Gabriel S; T2D-GENES Consortium, Abboud HE, Cortes ML, Revilla-Monsalve C, Islas-Andrade S, Soberon X, Curran JE, Jenkinson CP, DeFronzo RA, Lehman DM, Hanis CL, Bell GI, Boehnke M, Blangero J, Duggirala R, Saxena R, MacArthur D, Ferrer J, McCarroll SA, Torrents D, Knowler WC, Baier LJ, Burtt N, González-Villalpando C, Haiman CA, Aguilar-Salinas CA, Tusié-Luna T, Flannick J, Jacobs SBR, Orozco L, Altshuler D, Florez JC; SIGMA T2D Genetics Consortium. A Loss-of-Function Splice Acceptor Variant in IGF2 Is Protective for Type 2 Diabetes. Diabetes. 2017 Nov;66(11):2903-2914. doi: 10.2337/db17-0187. Epub 2017 Aug 24. PMID: 28838971  read article


Bick AG, Wakimoto H, Kamer KJ, Sancak Y, Goldberger O, Axelsson A, DeLaughter DM, Gorham JM, Mootha VK, Seidman JG, Seidman CE. Cardiovascular homeostasis dependence on MICU2, a regulatory subunit of the mitochondrial calcium uniporter. Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):E9096-E9104. doi: 10.1073/pnas.1711303114. Epub 2017 Oct 9. PMID: 29073106 PMCID: PMC5664535 read article


Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH. Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA. Cell Rep. 2017 Oct 3;21(1):236-245. doi: 10.1016/j.celrep.2017.09.033.
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Lai NY, Mills K, Chiu IM. Sensory neuron regulation of gastrointestinal inflammation and bacterial host defence. J Intern Med. 2017 Jul;282(1):5-23. doi: 10.1111/joim.12591. Epub 2017 Feb 2. PMID: 28155242 PMCID: PMC5474171 read article


Bodnar NO, Rapoport TA. Molecular Mechanism of Substrate Processing by the Cdc48 ATPase Complex. Cell. 2017 May 4;169(4):722-735.e9. doi: 10.1016/j.cell.2017.04.020. PMID: 28475898 PMCID: PMC5751438  read article


Bodnar N, Rapoport T. Toward an understanding of the Cdc48/p97 ATPase. F1000Res. 2017 Aug 3;6:1318. doi: 10.12688/f1000research.11683.1. eCollection 2017. PMID: 28815021 PMCID: PMC554342 read article


Tsherniak A, Vazquez F, Montgomery PG, Weir BA, Kryukov G, Cowley GS, Gill S, Harrington WF, Pantel S, Krill-Burger JM, Meyers RM, Ali L, Goodale A, Lee Y, Jiang G, Hsiao J, Gerath WFJ, Howell S, Merkel E, Ghandi M, Garraway LA, Root DE, Golub TR, Boehm JS, Hahn WC. Defining a Cancer Dependency Map. Cell. 2017 Jul 27;170(3):564-576.e16. doi: 10.1016/j.cell.2017.06.010. PMID: 28753430 PMCID: PMC5667678 read article


Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F; Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Syst. 2017 Nov 22;5(5):485-497.e3. doi: 10.1016/j.cels.2017.09.004. Epub 2017 Oct 4. PMID: 28988802 PMCID: PMC5814247 read article


Viswanathan VS, Ryan MJ, Dhruv HD, Gill S, Eichhoff OM, Seashore-Ludlow B, Kaffenberger SD, Eaton JK, Shimada K, Aguirre AJ, Viswanathan SR, Chattopadhyay S, Tamayo P, Yang WS, Rees MG, Chen S, Boskovic ZV, Javaid S, Huang C, Wu X, Tseng YY, Roider EM, Gao D, Cleary JM, Wolpin BM, Mesirov JP, Haber DA, Engelman JA, Boehm JS, Kotz JD, Hon CS, Chen Y, Hahn WC, Levesque MP, Doench JG, Berens ME, Shamji AF, Clemons PA, Stockwell BR, Schreiber SL. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature. 2017 Jul 27;547(7664):453-457. doi: 10.1038/nature23007. Epub 2017 Jul 5. PMID: 28678785 PMCID: PMC5667900 read article


Meyers RM, Bryan JG, McFarland JM, Weir BA, Sizemore AE, Xu H, Dharia NV, Montgomery PG, Cowley GS, Pantel S, Goodale A, Lee Y, Ali LD, Jiang G, Lubonja R, Harrington WF, Strickland M, Wu T, Hawes DC, Zhivich VA, Wyatt MR, Kalani Z, Chang JJ, Okamoto M, Stegmaier K, Golub TR, Boehm JS, Vazquez F, Root DE, Hahn WC, Tsherniak A. Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. Nat Genet. 2017 Dec;49(12):1779-1784. doi: 10.1038/ng.3984. Epub 2017 Oct 30. PMID: 29083409 PMCID: PMC5709193 read article


Kim JW, Abudayyeh OO, Yeerna H, Yeang CH, Stewart M, Jenkins RW, Kitajima S, Konieczkowski DJ, Medetgul-Ernar K, Cavazos T, Mah C, Ting S, Van Allen EM, Cohen O, Mcdermott J, Damato E, Aguirre AJ, Liang J, Liberzon A, Alexe G, Doench J, Ghandi M, Vazquez F, Weir BA, Tsherniak A, Subramanian A, Meneses-Cime K, Park J, Clemons P, Garraway LA, Thomas D, Boehm JS, Barbie DA, Hahn WC, Mesirov JP, Tamayo P. Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States. Cell Syst. 2017 Aug 23;5(2):105-118.e9. doi: 10.1016/j.cels.2017.08.002. PMID: 28837809 PMCID: PMC5639711 read article


Briggs JA, Li VC, Lee S, Woolf CJ, Klein A, Kirschner MW. Mouse embryonic stem cells can differentiate via multiple paths to the same state. Elife. 2017 Oct 9;6. pii: e26945. doi: 10.7554/eLife.26945. PMID: 28990928 PMCID: PMC5648529 read article


Barry G, Briggs JA, Hwang DW, Nayler SP, Fortuna PR, Jonkhout N, Dachet F, Maag JL, Mestdagh P, Singh EM, Avesson L, Kaczorowski DC, Ozturk E, Jones NC, Vetter I, Arriola-Martinez L, Hu J, Franco GR, Warn VM, Gong A, Dinger ME, Rigo F, Lipovich L, Morris MJ, O'Brien TJ, Lee DS, Loeb JA, Blackshaw S, Mattick JS, Wolvetang EJ. The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states. Sci Rep. 2017 Jan 5;7:40127. doi: 10.1038/srep40127. PMID: 28054653 PMCID: PMC5214838 read article


Hennessy ML, Corcoran AE, Brust RD, Chang Y, Nattie EE, Dymecki SM. Activity of Tachykinin1-Expressing Pet1 Raphe Neurons Modulates the Respiratory Chemoreflex. J Neurosci. 2017 Feb 15;37(7):1807-1819. doi: 10.1523/JNEUROSCI.2316-16.2016. Epub 2017 Jan 16. PMID: 28073937 PMCID: PMC5320611 read article


Saltman AJ, Barakat M, Bryant DM, Brodovskaya A, Whited JL. DiI Perfusion as a Method for Vascular Visualization in Ambystoma mexicanum. J Vis Exp. 2017 Jun 16;(124). doi: 10.3791/55740. PMID: 28654050 PMCID: PMC5608450 [Available on 2019-06-16] read article


Bryant DM, Sousounis K, Farkas JE, Bryant S, Thao N, Guzikowski AR, Monaghan JR, Levin M, Whited JL. Repeated removal of developing limb buds permanently reduces appendage size in the highly-regenerative axolotl. Dev Biol. 2017 Apr 1;424(1):1-9. doi: 10.1016/j.ydbio.2017.02.013. Epub 2017 Feb 21. PMID: 28235582 PMCID: PMC5707178 read article


Yoon SO, Shin S, Karreth FA, Buel GR, Jedrychowski MP, Plas DR, Dedhar S, Gygi SP, Roux PP, Dephoure N, Blenis J. Focal Adhesion- and IGF1R-Dependent Survival and Migratory Pathways Mediate Tumor Resistance to mTORC1/2 Inhibition. Mol Cell. 2017 Aug 3;67(3):512-527.e4. doi: 10.1016/j.molcel.2017.06.033. Epub 2017 Jul 27. PMID: 28757207 PMCID: PMC5698809 read article


Bullman S, Pedamallu CS, Sicinska E, Clancy TE, Zhang X, Cai D, Neuberg D, Huang K, Guevara F, Nelson T, Chipashvili O, Hagan T, Walker M, Ramachandran A, Diosdado B, Serna G, Mulet N, Landolfi S, Ramon Y Cajal S, Fasani R, Aguirre AJ, Ng K, Élez E, Ogino S, Tabernero J, Fuchs CS, Hahn WC, Nuciforo P, Meyerson M. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science. 2017 Dec 15;358(6369):1443-1448. doi: 10.1126/science.aal5240. Epub 2017 Nov 23. PMID: 29170280 PMCID: PMC5823247 read article


Lessard S, Francioli L, Alfoldi J, Tardif JC, Ellinor PT, MacArthur DG, Lettre G, Orkin SH, Canver MC. Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci. Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):E11257-E11266. doi: 10.1073/pnas.1714640114. Epub 2017 Dec 11. PMID: 29229813 PMCID: PMC5748207 read article


Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, A Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE, Orkin SH. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet. 2017 Apr;49(4):625-634. doi: 10.1038/ng.3793. Epub 2017 Feb 20. PMID: 28218758 PMCID: PMC5374001 read article


Canver MC, Bauer DE, Orkin SH. Functional interrogation of non-coding DNA through CRISPR genome editing. Methods. 2017 May 15;121-122:118-129. doi: 10.1016/j.ymeth.2017.03.008. Epub 2017 Mar 10. PMID: 28288828 PMCID: PMC5483188 read article


Canver MC, Bauer DE, Dass A, Yien YY, Chung J, Masuda T, Maeda T, Paw BH, Orkin SH. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J Biol Chem. 2017 Feb 10;292(6):2556. doi: 10.1074/jbc.A114.564625. PMID: 28188222 PMCID: PMC5313121 read article


Nakayama RT, Pulice JL, Valencia AM, McBride MJ, McKenzie ZM, Gillespie MA, Ku WL, Teng M, Cui K, Williams RT, Cassel SH, Qing H, Widmer CJ, Demetri GD, Irizarry RA, Zhao K, Ranish JA, Kadoch C. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nat Genet. 2017 Nov;49(11):1613-1623. doi: 10.1038/ng.3958. Epub 2017 Sep 25. PMID: 28945250 PMCID: PMC5803080 read article


Webster CM, Pino EC, Carr CE, Wu L, Zhou B, Cedillo L, Kacergis MC, Curran SP, Soukas AA. Genome-wide RNAi Screen for Fat Regulatory Genes in C. elegans Identifies a Proteostasis-AMPK Axis Critical for Starvation Survival. Cell Rep. 2017 Jul 18;20(3):627-640. doi: 10.1016/j.celrep.2017.06.068. PMID: 28723566 PMCID: PMC5578715 read article


Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP. A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA. 2017 Mar;23(3):270-283. doi: 10.1261/rna.059105.116. Epub 2016 Dec 19. PMID: 27994090 PMCID: PMC5311483 read article


McGurk PD, Swartz ME, Chen JW, Galloway JL, Eberhart JK. In vivo zebrafish morphogenesis shows Cyp26b1 promotes tendon condensation and musculoskeletal patterning in the embryonic jaw. PLoS Genet. 2017 Dec 11;13(12):e1007112. doi: 10.1371/journal.pgen.1007112. eCollection 2017 Dec. PMID: 29227993 PMCID: PMC5739505 read article


Dreijerink KMA, Groner AC, Vos ESM, Font-Tello A, Gu L, Chi D, Reyes J, Cook J, Lim E, Lin CY, de Laat W, Rao PK, Long HW, Brown M. Enhancer-Mediated Oncogenic Function of the Menin Tumor Suppressor in Breast Cancer. Cell Rep. 2017 Mar 7;18(10):2359-2372. doi: 10.1016/j.celrep.2017.02.025. PMID: 28273452 PMCID: PMC5609449 read article


Lubner JM, Dodge-Kafka KL, Carlson CR, Church GM, Chou MF, Schwartz D. Cushing's syndrome mutant PKAL205R exhibits altered substrate specificity. FEBS Lett. 2017 Feb;591(3):459-467. doi: 10.1002/1873-3468.12562. Epub 2017 Feb 3. PMID: 28100013 PMCID: PMC5321106 read article


Chan Y, Tung M, Garruss AS, Zaranek SW, Chan YK, Lunshof JE, Zaranek AW, Ball MP, Chou MF, Lim ET, Church GM. An unbiased index to quantify participant's phenotypic contribution to an open-access cohort. Sci Rep. 2017 Apr 7;7:46148. doi: 10.1038/srep46148. PMID: 28387241 PMCID: PMC5384003 read article


Miller K, Chou VT, Vactor DV. Liprin-α and Assembly of the Synaptic Cytomatrix. doi.(2017) org/10.1016/B978-0-12-809324-5.02406-8


Ciarlo C, Kaufman CK, Kinikoglu B, Michael J, Yang S, D Amato C, Blokzijl-Franke S, den Hertog J, Schlaeger TM, Zhou Y, Liao E, Zon LI. A chemical screen in zebrafish embryonic cells establishes that Akt activation is required for neural crest development. Elife. 2017 Aug 23;6. pii: e29145. doi: 10.7554/eLife.29145. PMID: 28832322 PMCID: PMC5599238 read article


Bluteau D, Masliah-Planchon J, Clairmont C, Rousseau A, Ceccaldi R, d'Enghien CD, Bluteau O, Cuccuini W, Gachet S, de Latour RP, Leblanc T, Socié G, Baruchel A, Stoppa-Lyonnet D, D'Andrea AD, Soulier J. Biallelic inactivation of REV7 is associated with Fanconi anemia. J Clin Invest. 2017 Mar 1;127(3):1117. doi: 10.1172/JCI92946. Epub 2017 Mar 1. PMID: 28248207 PMCID: PMC5330734  read article


Zhou Y, Castonguay P, Sidhom EH, Clark AR, Dvela-Levitt M, Kim S, Sieber J, Wieder N, Jung JY, Andreeva S, Reichardt J, Dubois F, Hoffmann SC, Basgen JM, Montesinos MS, Weins A, Johnson AC, Lander ES, Garrett MR, Hopkins CR, Greka A. A small-molecule inhibitor of TRPC5 ion channels suppresses progressive kidney disease in animal models. Science. 2017 Dec 8;358(6368):1332-1336. doi: 10.1126/science.aal4178. PMID: 29217578 PMCID: PMC6014699  read article


Sunwoo H, Colognori D, Froberg JE, Jeon Y, Lee JT Repeat E anchors Xist RNA to the inactive X chromosomal compartment through CDKN1A-interacting protein (CIZ1). Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):10654-10659. doi: 10.1073/pnas.1711206114. Epub 2017 Sep 18. PMID: 28923964 PMCID: PMC5635913  read article


Savol AJ, Wang PI, Jeon Y, Colognori D, Yildirim E, Pinter SF, Payer B, Lee JT, Sadreyev RI. Genome-wide identification of autosomal genes with allelic imbalance of chromatin state. PLoS One. 2017 Aug 10;12(8):e0182568. doi: 10.1371/journal.pone.0182568. eCollection 2017. PMID: 28796844 PMCID: PMC5552117  read article


Lyons SM, Gudanis D, Coyne SM, Gdaniec Z, Ivanov P. Author Correction: Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs. Nat Commun. 2017 Dec 5;8(1):2020. doi: 10.1038/s41467-017-02140-9. PMID: 29209051 PMCID: PMC5717102  read article


Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo TH, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RM Jr, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL. A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. Cell Rep. 2017 Jan 17;18(3):762-776. doi: 10.1016/j.celrep.2016.12.063. PMID: 28099853 PMCID: PMC5419050  read article


Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)-Analysis Working Group; Statistical Methods groups-Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site-NDRI; Biospecimen Collection Source Site-RPCI; Biospecimen Core Resource-VARI; Brain Bank Repository-University of Miami Brain Endowment Bank; Leidos Biomedical-Project Management; ELSI Study; Genome Browser Data Integration & Visualization-EBI; Genome Browser Data Integration & Visualization-UCSC Genomics Institute, University of California Santa Cruz, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Landscape of X chromosome inactivation across human tissues. Nature. 2017 Oct 11;550(7675):244-248. doi: 10.1038/nature24265. PMID: 29022598 PMCID: PMC5685192
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Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoort S, Foley AR, Bolduc V, Waddell LB, Sandaradura SA, O"Grady GL, Estrella E, Reddy HM, Zhao F, Weisburd B, Karczewski KJ, O"Donnell-Luria AH, Birnbaum D, Sarkozy A, Hu Y, Gonorazky H, Claeys K, Joshi H, Bournazos A, Oates EC, Ghaoui R, Davis MR, Laing NG, Topf A; Genotype-Tissue Expression Consortium, Kang PB, Beggs AH, North KN, Straub V, Dowling JJ, Muntoni F, Clarke NF, Cooper ST, Bönnemann CG, MacArthur DG. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Sci Transl Med. 2017 Apr 19;9(386). pii: eaal5209. doi: 10.1126/scitranslmed.aal5209. PMID: 28424332 PMCID: PMC5548421
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Walton T, Szostak JW. A Kinetic Model of Nonenzymatic RNA Polymerization by Cytidine-5'-phosphoro-2-aminoimidazolide. Biochemistry. 2017 Oct 31;56(43):5739-5747. doi: 10.1021/acs.biochem.7b00792. Epub 2017 Oct 19. PMID: 29022704 PMCID: PMC6340129 read article


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Petrov K, Wierbowski BM, Salic A. Sending and Receiving Hedgehog Signals. Annu Rev Cell Dev Biol. 2017 Oct 6;33:145-168. doi: 10.1146/annurev-cellbio-100616-060847. Epub 2017 Jul 10. PMID: 28693388 read article


Tripathi P, Rodriguez-Muela N, Klim JR, de Boer AS, Agrawal S, Sandoe J, Lopes CS, Ogliari KS, Williams LA, Shear M, Rubin LL, Eggan K, Zhou Q. Reactive Astrocytes Promote ALS-like Degeneration and Intracellular Protein Aggregation in Human Motor Neurons by Disrupting Autophagy through TGF-β1. Stem Cell Reports. 2017 Aug 8;9(2):667-680. doi: 10.1016/j.stemcr.2017.06.008. Epub 2017 Jul 14. PMID: 28712846 PMCID: PMC5549875 read article


Adams BD, Parsons C, Walker L, Zhang WC, Slack FJ. Targeting noncoding RNAs in disease. J Clin Invest. 2017 Mar 1;127(3):761-771. doi: 10.1172/JCI84424. Epub 2017 Mar 1. PMID: 28248199 PMCID: PMC5330746 read article


Gomez JE, Kaufmann-Malaga BB, Wivagg CN, Kim PB, Silvis MR, Renedo N, Ioerger TR, Ahmad R, Livny J, Fishbein S, Sacchettini JC, Carr SA, Hung DT. Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment. Elife. 2017 Feb 21;6. pii: e20420. doi: 10.7554/eLife.20420. PMID: 28220755 PMCID: PMC5319836 read article


Wu X, Zhang Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat Rev Genet. 2017 Sep;18(9):517-534. doi: 10.1038/nrg.2017.33. Epub 2017 May 30. PMID: 28555658 read article


Chen R, Wu X, Jiang L, Zhang Y. Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity. Cell Rep. 2017 Mar 28;18(13):3227-3241. doi: 10.1016/j.celrep.2017.03.004. PMID: 28355573 PMCID: PMC5782816 read article


Xu C, Luo J, He L, Montell C, Perrimon N. Oxidative stress induces stem cell proliferation via TRPA1/RyR-mediated Ca2+ signaling in the Drosophila midgut. Elife. 2017 May 31;6. pii: e22441. doi: 10.7554/eLife.22441. PMID: 28561738 PMCID: PMC5451214 read article


Yang T, Li S, Xu H, Walsh DM, Selkoe DJ. Large Soluble Oligomers of Amyloid β-Protein from Alzheimer Brain Are Far Less Neuroactive Than the Smaller Oligomers to Which They Dissociate. J Neurosci. 2017 Jan 4;37(1):152-163. doi: 10.1523/JNEUROSCI.1698-16.2016. PMID: 28053038 PMCID: PMC5214627 read article


Harper J, Lloyd C, Dimasi N, Toader D, Marwood R, Lewis L, Bannister D, Jovanovic J, Fleming R, D'Hooge F, Mao S, Marrero AM, Korade M, Strout P, Xu L, Chen C, Wetzel L, Breen S, van Vlerken-Ysla L, Jalla S, Rebelatto M, Zhong H, Hurt EM, Hinrichs MJ, Huang K, Howard PW, Tice DA, Hollingsworth RE, Herbst R, Kamal A. Preclinical Evaluation of MEDI0641, a Pyrrolobenzodiazepine-Conjugated Antibody-Drug Conjugate Targeting 5T4. Mol Cancer Ther. 2017 Aug;16(8):1576-1587. doi: 10.1158/1535-7163.MCT-16-0825. Epub 2017 May 18. PMID: 28522587  read article


Joyce CE, Yanez AG, Mori A, Yoda A, Carroll JS, Novina CD. Differential Regulation of the Melanoma Proteome by eIF4A1 and eIF4E. Cancer Res. 2017 Feb 1;77(3):613-622. doi: 10.1158/0008-5472.CAN-16-1298. Epub 2016 Nov 22. PMID: 27879264 PMCID: PMC5362820  read article


Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G. Corrigendum: Engineering and optimising deaminase fusions for genome editing. Nat Commun. 2017 Oct 9;8:16169. doi: 10.1038/ncomms16169. PMID: 28991237 PMCID: PMC5635175 read article


Wang G, Yang L, Grishin D, Rios X, Ye LY, Hu Y, Li K, Zhang D, Church GM, Pu WT. Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies. Nat Protoc. 2017 Jan;12(1):88-103. doi: 10.1038/nprot.2016.152. Epub 2016 Dec 8. PMID: 27929521 PMCID: PMC5352979 read article


Güell M, Niu D, Kan Y, George H, Wang T, Lee IH, Wang G, Church G, Yang L. PERV inactivation is necessary to guarantee absence of pig-to-patient PERVs transmission in xenotransplantation. Xenotransplantation. 2017 Nov;24(6). doi: 10.1111/xen.12366. Epub 2017 Nov 23. PMID: 29171094 read article


Niu D, Wei HJ, Lin L, George H, Wang T, Lee IH, Zhao HY, Wang Y, Kan Y, Shrock E, Lesha E, Wang G, Luo Y, Qing Y, Jiao D, Zhao H, Zhou X, Wang S, Wei H, Güell M, Church GM, Yang L. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science. 2017 Sep 22;357(6357):1303-1307. doi: 10.1126/science.aan4187. Epub 2017 Aug 10. PMID: 28798043 PMCID: PMC5813284 read article


Erb MA, Scott TG, Li BE, Xie H, Paulk J, Seo HS, Souza A, Roberts JM, Dastjerdi S, Buckley DL, Sanjana NE, Shalem O, Nabet B, Zeid R, Offei-Addo NK, Dhe-Paganon S, Zhang F, Orkin SH, Winter GE, Bradner JE. Transcription control by the ENL YEATS domain in acute leukaemia. Nature. 2017 Mar 9;543(7644):270-274. doi: 10.1038/nature21688. Epub 2017 Mar 1. PMID: 28241139 PMCID: PMC5497220 read article


Winter GE, Mayer A, Buckley DL, Erb MA, Roderick JE, Vittori S, Reyes JM, di Iulio J, Souza A, Ott CJ, Roberts JM, Zeid R, Scott TG, Paulk J, Lachance K, Olson CM, Dastjerdi S, Bauer S, Lin CY, Gray NS, Kelliher MA, Churchman LS, Bradner JE. BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment. Mol Cell. 2017 Jul 6;67(1):5-18.e19. doi: 10.1016/j.molcel.2017.06.004. Epub 2017 Jun 29. PMID: 28673542 PMCID: PMC5663500 read article


Cheng J, Park DE, Berrios C, White EA, Arora R, Yoon R, Branigan T, Xiao T, Westerling T, Federation A, Zeid R, Strober B, Swanson SK, Florens L, Bradner JE, Brown M, Howley PM, Padi M, Washburn MP, DeCaprio JA. Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis. PLoS Pathog. 2017 Oct 13;13(10):e1006668. doi: 10.1371/journal.ppat.1006668. eCollection 2017 Oct. PMID: 29028833 PMCID: PMC5640240 read article


Li H, Mar BG, Zhang H, Puram RV, Vazquez F, Weir BA, Hahn WC, Ebert B, Pellman D. The EMT regulator ZEB2 is a novel dependency of human and murine acute myeloid leukemia. Blood. 2017 Jan 26;129(4):497-508. doi: 10.1182/blood-2016-05-714493. Epub 2016 Oct 18. PMID: 27756750 PMCID: PMC5270388 read article


2016


Amamoto R, Huerta VG, Takahashi E, Dai G, Grant AK, Fu Z, Arlotta P. Adult axolotls can regenerate original neuronal diversity in response to brain injury. Elife. 2016 May 9;5. pii: e13998. doi: 10.7554/eLife.13998. PMID: 27156560 PMCID: PMC4861602 read article


Ariyachet C, Tovaglieri A, Xiang G, Lu J, Shah MS, Richmond CA, Verbeke C, Melton DA, Stanger BZ, Mooney D, Shivdasani RA, Mahony S, Xia Q, Breault DT, Zhou Q. Reprogrammed Stomach Tissue as a Renewable Source of Functional β Cells for Blood Glucose Regulation. Cell Stem Cell. 2016 Mar 3;18(3):410-21. doi: 10.1016/j.stem.2016.01.003. Epub 2016 Feb 18. PMID: 26908146 PMCID: PMC4779391 read article


Niederkofler V, Asher TE, Okaty BW, Rood BD, Narayan A, Hwa LS, Beck SG, Miczek KA, Dymecki SM. Identification of Serotonergic Neuronal Modules that Affect Aggressive Behavior. Cell Rep. 2016 Nov 15;17(8):1934-1949. doi: 10.1016/j.celrep.2016.10.063. PMID: 27851959 PMCID: PMC5156533 read article


Rose CM, Isasa M, Ordureau A, Prado MA, Beausoleil SA, Jedrychowski MP, Finley DJ, Harper JW, Gygi SP. Highly Multiplexed Quantitative Mass Spectrometry Analysis of Ubiquitylomes. Cell Syst. 2016 Oct 26;3(4):395-403.e4. doi: 10.1016/j.cels.2016.08.009. Epub 2016 Sep 22. PMID: 27667366 PMCID: PMC5241079  read article


Beier KT, Mundell NA, Pan YA, Cepko CL. Anterograde or Retrograde Transsynaptic Circuit Tracing in Vertebrates with Vesicular Stomatitis Virus Vectors. Curr Protoc Neurosci. 2016 Jan 4;74:1.26.1-27. doi: 10.1002/0471142301.ns0126s74. PMID: 26729030 PMCID: PMC4776322 read article


Wang S, Su JH, Beliveau BJ, Bintu B, Moffitt JR, Wu CT, Zhuang X. Spatial organization of chromatin domains and compartments in single chromosomes. Science. 2016 Aug 5;353(6299):598-602. doi: 10.1126/science.aaf8084. Epub 2016 Jul 21. PMID: 27445307 PMCID: PMC4991974 read article


Sekar A, Bialas AR, de Rivera H, Davis A, Hammond TR, Kamitaki N, Tooley K, Presumey J, Baum M, Van Doren V, Genovese G, Rose SA, Handsaker RE; Schizophrenia Working Group of the Psychiatric Genomics Consortium, Daly MJ, Carroll MC, Stevens B, McCarroll SA. Schizophrenia risk from complex variation of complement component 4. Nature. 2016 Feb 11;530(7589):177-83. doi: 10.1038/nature16549. Epub 2016 Jan 27. PMID: 26814963  read article


DeLaughter DM, Bick AG, Wakimoto H, McKean D, Gorham JM, Kathiriya IS, Hinson JT, Homsy J, Gray J, Pu W, Bruneau BG, Seidman JG, Seidman CE. Single-Cell Resolution of Temporal Gene Expression during Heart Development. Dev Cell. 2016 Nov 21;39(4):480-490. doi: 10.1016/j.devcel.2016.10.001. Epub 2016 Nov 10. PMID: 27840107 PMCID: PMC5198784 read article


Natarajan P, Gold NB, Bick AG, McLaughlin H, Kraft P, Rehm HL, Peloso GM, Wilson JG, Correa A, Seidman JG, Seidman CE, Kathiresan S, Green RC. Aggregate penetrance of genomic variants for actionable disorders in European and African Americans. Sci Transl Med. 2016 Nov 9;8(364):364ra151. PMID: 27831900 PMCID: PMC5823271 read article


Prywes N, Blain JC, Del Frate F, Szostak JW. Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides. Elife. 2016 Jun 28;5. pii: e17756. doi: 10.7554/eLife.17756. PMID: 27351102 PMCID: PMC4959843 read article


Baral P, Mills K, Pinho-Ribeiro FA, Chiu IM. Pain and Itch: Beneficial or Harmful to Antimicrobial Defense? Cell Host Microbe. 2016 Jun 8;19(6):755-9. doi: 10.1016/j.chom.2016.05.010. PMID: 27281567 read article


Tan D, Blok NB, Rapoport TA, Walz T. Structures of the double-ring AAA ATPase Pex1-Pex6 involved in peroxisome biogenesis. FEBS J. 2016 Mar;283(6):986-92. doi: 10.1111/febs.13569. Epub 2015 Nov 12. PMID: 26476099 PMCID: PMC4803591 read article


Kim JW, Botvinnik OB, Abudayyeh O, Birger C, Rosenbluh J, Shrestha Y, Abazeed ME, Hammerman PS, DiCara D, Konieczkowski DJ, Johannessen CM, Liberzon A, Alizad-Rahvar AR, Alexe G, Aguirre A, Ghandi M, Greulich H, Vazquez F, Weir BA, Van Allen EM, Tsherniak A, Shao DD, Zack TI, Noble M, Getz G, Beroukhim R, Garraway LA, Ardakani M, Romualdi C, Sales G, Barbie DA, Boehm JS, Hahn WC, Mesirov JP, Tamayo P. Characterizing genomic alterations in cancer by complementary functional associations. Nat Biotechnol. 2016 May;34(5):539-46. doi: 10.1038/nbt.3527. Epub 2016 Apr 18. PMID: 27088724 PMCID: PMC4868596 read article


Rosenbluh J, Mercer J, Shrestha Y, Oliver R, Tamayo P, Doench JG, Tirosh I, Piccioni F, Hartenian E, Horn H, Fagbami L, Root DE, Jaffe J, Lage K, Boehm JS, Hahn WC. Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers. Cell Syst. 2016 Sep 28;3(3):302-316.e4. doi: 10.1016/j.cels.2016.09.001. PMID: 27684187 PMCID: PMC5455996 read article


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Hong AL, Tseng YY, Cowley GS, Jonas O, Cheah JH, Kynnap BD, Doshi MB, Oh C, Meyer SC, Church AJ, Gill S, Bielski CM, Keskula P, Imamovic A, Howell S, Kryukov GV, Clemons PA, Tsherniak A, Vazquez F, Crompton BD, Shamji AF, Rodriguez-Galindo C, Janeway KA, Roberts CW, Stegmaier K, van Hummelen P, Cima MJ, Langer RS, Garraway LA, Schreiber SL, Root DE, Hahn WC, Boehm JS. Integrated genetic and pharmacologic interrogation of rare cancers. Nat Commun. 2016 Jun 22;7:11987. doi: 10.1038/ncomms11987. PMID: 27329820 PMCID: PMC4917959 read article


Kim E, Ilic N, Shrestha Y, Zou L, Kamburov A, Zhu C, Yang X, Lubonja R, Tran N, Nguyen C, Lawrence MS, Piccioni F, Bagul M, Doench JG, Chouinard CR, Wu X, Hogstrom L, Natoli T, Tamayo P, Horn H, Corsello SM, Lage K, Root DE, Subramanian A, Golub TR, Getz G, Boehm JS, Hahn WC. Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles. Cancer Discov. 2016 Jul;6(7):714-26. doi: 10.1158/2159-8290.CD-16-0160. Epub 2016 May 4. PMID: 27147599 PMCID: PMC4930723 read article


Howard TP, Vazquez F, Tsherniak A, Hong AL, Rinne M, Aguirre AJ, Boehm JS, Hahn WC. Functional Genomic Characterization of Cancer Genomes. Cold Spring Harb Symp Quant Biol. 2016;81:237-246. doi: 10.1101/sqb.2016.81.031070. Epub 2016 Nov 4. PMID: 27815544 read article


Boettger LM, Salem RM, Handsaker RE, Peloso GM, Kathiresan S, Hirschhorn JN, McCarroll SA. Recurring exon deletions in the HP (haptoglobin) gene contribute to lower blood cholesterol levels. Nat Genet. 2016 Apr;48(4):359-66. doi: 10.1038/ng.3510. Epub 2016 Feb 22. PMID: 26901066 PMCID: PMC4811681 read article


Markovski M, Bohrhunter JL, Lupoli TJ, Uehara T, Walker S, Kahne DE, Bernhardt TG. Cofactor bypass variants reveal a conformational control mechanism governing cell wall polymerase activity. Proc Natl Acad Sci U S A. 2016 Apr 26;113(17):4788-93. doi: 10.1073/pnas.1524538113. Epub 2016 Apr 11. PubMed PMID: 27071112
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Barrett KT, Dosumu-Johnson RT, Daubenspeck JA, Brust RD, Kreouzis V, Kim JC, Li A, Dymecki SM, Nattie EE. Partial Raphe Dysfunction in Neurotransmission Is Sufficient to Increase Mortality after Anoxic Exposures in Mice at a Critical Period in Postnatal Development. J Neurosci. 2016 Apr 6;36(14):3943-53. doi: 10.1523/JNEUROSCI.1796-15.2016. PMID: 27053202 PMCID: PMC4821907 read article


Farkas JE, Freitas PD, Bryant DM, Whited JL, Monaghan JR. Neuregulin-1 signaling is essential for nerve-dependent axolotl limb regeneration. Development. 2016 Aug 1;143(15):2724-31. doi: 10.1242/dev.133363. Epub 2016 Jun 17. PMID: 27317805 read article


Buel GR, Blenis J. CELL SIGNALING. Seeing mTORC1 specificity. Science. 2016 Jan 1;351(6268):25-6. doi: 10.1126/science.aad9696. PMID: 26721988  read article


Bui DA, Lee W, White AE, Harper JW, Schackmann RC, Overholtzer M, Selfors LM, Brugge JS. Cytokinesis involves a nontranscriptional function of the Hippo pathway effector YAP. Sci Signal. 2016 Mar 1;9(417):ra23. doi: 10.1126/scisignal.aaa9227. PMID: 26933062 PMCID: PMC5455055 read article


Burrill DR, Vernet A, Collins JJ, Silver PA, Way JC. Targeted erythropoietin selectively stimulates red blood cell expansion in vivo. Proc Natl Acad Sci U S A. 2016 May 10;113(19):5245-50. doi: 10.1073/pnas.1525388113. Epub 2016 Apr 25. PMID: 27114509 PMCID: PMC4868492 read article


Brendel C, Guda S, Renella R, Bauer DE, Canver MC, Kim YJ, Heeney MM, Klatt D, Fogel J, Milsom MD, Orkin SH, Gregory RI, Williams DA. Lineage-specific BCL11A knockdown circumvents toxicities and reverses sickle phenotype. J Clin Invest. 2016 Oct 3;126(10):3868-3878. doi: 10.1172/JCI87885. Epub 2016 Sep 6. PMID: 27599293 PMCID: PMC5096824 read article


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Canver MC, Orkin SH. Customizing the genome as therapy for the β-hemoglobinopathies. Blood. 2016 May 26;127(21):2536-45. doi: 10.1182/blood-2016-01-678128. Epub 2016 Apr 6. PMID: 27053533 PMCID: PMC4882803 read article


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Chan YK, Gack MU. Viral evasion of intracellular DNA and RNA sensing. Nat Rev Microbiol. 2016 Jun;14(6):360-73. doi: 10.1038/nrmicro.2016.45. Epub 2016 May 13. PMID: 27174148 PMCID: PMC5072394 read article


Chan YK, Gack MU. A phosphomimetic-based mechanism of dengue virus to antagonize innate immunity. Nat Immunol. 2016 May;17(5):523-30. doi: 10.1038/ni.3393. Epub 2016 Mar 21. PMID: 26998762 PMCID: PMC4837045 read article


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Leriche G, Chen AC, Kim S, Selkoe DJ, Yang J. Fluorescent Analogue of Batimastat Enables Imaging of α-Secretase in Living Cells. ACS Chem Neurosci. 2016 Jan 20;7(1):40-5. doi: 10.1021/acschemneuro.5b00283. Epub 2015 Nov 18. PMID: 26559179 PMCID: PMC4720558 read article


Chew CL, Chen M, Pandolfi PP. Endosome and INPP4B. Oncotarget. 2016 Jan 5;7(1):5-6. doi: 10.18632/oncotarget.6663. PMID: 26700619 PMCID: PMC4807978  read article


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Grant SS, Wellington S, Kawate T, Desjardins CA, Silvis MR, Wivagg C, Thompson M, Gordon K, Kazyanskaya E, Nietupski R, Haseley N, Iwase N, Earl AM, Fitzgerald M, Hung DT. Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors. Cell Chem Biol. 2016 Jun 23;23(6):666-77. doi: 10.1016/j.chembiol.2016.05.011. Epub 2016 Jun 16. PMID: 27321573 PMCID: PMC4920728 read article


Wivagg CN, Wellington S, Gomez JE, Hung DT. Loss of a Class A Penicillin-Binding Protein Alters β-Lactam Susceptibilities in Mycobacterium tuberculosis. ACS Infect Dis. 2016 Feb 12;2(2):104-10. doi: 10.1021/acsinfecdis.5b00119. Epub 2015 Dec 21. PMID: 27624961 read article


Greig LC, Woodworth MB, Greppi C, Macklis JD. Ctip1 Controls Acquisition of Sensory Area Identity and Establishment of Sensory Input Fields in the Developing Neocortex. Neuron. 2016 Apr 20;90(2):261-77. doi: 10.1016/j.neuron.2016.03.008. PMID: 27100196 PMCID: PMC4873772 read article


Smith EC, Luc S, Croney DM, Woodworth MB, Greig LC, Fujiwara Y, Nguyen M, Sher F, Macklis JD, Bauer DE, Orkin SH. Strict in vivo specificity of the Bcl11a erythroid enhancer. Blood. 2016 Nov 10;128(19):2338-2342. doi: 10.1182/blood-2016-08-736249. Epub 2016 Oct 5. PMID: 27707736 PMCID: PMC5106112 read article


Woodworth MB, Greig LC, Liu KX, Ippolito GC, Tucker HO, Macklis JD. Ctip1 Regulates the Balance between Specification of Distinct Projection Neuron Subtypes in Deep Cortical Layers. Cell Rep. 2016 May 3;15(5):999-1012. doi: 10.1016/j.celrep.2016.03.064. Epub 2016 Apr 21. PMID: 27117402 PMCID: PMC4873759 read article


Lee RE, Qasaimeh MA, Xia X, Juncker D, Gaudet S. NF-κB signalling and cell fate decisions in response to a short pulse of tumour necrosis factor. Sci Rep. 2016 Dec 22;6:39519. doi: 10.1038/srep39519. PMID: 28004761 PMCID: PMC5177917 read article


Xiang M, Kim H, Ho VT, Walker SR, Bar-Natan M, Anahtar M, Liu S, Toniolo PA, Kroll Y, Jones N, Giaccone ZT, Heppler LN, Ye DQ, Marineau JJ, Shaw D, Bradner JE, Blonquist T, Neuberg D, Hetz C, Stone RM, Soiffer RJ, Frank DA. Gene expression-based discovery of atovaquone as a STAT3 inhibitor and anticancer agent. Blood. 2016 Oct 6;128(14):1845-1853. doi: 10.1182/blood-2015-07-660506. Epub 2016 Aug 16. PMID: 27531676 PMCID: PMC5054697 read article


Xu H, Gelyana E, Rajsombath M, Yang T, Li S, Selkoe D. Environmental Enrichment Potently Prevents Microglia-Mediated Neuroinflammation by Human Amyloid β-Protein Oligomers. J Neurosci. 2016 Aug 31;36(35):9041-56. doi: 10.1523/JNEUROSCI.1023-16.2016. PMID: 27581448 PMCID: PMC5005718 read article


Lei M, Xu H, Li Z, Wang Z, O'Malley TT, Zhang D, Walsh DM, Xu P, Selkoe DJ, Li S. Soluble Aβ oligomers impair hippocampal LTP by disrupting glutamatergic/GABAergic balance. Neurobiol Dis. 2016 Jan;85:111-121. doi: 10.1016/j.nbd.2015.10.019. Epub 2015 Oct 22. PMID: 26525100 PMCID: PMC4778388 read article


Jiang Q, Lu W, Yang K, Hadadi C, Fu X, Chen Y, Yun X, Zhang J, Li M, Xu L, Tang H, Yuan JX, Wang J, Sun D. Sodium tanshinone IIA sulfonate inhibits hypoxia-induced enhancement of SOCE in pulmonary arterial smooth muscle cells via the PKG-PPAR-γ signaling axis. Am J Physiol Cell Physiol. 2016 Jul 1;311(1):C136-49. doi: 10.1152/ajpcell.00252.2015. Epub 2016 May 18. PMID: 27194472 PMCID: PMC4967135  read article


Yang L, Kirby JE, Sunwoo H, Lee JT. Female mice lacking Xist RNA show partial dosage compensation and survive to term. Genes Dev. 2016 Aug 1;30(15):1747-60. doi: 10.1101/gad.281162.116. PMID: 27542829 PMCID: PMC5002979  read article


Yang L, Briggs AW, Chew WL, Mali P, Guell M, Aach J, Goodman DB, Cox D, Kan Y, Lesha E, Soundararajan V, Zhang F, Church G. Engineering and optimising deaminase fusions for genome editing. Nat Commun. 2016 Nov 2;7:13330. doi: 10.1038/ncomms13330. PMID: 27804970 PMCID: PMC5097136 read article


Hinson JT, Chopra A, Nafissi N, Polacheck WJ, Benson CC, Swist S, Gorham J, Yang L, Schafer S, Sheng CC, Haghighi A, Homsy J, Hubner N, Church G, Cook SA, Linke WA, Chen CS, Seidman JG, Seidman CE. HEART DISEASE. Titin mutations in iPS cells define sarcomere insufficiency as a cause of dilated cardiomyopathy. Science. 2015 Aug 28;349(6251):982-6. doi: 10.1126/science.aaa5458. PMID: 26315439 PMCID: PMC4618316 read article


Mathew RS, Tatarakis A, Rudenko A, Johnson-Venkatesh EM, Yang YJ, Murphy EA, Todd TP, Schepers ST, Siuti N, Martorell AJ, Falls WA, Hammack SE, Walsh CA, Tsai LH, Umemori H, Bouton ME, Moazed D. A microRNA negative feedback loop downregulates vesicle transport and inhibits fear memory. Elife. 2016 Dec 21;5. pii: e22467. doi: 10.7554/eLife.22467. PMID: 28001126 PMCID: PMC5293492 read article


Toniolo PA, Liu S, Yeh JE, Ye DQ, Barbuto JA, Frank DA. Deregulation of SOCS5 suppresses dendritic cell function in chronic lymphocytic leukemia. Oncotarget. 2016 Jul 19;7(29):46301-46314. doi: 10.18632/oncotarget.10093. PMID: 27317770 PMCID: PMC5216799 read article


Yu R, Moazed D. CSR-1 Slices a Balance. Cell. 2016 Apr 7;165(2):267-9. doi: 10.1016/j.cell.2016.03.019. PMID: 27058659 read article


Tsui HC, Zheng JJ, Magallon AN, Ryan JD, Yunck R, Rued BE, Bernhardt TG, Winkler ME. Suppression of a deletion mutation in the gene encoding essential PBP2b reveals a new lytic transglycosylase involved in peripheral peptidoglycan synthesis in Streptococcus pneumoniae D39. Mol Microbiol. 2016 Jun;100(6):1039-65. doi: 10.1111/mmi.13366. Epub 2016 Apr 15. PMID: 26933838 PMCID: PMC5063045 read article


Lin CY, Erkek S, Tong Y, Yin L, Federation AJ, Zapatka M, Haldipur P, Kawauchi D, Risch T, Warnatz HJ, Worst BC, Ju B, Orr BA, Zeid R, Polaski DR, Segura-Wang M, Waszak SM, Jones DT, Kool M, Hovestadt V, Buchhalter I, Sieber L, Johann P, Chavez L, Gröschel S, Ryzhova M, Korshunov A, Chen W, Chizhikov VV, Millen KJ, Amstislavskiy V, Lehrach H, Yaspo ML, Eils R, Lichter P, Korbel JO, Pfister SM, Bradner JE, Northcott PA. Active medulloblastoma enhancers reveal subgroup-specific cellular origins. Nature. 2016 Feb 4;530(7588):57-62. doi: 10.1038/nature16546. Epub 2016 Jan 27. PMID: 26814967 PMCID: PMC5168934 read article


Bandopadhayay P, Ramkissoon LA, Jain P, Bergthold G, Wala J, Zeid R, Schumacher SE, Urbanski L, O'Rourke R, Gibson WJ, Pelton K, Ramkissoon SH, Han HJ, Zhu Y, Choudhari N, Silva A, Boucher K, Henn RE, Kang YJ, Knoff D, Paolella BR, Gladden-Young A, Varlet P, Pages M, Horowitz PM, Federation A, Malkin H, Tracy AA, Seepo S, Ducar M, Van Hummelen P, Santi M, Buccoliero AM, Scagnet M, Bowers DC, Giannini C, Puget S, Hawkins C, Tabori U, Klekner A, Bognar L, Burger PC, Eberhart C, Rodriguez FJ, Hill DA, Mueller S, Haas-Kogan DA, Phillips JJ, Santagata S, Stiles CD, Bradner JE, Jabado N, Goren A, Grill J, Ligon AH, Goumnerova L, Waanders AJ, Storm PB, Kieran MW, Ligon KL, Beroukhim R, Resnick AC. MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism. Nat Genet. 2016 Mar;48(3):273-82. doi: 10.1038/ng.3500. Epub 2016 Feb 1. PMID: 26829751 PMCID: PMC4767685  read article


Liu C, Colón BC, Ziesack M, Silver PA, Nocera DG. Water splitting-biosynthetic system with CO₂ reduction efficiencies exceeding photosynthesis. Science. 2016 Jun 3;352(6290):1210-3. doi: 10.1126/science.aaf5039. PMID: 27257255  read article


2015


Diaz MF, Li N, Lee HJ, Adamo L, Evans SM, Willey HE, Arora N, Torisawa YS, Vickers DA, Morris SA, Naveiras O, Murthy SK, Ingber DE, Daley GQ, García-Cardeña G, Wenzel PL. Biomechanical forces promote blood development through prostaglandin E2 and the cAMP-PKA signaling axis. J Exp Med. 2015 May 4;212(5):665-80. doi: 10.1084/jem.20142235. Epub 2015 Apr 13. PMID: 25870199 PMCID: PMC4419354 read article


Izhar L, Adamson B, Ciccia A, Lewis J, Pontano-Vaites L, Leng Y, Liang AC, Westbrook TF, Harper JW, Elledge SJ. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors. Cell Rep. 2015 Jun 9;11(9):1486-500. doi: 10.1016/j.celrep.2015.04.053. Epub 2015 May 21. PMID: 26004182 PMCID: PMC4464939 read article


Niederkofler V, Asher TE, Dymecki SM. Functional Interplay between Dopaminergic and Serotonergic Neuronal Systems during Development and Adulthood. ACS Chem Neurosci. 2015 Jul 15;6(7):1055-1070. doi: 10.1021/acschemneuro.5b00021. Epub 2015 Mar 18. PMID: 25747116 PMCID: PMC4791184 read article


Aspiras AC, Rohner N, Martineau B, Borowsky RL, Tabin CJ. Melanocortin 4 receptor mutations contribute to the adaptation of cavefish to nutrient-poor conditions. Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):9668-73. doi: 10.1073/pnas.1510802112. PMID: 26170297 PMCID: PMC4534248 read article


Chiasson-MacKenzie C, Morris ZS, Baca Q, Morris B, Coker JK, Mirchev R, Jensen AE, Carey T, Stott SL, Golan DE, McClatchey AI. NF2/Merlin mediates contact-dependent inhibition of EGFR mobility and internalization via cortical actomyosin. J Cell Biol. 2015 Oct 26;211(2):391-405. doi: 10.1083/jcb.201503081. Epub 2015 Oct 19. PMID: 26483553 PMCID: PMC4621825 read article


Kwon M, Bagonis M, Danuser G, Pellman D. Direct Microtubule-Binding by Myosin-10 Orients Centrosomes toward Retraction Fibers and Subcortical Actin Clouds. Dev Cell. 2015 Aug 10;34(3):323-37. doi: 10.1016/j.devcel.2015.06.013. PMID: 26235048  read article


Barclay LA, Wales TE, Garner TP, Wachter F, Lee S, Guerra RM, Stewart ML, Braun CR, Bird GH, Gavathiotis E, Engen JR, Walensky LD. Inhibition of Pro-apoptotic BAX by a noncanonical interaction mechanism. Mol Cell. 2015 Mar 5;57(5):873-886. doi: 10.1016/j.molcel.2015.01.014. Epub 2015 Feb 12. PMID: 25684204 PMCID: PMC4384643 read article


Chen Y, Bauer BW, Rapoport TA, Gumbart JC. Conformational Changes of the Clamp of the Protein Translocation ATPase SecA. J Mol Biol. 2015 Jul 17;427(14):2348-59. doi: 10.1016/j.jmb.2015.05.003. Epub 2015 May 14. PMID: 25982945 PMCID: PMC4472001  read article


Paulo JA, McAllister FE, Everley RA, Beausoleil SA, Banks AS, Gygi SP. Effects
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Mundell NA, Beier KT, Pan YA, Lapan SW, Göz Aytürk D, Berezovskii VK, Wark AR, Drokhlyansky E, Bielecki J, Born RT, Schier AF, Cepko CL. Vesicular stomatitis virus enables gene transfer and transsynaptic tracing in a wide range of organisms. J Comp Neurol. 2015 Aug 1;523(11):1639-63. doi: 10.1002/cne.23761. Epub 2015 Apr 2. PMID: 25688551 PMCID: PMC4458151 read article


Nassi JJ, Cepko CL, Born RT, Beier KT. Neuroanatomy goes viral! Front Neuroanat. 2015 Jul 1;9:80. doi: 10.3389/fnana.2015.00080. eCollection 2015. PMID: 26190977 PMCID: PMC4486834  read article


Schmidt TL, Beliveau BJ, Uca YO, Theilmann M, Da Cruz F, Wu CT, Shih WM. Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries. Nat Commun. 2015 Nov 16;6:8634. doi: 10.1038/ncomms9634. PMID: 26567534 PMCID: PMC4660042  read article


Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu CT, Lee JT. Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome. Genetics. 2015 Jun;200(2):537-49. doi: 10.1534/genetics.115.176263. Epub 2015 Apr 9. PMID: 25858912 PMCID: PMC4492378 read article


Roberts AM, Ware JS, Herman DS, Schafer S, Baksi J, Bick AG, Buchan RJ, Walsh R, John S, Wilkinson S, Mazzarotto F, Felkin LE, Gong S, MacArthur JA, Cunningham F, Flannick J, Gabriel SB, Altshuler DM, Macdonald PS, Heinig M, Keogh AM, Hayward CS, Banner NR, Pennell DJ, O'Regan DP, San TR, de Marvao A, Dawes TJ, Gulati A, Birks EJ, Yacoub MH, Radke M, Gotthardt M, Wilson JG, O'Donnell CJ, Prasad SK, Barton PJ, Fatkin D, Hubner N, Seidman JG, Seidman CE, Cook SA. Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease. Sci Transl Med. 2015 Jan 14;7(270):270ra6. doi: 10.1126/scitranslmed.3010134. PMID: 25589632 PMCID: PMC4560092 read article


Black JC, Atabakhsh E, Kim J, Biette KM, Van Rechem C, Ladd B, Burrowes PD, Donado C, Mattoo H, Kleinstiver BP, Song B, Andriani G, Joung JK, Iliopoulos O, Montagna C, Pillai S, Getz G, Whetstine JR. Hypoxia drives transient site-specific copy gain and drug-resistant gene expression. Genes Dev. 2015 May 15;29(10):1018-31. doi: 10.1101/gad.259796.115.


Vincent BJ, Scholes C, Staller MV, Wunderlich Z, Estrada J, Park J, Bragdon MD, Lopez Rivera F, Biette KM, DePace AH. Yearly planning meetings: individualized development plans aren't just more paperwork. Mol Cell. 2015 Jun 4;58(5):718-21. doi: 10.1016/j.molcel.2015.04.025.


Björkbom A, Lelyveld VS, Zhang S, Zhang W, Tam CP, Blain JC, Szostak JW. Bidirectional Direct Sequencing of Noncanonical RNA by Two-Dimensional Analysis of Mass Chromatograms. J Am Chem Soc. 2015 Nov 18;137(45):14430-8. doi: 10.1021/jacs.5b09438. Epub 2015 Nov 9. PMID: 26495937 read article


Izgu EC, Fahrenbach AC, Zhang N, Li L, Zhang W, Larsen AT, Blain JC, Szostak JW. Uncovering the thermodynamics of monomer binding for RNA replication. J Am Chem Soc. 2015 May 20;137(19):6373-82. doi: 10.1021/jacs.5b02707. Epub 2015 May 7. PMID: 25901790 PMCID: PMC4984997 read article


Blok NB, Tan D, Wang RY, Penczek PA, Baker D, DiMaio F, Rapoport TA, Walz T. Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy. Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):E4017-25. doi: 10.1073/pnas.1500257112. Epub 2015 Jul 13. PMID: 26170309 PMCID: PMC4522808 read article


Moody SE, Schinzel AC, Singh S, Izzo F, Strickland MR, Luo L, Thomas SR, Boehm JS, Kim SY, Wang ZC, Hahn WC. PRKACA mediates resistance to HER2-targeted therapy in breast cancer cells and restores anti-apoptotic signaling. Oncogene. 2015 Apr 16;34(16):2061-71. doi: 10.1038/onc.2014.153. Epub 2014 Jun 9. PMID: 24909179 PMCID: PMC4261061 read article


Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, Boettger LM, McCarroll SA. Large multiallelic copy number variations in humans. Nat Genet. 2015 Mar;47(3):296-303. doi: 10.1038/ng.3200. Epub 2015 Jan 26. PMID: 25621458 PMCID: PMC4405206 read article


Briggs JA, Wolvetang EJ, Mattick JS, Rinn JL, Barry G. Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution. Neuron. 2015 Dec 2;88(5):861-877. doi: 10.1016/j.neuron.2015.09.045. PMID: 26637795 read article


Brubaker SW, Bonham KS, Zanoni I, Kagan JC. Innate immune pattern recognition: a cell biological perspective. Annu Rev Immunol. 2015;33:257-90. doi: 10.1146/annurev-immunol-032414-112240. Epub 2015 Jan 2. PMID: 25581309 PMCID: PMC5146691 read article


Okaty BW, Freret ME, Rood BD, Brust RD, Hennessy ML, deBairos D, Kim JC, Cook MN, Dymecki SM. Multi-Scale Molecular Deconstruction of the Serotonin Neuron System. Neuron. 2015 Nov 18;88(4):774-91. doi: 10.1016/j.neuron.2015.10.007. Epub 2015 Nov 5. PMID: 26549332 PMCID: PMC4809055 read article


Bryant DM, O'Meara CC, Ho NN, Gannon J, Cai L, Lee RT. Response to "Comment to the article 'A systematic analysis of neonatal mouse heart regeneration after apical resection'". J Mol Cell Cardiol. 2015 May;82:184-5. doi: 10.1016/j.yjmcc.2015.03.003. Epub 2015 Mar 11. PMID: 25771145  read article


Shin S, Buel GR, Wolgamott L, Plas DR, Asara JM, Blenis J, Yoon SO. ERK2 Mediates Metabolic Stress Response to Regulate Cell Fate. Mol Cell. 2015 Aug 6;59(3):382-98. doi: 10.1016/j.molcel.2015.06.020. Epub 2015 Jul 16. PMID: 26190261 PMCID: PMC4530034 read article


Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CA. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science. 2015 Oct 2;350(6256):94-98. doi: 10.1126/science.aab1785. PMID: 26430121 PMCID: PMC4664477 read article


Evrony GD, Lee E, Mehta BK, Benjamini Y, Johnson RM, Cai X, Yang L, Haseley P, Lehmann HS, Park PJ, Walsh CA. Cell lineage analysis in human brain using endogenous retroelements. Neuron. 2015 Jan 7;85(1):49-59. doi: 10.1016/j.neuron.2014.12.028. PMID: 25569347 PMCID: PMC4299461 read article


Cai X, Evrony GD, Lehmann HS, Elhosary PC, Mehta BK, Poduri A, Walsh CA. Erratum: Single-cell, genome-wide sequencing identifies clonal somatic copy-number variation in the human brain. Cell Rep. 2015 Feb 3;10(4):645. doi: 10.1016/j.celrep.2015.01.028. Epub 2015 Feb 3. PMID: 25832109 read article


Baffour-Awuah NY, Fleet S, Montgomery RK, Baker SS, Butler JL, Campbell C, Tischfield S, Mitchell PD, Allende-Richter S, Moon JE, Fishman L, Bousvaros A, Fox V, Kuokkanen M, Grand RJ, Hirschhorn JN. Functional significance of single nucleotide polymorphisms in the lactase gene in diverse US patients and evidence for a novel lactase persistence allele at -13909 in those of European ancestry. J Pediatr Gastroenterol Nutr. 2015 Feb;60(2):182-91. doi: 10.1097/MPG.0000000000000595. PMID: 25625576 PMCID: PMC4308731 read article


Bauer DE, Canver MC, Orkin SH. Generation of genomic deletions in mammalian cell lines via CRISPR/Cas9. J Vis Exp. 2015 Jan 3;(95):e52118. doi: 10.3791/52118. PMID: 25549070 PMCID: PMC4279820 read article


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Canver MC, Bauer DE, Orkin SH. Embryonic stem cells as sources of donor-independent platelets. J Clin Invest. 2015 Jun;125(6):2261-3. doi: 10.1172/JCI82348. Epub 2015 May 11. PMID: 25961451 PMCID: PMC4497771 read article


Renneville A, Van Galen P, Canver MC, McConkey M, Krill-Burger JM, Dorfman DM, Holson EB, Bernstein BE, Orkin SH, Bauer DE, Ebert BL. EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression. Blood. 2015 Oct 15;126(16):1930-9. doi: 10.1182/blood-2015-06-649087. Epub 2015 Aug 28. PMID: 26320100 PMCID: PMC4608240 read article


Guda S, Brendel C, Renella R, Du P, Bauer DE, Canver MC, Grenier JK, Grimson AW, Kamran SC, Thornton J, de Boer H, Root DE, Milsom MD, Orkin SH, Gregory RI, Williams DA. miRNA-embedded shRNAs for Lineage-specific BCL11A Knockdown and Hemoglobin F Induction. Mol Ther. 2015 Sep;23(9):1465-74. doi: 10.1038/mt.2015.113. Epub 2015 Jun 17. PMID: 26080908 PMCID: PMC4817887 read article


Esain V, Kwan W, Carroll KJ, Cortes M, Liu SY, Frechette GM, Sheward LM, Nissim S, Goessling W, North TE. Cannabinoid Receptor-2 Regulates Embryonic Hematopoietic Stem Cell Development via Prostaglandin E2 and P-Selectin Activity. Stem Cells. 2015 Aug;33(8):2596-612. doi: 10.1002/stem.2044. Epub 2015 May 26. PMID: 25931248 PMCID: PMC4781665 read article


Chan YK, Gack MU. RIG-I-like receptor regulation in virus infection and immunity. Curr Opin Virol. 2015 Jun;12:7-14. doi: 10.1016/j.coviro.2015.01.004. Epub 2015 Jan 30. PMID: 25644461 PMCID: PMC5076476 read article


Kieser KJ, Baranowski C, Chao MC, Long JE, Sassetti CM, Waldor MK, Sacchettini JC, Ioerger TR, Rubin EJ. Peptidoglycan synthesis in Mycobacterium tuberculosis is organized into networks with varying drug susceptibility. Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):13087-92. doi: 10.1073/pnas.1514135112. Epub 2015 Oct 5. PMID: 26438867 PMCID: PMC4620856 read article


Kieser KJ, Boutte CC, Kester JC, Baer CE, Barczak AK, Meniche X, Chao MC, Rego EH, Sassetti CM, Fortune SM, Rubin EJ. Phosphorylation of the Peptidoglycan Synthase PonA1 Governs the Rate of Polar Elongation in Mycobacteria. PLoS Pathog. 2015 Jun 26;11(6):e1005010. doi: 10.1371/journal.ppat.1005010. eCollection 2015 Jun. PMID: 26114871 PMCID: PMC4483258 read article


Chau KF, Springel MW, Broadbelt KG, Park HY, Topal S, Lun MP, Mullan H, Maynard T, Steen H, LaMantia AS, Lehtinen MK. Progressive Differentiation and Instructive Capacities of Amniotic Fluid and Cerebrospinal Fluid Proteomes following Neural Tube Closure. Dev Cell. 2015 Dec 21;35(6):789-802. doi: 10.1016/j.devcel.2015.11.015. PMID: 26702835 PMCID: PMC4691285 read article


Chen AC, Kim S, Shepardson N, Patel S, Hong S, Selkoe DJ. Physical and functional interaction between the α- and γ-secretases: A new model of regulated intramembrane proteolysis. J Cell Biol. 2015 Dec 21;211(6):1157-76. doi: 10.1083/jcb.201502001. PMID: 26694839 PMCID: PMC4687875 read article


Schlaeger TM, Daheron L, Brickler TR, Entwisle S, Chan K, Cianci A, DeVine A, Ettenger A, Fitzgerald K, Godfrey M, Gupta D, McPherson J, Malwadkar P, Gupta M, Bell B, Doi A, Jung N, Li X, Lynes MS, Brookes E, Cherry AB, Demirbas D, Tsankov AM, Zon LI, Rubin LL, Feinberg AP, Meissner A, Cowan CA, Daley GQ. A comparison of non-integrating reprogramming methods. Nat Biotechnol. 2015 Jan;33(1):58-63. doi: 10.1038/nbt.3070. Epub 2014 Dec 1. PMID: 25437882 PMCID: PMC4329913 read article


Choi S, Taylor KP, Chatzigeorgiou M, Hu Z, Schafer WR, Kaplan JM. Sensory Neurons Arouse C. elegans Locomotion via Both Glutamate and Neuropeptide Release. PLoS Genet. 2015 Jul 8;11(7):e1005359. doi: 10.1371/journal.pgen.1005359. eCollection 2015 Jul. PMID: 26154367 PMCID: PMC4495980 read article


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Vincent BJ, Scholes C, Staller MV, Wunderlich Z, Estrada J, Park J, Bragdon MD, Lopez Rivera F, Biette KM, DePace AH. Yearly planning meetings: individualized development plans aren't just more paperwork. Mol Cell. 2015 Jun 4;58(5):718-21. doi: 10.1016/j.molcel.2015.04.025. PMID: 26046646 read article


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Staller MV, Vincent BJ, Bragdon MD, Lydiard-Martin T, Wunderlich Z, Estrada J, DePace AH. Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo. Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):785-90. doi: 10.1073/pnas.1413877112. Epub 2015 Jan 6. PMID: 25564665 PMCID: PMC4311800 read article


Tu HC, Schwitalla S, Qian Z, LaPier GS, Yermalovich A, Ku YC, Chen SC, Viswanathan SR, Zhu H, Nishihara R, Inamura K, Kim SA, Morikawa T, Mima K, Sukawa Y, Yang J, Meredith G, Fuchs CS, Ogino S, Daley GQ. LIN28 cooperates with WNT signaling to drive invasive intestinal and colorectal adenocarcinoma in mice and humans. Genes Dev. 2015 May 15;29(10):1074-86. doi: 10.1101/gad.256693.114. Epub 2015 May 8. PMID: 25956904 PMCID: PMC4441054  read article


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Li L, Walsh RM, Wagh V, James MF, Beauchamp RL, Chang YS, Gusella JF, Hochedlinger K, Ramesh V. Mediator Subunit Med28 Is Essential for Mouse Peri-Implantation Development and Pluripotency. PLoS One. 2015 Oct 7;10(10):e0140192. doi: 10.1371/journal.pone.0140192. eCollection 2015. PMID: 26445504 PMCID: PMC4596692 read article


Do R, Stitziel NO, Won HH, Jørgensen AB, Duga S, Angelica Merlini P, Kiezun A, Farrall M, Goel A, Zuk O, Guella I, Asselta R, Lange LA, Peloso GM, Auer PL; NHLBI Exome Sequencing Project, Girelli D, Martinelli N, Farlow DN, DePristo MA, Roberts R, Stewart AF, Saleheen D, Danesh J, Epstein SE, Sivapalaratnam S, Hovingh GK, Kastelein JJ, Samani NJ, Schunkert H, Erdmann J, Shah SH, Kraus WE, Davies R, Nikpay M, Johansen CT, Wang J, Hegele RA, Hechter E, Marz W, Kleber ME, Huang J, Johnson AD, Li M, Burke GL, Gross M, Liu Y, Assimes TL, Heiss G, Lange EM, Folsom AR, Taylor HA, Olivieri O, Hamsten A, Clarke R, Reilly DF, Yin W, Rivas MA, Donnelly P, Rossouw JE, Psaty BM, Herrington DM, Wilson JG, Rich SS, Bamshad MJ, Tracy RP, Cupples LA, Rader DJ, Reilly MP, Spertus JA, Cresci S, Hartiala J, Tang WH, Hazen SL, Allayee H, Reiner AP, Carlson CS, Kooperberg C, Jackson RD, Boerwinkle E, Lander ES, Schwartz SM, Siscovick DS, McPherson R, Tybjaerg-Hansen A, Abecasis GR, Watkins H, Nickerson DA, Ardissino D, Sunyaev SR, O'Donnell CJ, Altshuler D, Gabriel S, Kathiresan S. Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction. Nature. 2015 Feb 5;518(7537):102-6. doi: 10.1038/nature13917. Epub 2014 Dec 10. PMID: 25487149 PMCID: PMC4319990  read article


Johnson MB, Wang PP, Atabay KD, Murphy EA, Doan RN, Hecht JL, Walsh CA. Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex. Nat Neurosci. 2015 May;18(5):637-46. doi: 10.1038/nn.3980. Epub 2015 Mar 3. PMID: 25734491 PMCID: PMC5568903 read article


Wang SR, Jacobsen CM, Carmichael H, Edmund AB, Robinson JW, Olney RC, Miller TC, Moon JE, Mericq V, Potter LR, Warman ML, Hirschhorn JN, Dauber A. Heterozygous mutations in natriuretic peptide receptor-B (NPR2) gene as a cause of short stature. Hum Mutat. 2015 Apr;36(4):474-81. doi: 10.1002/humu.22773. Epub 2015 Mar 16. PMID: 25703509 PMCID: PMC4382411 read article


Goldman SR, Nair NU, Wells CD, Nickels BE, Hochschild A. The primary σ factor in Escherichia coli can access the transcription elongation complex from solution in vivo. Elife. 2015 Sep 15;4. doi: 10.7554/eLife.10514. PMID: 26371553 PMCID: PMC4604602 read article


Walker SR, Liu S, Xiang M, Nicolais M, Hatzi K, Giannopoulou E, Elemento O, Cerchietti L, Melnick A, Frank DA. The transcriptional modulator BCL6 as a molecular target for breast cancer therapy. Oncogene. 2015 Feb 26;34(9):1073-82. doi: 10.1038/onc.2014.61. Epub 2014 Mar 24. PMID: 24662818 PMCID: PMC4175367 read article


Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc. 2015 Mar;10(3):442-58. doi: 10.1038/nprot.2014.191. Epub 2015 Feb 12. PMID: 25675209 PMCID: PMC4327781 read article


Yang L, Güell M, Niu D, George H, Lesha E, Grishin D, Aach J, Shrock E, Xu W, Poci J, Cortazio R, Wilkinson RA, Fishman JA, Church G. Genome-wide inactivation of porcine endogenous retroviruses (PERVs). Science. 2015 Nov 27;350(6264):1101-4. doi: 10.1126/science.aad1191. Epub 2015 Oct 11. PMID: 26456528 read article


Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes Dev. 2015 Mar 1;29(5):501-12. doi: 10.1101/gad.258483.115. PMID: 25737280 PMCID: PMC4358403 read article


Toniolo PA, Liu S, Yeh JE, Moraes-Vieira PM, Walker SR, Vafaizadeh V, Barbuto JA, Frank DA. Inhibiting STAT5 by the BET bromodomain inhibitor JQ1 disrupts human dendritic cell maturation. J Immunol. 2015 Apr 1;194(7):3180-90. doi: 10.4049/jimmunol.1401635. Epub 2015 Feb 27. PMID: 25725100 PMCID: PMC4369449 read article


Yeh JE, Frank DA. STAT3-Interacting Proteins as Modulators of Transcription Factor Function: Implications to Targeted Cancer Therapy. ChemMedChem. 2016 Apr 19;11(8):795-801. doi: 10.1002/cmdc.201500482. Epub 2015 Dec 10. PMID: 26662504 read article


Hu T, Yeh JE, Pinello L, Jacob J, Chakravarthy S, Yuan GC, Chopra R, Frank DA. Impact of the N-Terminal Domain of STAT3 in STAT3-Dependent Transcriptional Activity. Mol Cell Biol. 2015 Oct;35(19):3284-300. doi: 10.1128/MCB.00060-15. Epub 2015 Jul 13. PMID: 26169829 PMCID: PMC4561728 read article


Yeh JE, Kreimer S, Walker SR, Emori MM, Krystal H, Richardson A, Ivanov AR, Frank DA. Granulin, a novel STAT3-interacting protein, enhances STAT3 transcriptional function and correlates with poorer prognosis in breast cancer. Genes Cancer. 2015 Mar;6(3-4):153-68. PMID: 26000098 PMCID: PMC4426952  read article


Huh SJ, Clement K, Jee D, Merlini A, Choudhury S, Maruyama R, Yoo R, Chytil A, Boyle P, Ran FA, Moses HL, Barcellos-Hoff MH, Jackson-Grusby L, Meissner A, Polyak K. Age- and pregnancy-associated DNA methylation changes in mammary epithelial cells. Stem Cell Reports. 2015 Feb 10;4(2):297-311. doi: 10.1016/j.stemcr.2014.12.009. Epub 2015 Jan 22. PMID: 25619437 PMCID: PMC4325231 read article


Yunck R, Cho H, Bernhardt TG. Identification of MltG as a potential terminase for peptidoglycan polymerization in bacteria. Mol Microbiol. 2016 Feb;99(4):700-18. doi: 10.1111/mmi.13258. Epub 2015 Nov 19. PMID: 26507882 PMCID: PMC4752859 read article


Hays SG, Patrick WG, Ziesack M, Oxman N, Silver PA. Better together: engineering and application of microbial symbioses. Curr Opin Biotechnol. 2015 Dec;36:40-9. doi: 10.1016/j.copbio.2015.08.008. Epub 2015 Aug 28. Review. PMID: 26319893  read article


2014


Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014 Mar 21;343(6177):1360-3. doi: 10.1126/science.1250212. Epub 2014 Feb 27. PMID: 24578530 PMCID: PMC4140943 read article


Amamoto R, Arlotta P. Development-inspired reprogramming of the mammalian central nervous system. Science. 2014 Jan 31;343(6170):1239882. doi: 10.1126/science.1239882. PMID: 24482482 PMCID: PMC4122114 read article


Tschopp P, Sherratt E, Sanger TJ, Groner AC, Aspiras AC, Hu JK, Pourquié O, Gros J, Tabin CJ. A relative shift in cloacal location repositions external genitalia in amniote evolution. Nature. 2014 Dec 18;516(7531):391-4. doi: 10.1038/nature13819. Epub 2014 Nov 5. PMID: 25383527 read article


Prandi D, Baca SC, Romanel A, Barbieri CE, Mosquera JM, Fontugne J, Beltran H, Sboner A, Garraway LA, Rubin MA, Demichelis F. Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biol. 2014 Aug 26;15(8):439. doi: 10.1186/s13059-014-0439-6. PMID: 25160065 PMCID: PMC4167267  read article


Theurillat JP, Udeshi ND, Errington WJ, Svinkina T, Baca SC, Pop M, Wild PJ, Blattner M, Groner AC, Rubin MA, Moch H, Prive GG, Carr SA, Garraway LA. Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer. Science. 2014 Oct 3;346(6205):85-89. doi: 10.1126/science.1250255. Epub 2014 Oct 2. PMID: 25278611 PMCID: PMC4257137 read article


Perry JA, Kiezun A, Tonzi P, Van Allen EM, Carter SL, Baca SC, Cowley GS, Bhatt AS, Rheinbay E, Pedamallu CS, Helman E, Taylor-Weiner A, McKenna A, DeLuca DS, Lawrence MS, Ambrogio L, Sougnez C, Sivachenko A, Walensky LD, Wagle N, Mora J, de Torres C, Lavarino C, Dos Santos Aguiar S, Yunes JA, Brandalise SR, Mercado-Celis GE, Melendez-Zajgla J, Cárdenas-Cardós R, Velasco-Hidalgo L, Roberts CW, Garraway LA, Rodriguez-Galindo C, Gabriel SB, Lander ES, Golub TR, Orkin SH, Getz G, Janeway KA. Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):E5564-73. doi: 10.1073/pnas.1419260111. Epub 2014 Dec 15. PMID: 25512523 PMCID: PMC4280630 read article


Bauer BW, Shemesh T, Chen Y, Rapoport TA. A "push and slide" mechanism allows sequence-insensitive translocation of secretory proteins by the SecA ATPase. Cell. 2014 Jun 5;157(6):1416-29. doi: 10.1016/j.cell.2014.03.063. PMID: 24906156 PMCID: PMC4104599 read article


Knyazev DG, Winter L, Bauer BW, Siligan C, Pohl P. Ion conductivity of the bacterial translocation channel SecYEG engaged in translocation. J Biol Chem. 2014 Aug 29;289(35):24611-6. doi: 10.1074/jbc.M114.588491. Epub 2014 Jul 11. PMID: 25016015 PMCID: PMC4148884 read article


Ordureau A, Sarraf SA, Duda DM, Heo JM, Jedrychowski MP, Sviderskiy VO,
Olszewski JL, Koerber JT, Xie T,
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Beliveau BJ, Apostolopoulos N, Wu CT. Visualizing genomes with Oligopaint FISH probes. Curr Protoc Mol Biol. 2014 Jan 6;105:Unit 14.23. doi: 10.1002/0471142727.mb1423s105. PMID: 24510436 PMCID: PMC3928790 read article


Glessner JT, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, Mazaika E, Vardarajan B, Italia M, Leipzig J, DePalma SR, Golhar R, Sanders SJ, Yamrom B, Ronemus M, Iossifov I, Willsey AJ, State MW, Kaltman JR, White PS, Shen Y, Warburton D, Brueckner M, Seidman C, Goldmuntz E, Gelb BD, Lifton R, Seidman J, Hakonarson H, Chung WK. Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circ Res. 2014 Oct 24;115(10):884-896. doi: 10.1161/CIRCRESAHA.115.304458. Epub 2014 Sep 9. PMID: 25205790 PMCID: PMC4209190 read article


Ito K, Bick AG, Flannick J, Friedman DJ, Genovese G, Parfenov MG, Depalma SR, Gupta N, Gabriel SB, Taylor HA Jr, Fox ER, Newton-Cheh C, Kathiresan S, Hirschhorn JN, Altshuler DM, Pollak MR, Wilson JG, Seidman JG, Seidman C. Increased burden of cardiovascular disease in carriers of APOL1 genetic variants. Circ Res. 2014 Feb 28;114(5):845-50. doi: 10.1161/CIRCRESAHA.114.302347. Epub 2013 Dec 30. PMID: 24379297 PMCID: PMC3982584 read article


Blain JC, Szostak JW. Progress toward synthetic cells. Annu Rev Biochem. 2014;83:615-40. doi: 10.1146/annurev-biochem-080411-124036. Epub 2014 Mar 3. PMID: 24606140 read article


Sheng J, Larsen A, Heuberger BD, Blain JC, Szostak JW. Crystal structure studies of RNA duplexes containing s(2)U:A and s(2)U:U base pairs. J Am Chem Soc. 2014 Oct 1;136(39):13916-24. doi: 10.1021/ja508015a. Epub 2014 Sep 16. PMID: 25188906 PMCID: PMC4183603 read article


Blain JC, Ricardo A, Szostak JW. Synthesis and nonenzymatic template-directed polymerization of 2'-amino-2'-deoxythreose nucleotides. J Am Chem Soc. 2014 Feb 5;136(5):2033-9. doi: 10.1021/ja411950n. Epub 2014 Jan 22. PMID: 24409991 PMCID: PMC4105081 read article


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Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GS, Li T, Chabot MS, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS, Love JC. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat Biotechnol. 2014 May;32(5):479-84. doi: 10.1038/nbt.2892. Epub 2014 Apr 20. PMID: 24752078 PMCID: PMC4034575 read article


Bowen ME, Ayturk UM, Kurek KC, Yang W, Warman ML. SHP2 regulates chondrocyte terminal differentiation, growth plate architecture and skeletal cell fates. PLoS Genet. 2014 May 29;10(5):e1004364. doi: 10.1371/journal.pgen.1004364. eCollection 2014. PMID: 24875294 PMCID: PMC4038465 read article


Anger GJ, Crocker S, McKenzie K, Brown KK, Morton CC, Harrison K, MacKenzie JJ. X-linked deafness-2 (DFNX2) phenotype associated with a paracentric inversion upstream of POU3F4. Am J Audiol. 2014 Mar;23(1):1-6. doi: 10.1044/1059-0889(2013/13-0018). read article


Brubaker SW, Gauthier AE, Mills EW, Ingolia NT, Kagan JC. A bicistronic MAVS transcript highlights a class of truncated variants in antiviral immunity. Cell. 2014 Feb 13;156(4):800-11. doi: 10.1016/j.cell.2014.01.021. PMID: 24529381 PMCID: PMC3959641 read article


Brust RD, Corcoran AE, Richerson GB, Nattie E, Dymecki SM. Functional and developmental identification of a molecular subtype of brain serotonergic neuron specialized to regulate breathing dynamics. Cell Rep. 2014 Dec 24;9(6):2152-65. doi: 10.1016/j.celrep.2014.11.027. Epub 2014 Dec 11. PMID: 25497093 PMCID: PMC4351711 read article


Bryant DM, O'Meara CC, Ho NN, Gannon J, Cai L, Lee RT. A systematic analysis of neonatal mouse heart regeneration after apical resection. J Mol Cell Cardiol. 2015 Feb;79:315-8. doi: 10.1016/j.yjmcc.2014.12.011. Epub 2014 Dec 19. PMID: 25533939 PMCID: PMC4302033 read article


Cai X, Evrony GD, Lehmann HS, Elhosary PC, Mehta BK, Poduri A, Walsh CA. Single-cell, genome-wide sequencing identifies clonal somatic copy-number variation in the human brain. Cell Rep. 2014 Sep 11;8(5):1280-9. doi: 10.1016/j.celrep.2014.07.043. Epub 2014 Aug 21. PMID: 25159146 PMCID: PMC4272008  read article


Moroz N, Carmona JJ, Anderson E, Hart AC, Sinclair DA, Blackwell TK. Dietary restriction involves NAD⁺ -dependent mechanisms and a shift toward oxidative metabolism. Aging Cell. 2014 Dec;13(6):1075-85. doi: 10.1111/acel.12273. Epub 2014 Sep 25. PMID: 25257342 PMCID: PMC4244309 read article


Carroll KJ, North TE. Oceans of opportunity: exploring vertebrate hematopoiesis in zebrafish. Exp Hematol. 2014 Aug;42(8):684-96. doi: 10.1016/j.exphem.2014.05.002. Epub 2014 May 9. PMID: 24816275 PMCID: PMC4461861 read article


Pauli EK, Chan YK, Davis ME, Gableske S, Wang MK, Feister KF, Gack MU. The ubiquitin-specific protease USP15 promotes RIG-I-mediated antiviral signaling by deubiquitylating TRIM25. Sci Signal. 2014 Jan 7;7(307):ra3. doi: 10.1126/scisignal.2004577. PMID: 24399297 PMCID: PMC4008495
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Gostissa M, Schwer B, Chang A, Dong J, Meyers RM, Marecki GT, Choi VW, Chiarle R, Zarrin AA, Alt FW. IgH class switching exploits a general property of two DNA breaks to be joined in cis over long chromosomal distances. Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2644-9. doi: 10.1073/pnas.1324176111. Epub 2014 Feb 3. PMID: 24550291 PMCID: 24550291 read article


Pritchard JR, Chao MC, Abel S, Davis BM, Baranowski C, Zhang YJ, Rubin EJ, Waldor MK. ARTIST: high-resolution genome-wide assessment of fitness using transposon-insertion sequencing. PLoS Genet. 2014 Nov 6;10(11):e1004782. doi: 10.1371/journal.pgen.1004782. eCollection 2014 Nov. PMID: 25375795 PMCID: PMC4222735 read article


Chen JW, Galloway JL. The development of zebrafish tendon and ligament progenitors. Development. 2014 May;141(10):2035-45. doi: 10.1242/dev.104067. PMID: 24803652 PMCID: PMC4011085 read article


Wang SR, Agarwala V, Flannick J, Chiang CW, Altshuler D; GoT2D Consortium, Hirschhorn JN. Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland. Am J Hum Genet. 2014 May 1;94(5):710-20. doi: 10.1016/j.ajhg.2014.03.019. Epub 2014 Apr 24. PMID: 24768551 PMCID: PMC4067550 read article


Choi JE, Mostoslavsky R. Sirtuins, metabolism, and DNA repair. Curr Opin Genet Dev. 2014 Jun;26C:24-32. doi: 10.1016/j.gde.2014.05.005. Epub 2014 Jul 5. PMID: 25005742 PMCID: PMC4254145 read article


Choi Y, Mango SE. Hunting for Darwin's gemmules and Lamarck's fluid: Transgenerational signaling and histone methylation. Biochim Biophys Acta. 2014 Dec;1839(12):1440-53. doi: 10.1016/j.bbagrm.2014.05.011. Epub 2014 May 21. PMID: 24859459 read article


Ball MP, Bobe JR, Chou MF, Clegg T, Estep PW, Lunshof JE, Vandewege W, Zaranek A, Church GM. Harvard Personal Genome Project: lessons from participatory public research. Genome Med. 2014 Feb 28;6(2):10. doi: 10.1186/gm527. PMID: 24713084 PMCID: PMC3978420 read article


Christodoulou DC, Wakimoto H, Onoue K, Eminaga S, Gorham JM, DePalma SR, Herman DS, Teekakirikul P, Conner DA, McKean DM, Domenighetti AA, Aboukhalil A, Chang S, Srivastava G, McDonough B, De Jager PL, Chen J, Bulyk ML, Muehlschlegel JD, Seidman CE, Seidman JG. 5'RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy. J Clin Invest. 2014 Mar;124(3):1364-70. doi: 10.1172/JCI70108. Epub 2014 Feb 10. PMID: 24509080 PMCID: PMC3934171 read article


Domenighetti AA, Chu PH, Wu T, Sheikh F, Gokhin DS, Guo LT, Cui Z, Peter AK, Christodoulou DC, Parfenov MG, Gorham JM, Li DY, Banerjee I, Lai X, Witzmann FA, Seidman CE, Seidman JG, Gomes AV, Shelton GD, Lieber RL, Chen J. Loss of FHL1 induces an age-dependent skeletal muscle myopathy associated with myofibrillar and intermyofibrillar disorganization in mice. Hum Mol Genet. 2014 Jan 1;23(1):209-25. doi: 10.1093/hmg/ddt412. Epub 2013 Aug 23. PMID: 23975679 PMCID: PMC3916749 read article


Christofferson DE, Li Y, Yuan J. Control of life-or-death decisions by RIP1 kinase. Annu Rev Physiol. 2014;76:129-50. doi: 10.1146/annurev-physiol-021113-170259. Epub 2013 Sep 20. PMID: 24079414 read article


Clark AR, Toker A. Signalling specificity in the Akt pathway in breast cancer. Biochem Soc Trans. 2014 Oct;42(5):1349-55. doi: 10.1042/BST20140160. PMID: 25233414  read article


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Terrell SL, Pesola JM, Coen DM. Roles of conserved residues within the pre-NH2-terminal domain of herpes simplex virus 1 DNA polymerase in replication and latency in mice. J Gen Virol. 2014 Apr;95(Pt 4):940-7. doi: 10.1099/vir.0.061903-0. Epub 2014 Jan 10. PMID: 24413420 PMCID: PMC3973481 read article


Thomas MP, Whangbo J, McCrossan G, Deutsch AJ, Martinod K, Walch M, Lieberman J. Leukocyte protease binding to nucleic acids promotes nuclear localization and cleavage of nucleic acid binding proteins. J Immunol. 2014 Jun 1;192(11):5390-7. doi: 10.4049/jimmunol.1303296. Epub 2014 Apr 25. PMID: 24771851 PMCID: PMC4041364  read article


Guilinger JP, Thompson DB, Liu DR. Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol. 2014 Jun;32(6):577-582. doi: 10.1038/nbt.2909. Epub 2014 Apr 25. PMID: 24770324 PMCID: PMC4263420 read article


Thompson MN, MacDonald ME, Gusella JF, Myre MA. Huntingtin Supplies a csaA-Independent Function Essential for EDTA-Resistant Homotypic Cell Adhesion in Dictyostelium discoideum. J Huntingtons Dis. 2014;3(3):261-71. doi: 10.3233/JHD-140112. PMID: 25300330 read article


Kim LA, Amarnani D, Gnanaguru G, Tseng WA, Vavvas DG, D'Amore PA. Tamoxifen toxicity in cultured retinal pigment epithelial cells is mediated by concurrent regulated cell death mechanisms. Invest Ophthalmol Vis Sci. 2014 Jul 3;55(8):4747-58. doi: 10.1167/iovs.13-13662. PMID: 24994868 PMCID: PMC4122018 read article


Balasubramanian D, Kumari H, Jaric M, Fernandez M, Turner KH, Dove SL, Narasimhan G, Lory S, Mathee K. Deep sequencing analyses expands the Pseudomonas aeruginosa AmpR regulon to include small RNA-mediated regulation of iron acquisition, heat shock and oxidative stress response. Nucleic Acids Res. 2014 Jan;42(2):979-98. doi: 10.1093/nar/gkt942. Epub 2013 Oct 23. PMID: 24157832 PMCID: PMC3902932 read article


Umbarger MA, Kennedy CJ, Saunders P, Breton B, Chennagiri N, Emhoff J, Greger V, Hallam S, Maganzini D, Micale C, Nizzari MM, Towne CF, Church GM, Porreca GJ. Next-generation carrier screening. Genet Med. 2014 Feb;16(2):132-40. doi: 10.1038/gim.2013.83. Epub 2013 Jun 13 PMID: 23765052 PMCID: PMC3918543  read article


Cooper KL, Sears KE, Uygur A, Maier J, Baczkowski KS, Brosnahan M, Antczak D, Skidmore JA, Tabin CJ. Patterning and post-patterning modes of evolutionary digit loss in mammals. Nature. 2014 Jul 3;511(7507):41-5. doi: 10.1038/nature13496. Epub 2014 Jun 18. PMID: 24990742 PMCID: PMC4228958 read article


Valdez CN, Arboleda-Velasquez JF, Amarnani DS, Kim LA, D'Amore PA. Retinal microangiopathy in a mouse model of inducible mural cell loss. Am J Pathol. 2014 Oct;184(10):2618-26. doi: 10.1016/j.ajpath.2014.06.011. Epub 2014 Aug 1. PMID: 25092275 PMCID: PMC4715212 read article


Teo AK, Valdez IA, Dirice E, Kulkarni RN. Comparable generation of activin-induced definitive endoderm via additive Wnt or BMP signaling in absence of serum. Stem Cell Reports. 2014 Jun 12;3(1):5-14. doi: 10.1016/j.stemcr.2014.05.007. eCollection 2014. PMID: 25068117 PMCID: PMC4110751 read article


Ayala de la Peña F, Kanasaki K, Kanasaki M, Vong S, Rovira C, Kalluri R. Specific activation of K-RasG12D allele in the bladder urothelium results in lung alveolar and vascular defects. PLoS One. 2014 Apr 23;9(4):e95888. doi: 10.1371/journal.pone.0095888. eCollection 2014. PMID: 24760005 PMCID: PMC3997426 read article


Helming KC, Wang X, Wilson BG, Vazquez F, Haswell JR, Manchester HE, Kim Y, Kryukov GV, Ghandi M, Aguirre AJ, Jagani Z, Wang Z, Garraway LA, Hahn WC, Roberts CW. ARID1B is a specific vulnerability in ARID1A-mutant cancers. Nat Med. 2014 Mar;20(3):251-4. doi: 10.1038/nm.3480. Epub 2014 Feb 23. PMID: 24562383 PMCID: PMC3954704 read article


Wilson BG, Helming KC, Wang X, Kim Y, Vazquez F, Jagani Z, Hahn WC, Roberts CW. Residual complexes containing SMARCA2 (BRM) underlie the oncogenic drive of SMARCA4 (BRG1) mutation. Mol Cell Biol. 2014 Mar;34(6):1136-44. doi: 10.1128/MCB.01372-13. Epub 2014 Jan 13. PMID: 24421395 PMCID: PMC3958034 read article


Helming KC, Wang X, Roberts CW. Vulnerabilities of mutant SWI/SNF complexes in cancer. Cancer Cell. 2014 Sep 8;26(3):309-17. doi: 10.1016/j.ccr.2014.07.018. PMID: 25203320 PMCID: PMC4159614 read article


Bar-Nur O, Brumbaugh J, Verheul C, Apostolou E, Pruteanu-Malinici I, Walsh RM, Ramaswamy S, Hochedlinger K. Small molecules facilitate rapid and synchronous iPSC generation. Nat Methods. 2014 Nov;11(11):1170-6. doi: 10.1038/nmeth.3142. Epub 2014 Sep 24. PMID: 25262205 PMCID: PMC4326224 read article


Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415. PMID: 25164756 PMCID: PMC4227084 read article


Geng J, Picker J, Zheng Z, Zhang X, Wang J, Hisama F, Brown DW, Mullen MP, Harris D, Stoler J, Seman A, Miller DT, Fu Q1, Roberts AE, Shen Y. Chromosome microarray testing for patients with congenital heart defects reveals novel disease causing loci and high diagnostic yield. BMC Genomics. 2014 Dec 17;15:1127. doi: 10.1186/1471-2164-15-1127. PMID: 25516202 PMCID: PMC4378009  read article


Bae BI, Tietjen I, Atabay KD, Evrony GD, Johnson MB, Asare E, Wang PP, Murayama AY, Im K, Lisgo SN, Overman L, Sestan N, Chang BS, Barkovich AJ, Grant PE, Topçu M, Politsky J, Okano H, Piao X, Walsh CA. Evolutionarily dynamic alternative splicing of GPR56 regulates regional cerebral cortical patterning. Science. 2014 Feb 14;343(6172):764-8. doi: 10.1126/science.1244392. PMID: 24531968 read article


Dauber A, Ercan A, Lee J, James P, Jacobs PP, Ashline DJ, Wang SR, Miller T, Hirschhorn JN, Nigrovic PA, Sackstein R. Congenital disorder of fucosylation type 2c (LADII) presenting with short stature and developmental delay with minimal adhesion defect. Hum Mol Genet. 2014 Jun 1;23(11):2880-7. doi: 10.1093/hmg/ddu001. Epub 2014 Jan 8. PMID: 24403049 PMCID: PMC4014190 read article


Wang SR, Agarwala V, Flannick J, Chiang CW, Altshuler D; GoT2D Consortium, Hirschhorn JN. Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland. Am J Hum Genet. 2014 May 1;94(5):710-20. doi: 10.1016/j.ajhg.2014.03.019. Epub 2014 Apr 24. PMID: 24768551 PMCID: PMC4067550 read article


Chan Y, Lim ET, Sandholm N, Wang SR, McKnight AJ, Ripke S; DIAGRAM Consortium; GENIE Consortium; GIANT Consortium; IIBDGC Consortium; PGC Consortium, Daly MJ, Neale BM, Salem RM, Hirschhorn JN. An excess of risk-increasing low-frequency variants can be a signal of polygenic inheritance in complex diseases. Am J Hum Genet. 2014 Mar 6;94(3):437-52. doi: 10.1016/j.ajhg.2014.02.006. PMID: 24607388 PMCID: PMC3951950 read article


Kong X, Banks A, Liu T, Kazak L, Rao RR, Cohen P, Wang X, Yu S, Lo JC, Tseng YH, Cypess AM, Xue R, Kleiner S, Kang S, Spiegelman BM, Rosen ED. IRF4 is a key thermogenic transcriptional partner of PGC-1α. Cell. 2014 Jul 3;158(1):69-83. doi: 10.1016/j.cell.2014.04.049. PMID: 24995979 PMCID: PMC4116691 read article


Puebla-Osorio N, Kim J, Ojeda S, Zhang H, Tavana O, Li S, Wang Y, Ma Q, Schluns KS, Zhu C. A novel Ku70 function in colorectal homeostasis separate from nonhomologous end joining. Oncogene. 2014 May 22;33(21):2748-57. doi: 10.1038/onc.2013.234. Epub 2013 Jun 10. PMID: 23752193 PMCID: PMC5761319 read article


Rooks MG, Veiga P, Wardwell-Scott LH, Tickle T, Segata N, Michaud M, Gallini CA, Beal C, van Hylckama-Vlieg JE, Ballal SA, Morgan XC, Glickman JN, Gevers D, Huttenhower C, Garrett WS. Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission. ISME J. 2014 Jul;8(7):1403-17. doi: 10.1038/ismej.2014.3. Epub 2014 Feb 6. PMID: 24500617 PMCID: PMC4069400 read article


Wainger BJ, Kiskinis E, Mellin C, Wiskow O, Han SS, Sandoe J, Perez NP, Williams LA, Lee S, Boulting G, Berry JD, Brown RH Jr, Cudkowicz ME, Bean BP, Eggan K, Woolf CJ. Intrinsic membrane hyperexcitability of amyotrophic lateral sclerosis patient-derived motor neurons. Cell Rep. 2014 Apr 10;7(1):1-11. doi: 10.1016/j.celrep.2014.03.019. Epub 2014 Apr 3. PMID: 24703839 PMCID: PMC4023477 read article


Davis-Dusenbery BN, Williams LA, Klim JR, Eggan K. How to make spinal motor neurons. Development. 2014 Feb;141(3):491-501. doi: 10.1242/dev.097410. PMID: 24449832 read article


Wainger BJ, Kiskinis E, Mellin C, Wiskow O, Han SS, Sandoe J, Perez NP, Williams LA, Lee S, Boulting G, Berry JD, Brown RH Jr, Cudkowicz ME, Bean BP, Eggan K, Woolf CJ. Intrinsic membrane hyperexcitability of amyotrophic lateral sclerosis patient-derived motor neurons. Cell Rep. 2014 Apr 10;7(1):1-11. doi: 10.1016/j.celrep.2014.03.019. Epub 2014 Apr 3. PMID: 24703839 PMCID: PMC4023477 read article


Wivagg CN, Bhattacharyya RP, Hung DT. Mechanisms of β-lactam killing and resistance in the context of Mycobacterium tuberculosis. J Antibiot (Tokyo). 2014 Sep;67(9):645-54. doi: 10.1038/ja.2014.94. Epub 2014 Jul 23. PMID: 25052484 read article


Ringgaard S, Zepeda-Rivera M, Wu X, Schirner K, Davis BM, Waldor MK. ParP prevents dissociation of CheA from chemotactic signaling arrays and tethers them to a polar anchor. Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):E255-64. doi: 10.1073/pnas.1315722111. Epub 2013 Dec 30. PMID: 24379357 PMCID: PMC3896188 read article


Wu H, Wu X, Shen L, Zhang Y. Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing. Nat Biotechnol. 2014 Dec;32(12):1231-40. doi: 10.1038/nbt.3073. Epub 2014 Nov 2. PMID: 25362244 PMCID: PMC4269366 read article


Xia X, Owen MS, Lee RE, Gaudet S. Cell-to-cell variability in cell death: can systems biology help us make sense of it all? Cell Death Dis. 2014 May 29;5:e1261. doi: 10.1038/cddis.2014.199. PMID: 24874733 PMCID: PMC4047886 read article


Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM. Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev. 2014 Sep 1;28(17):1957-75. doi: 10.1101/gad.241620.114. PMID: 25184681 PMCID: PMC4197947 read article


Walker SR, Xiang M, Frank DA. Distinct roles of STAT3 and STAT5 in the pathogenesis and targeted therapy of breast cancer. Mol Cell Endocrinol. 2014 Jan 25;382(1):616-621. doi: 10.1016/j.mce.2013.03.010. Epub 2013 Mar 24. PMID: 23531638 PMCID: PMC3732813 read article


Liu S, Walker SR, Nelson EA, Cerulli R, Xiang M, Toniolo PA, Qi J, Stone RM, Wadleigh M, Bradner JE, Frank DA. Targeting STAT5 in hematologic malignancies through inhibition of the bromodomain and extra-terminal (BET) bromodomain protein BRD2. Mol Cancer Ther. 2014 May;13(5):1194-205. doi: 10.1158/1535-7163.MCT-13-0341. Epub 2014 Jan 16. PMID: 24435449 PMCID: PMC4013223 read article


Xiang M, Birkbak NJ, Vafaizadeh V, Walker SR, Yeh JE, Liu S, Kroll Y, Boldin M, Taganov K, Groner B, Richardson AL, Frank DA. STAT3 induction of miR-146b forms a feedback loop to inhibit the NF-κB to IL-6 signaling axis and STAT3-driven cancer phenotypes. Sci Signal. 2014 Jan 28;7(310):ra11. doi: 10.1126/scisignal.2004497. PMID: 24473196 PMCID: PMC4233120 read article


Walker SR, Xiang M, Frank DA. STAT3 Activity and Function in Cancer: Modulation by STAT5 and miR-146b. Cancers (Basel). 2014 Apr 23;6(2):958-68. doi: 10.3390/cancers6020958. PMID: 24762632 PMCID: PMC4074811 read article


Yang L, Yang JL, Byrne S, Pan J, Church GM. CRISPR/Cas9-Directed Genome Editing of Cultured Cells. Curr Protoc Mol Biol. 2014 Jul 1;107:31.1.1-31.1.17. doi: 10.1002/0471142727.mb3101s107. PMID: 24984853 read article


Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM. Highly multiplexed subcellular RNA sequencing in situ. Science. 2014 Mar 21;343(6177):1360-3. doi: 10.1126/science.1250212. Epub 2014 Feb 27. PMID: 24578530 PMCID: PMC4140943 read article


Kim H, Dejsuphong D, Adelmant G, Ceccaldi R, Yang K, Marto JA, D'Andrea AD. Transcriptional repressor ZBTB1 promotes chromatin remodeling and translesion DNA synthesis. Mol Cell. 2014 Apr 10;54(1):107-118. doi: 10.1016/j.molcel.2014.02.017. Epub 2014 Mar 20. PMID: 24657165 PMCID: PMC3989074 read article


Yang L, Grishin D, Wang G, Aach J, Zhang CZ, Chari R, Homsy J, Cai X, Zhao Y, Fan JB, Seidman C, Seidman J, Pu W, Church G. Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells. Nat Commun. 2014 Nov 26;5:5507. doi: 10.1038/ncomms6507. PMID: 25425480 PMCID: PMC4352754 read article


Güell M, Yang L, Church GM. Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA). Bioinformatics. 2014 Oct 15;30(20):2968-70. doi: 10.1093/bioinformatics/btu427. Epub 2014 Jul 1. PMID: 24990609 PMCID: PMC4184265 read article


Wang G, McCain ML, Yang L, He A, Pasqualini FS, Agarwal A, Yuan H, Jiang D, Zhang D, Zangi L, Geva J, Roberts AE, Ma Q, Ding J, Chen J, Wang DZ, Li K, Wang J, Wanders RJ, Kulik W, Vaz FM, Laflamme MA, Murry CE, Chien KR, Kelley RI, Church GM, Parker KK, Pu WT. Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies. Nat Med. 2014 Jun;20(6):616-23. doi: 10.1038/nm.3545. Epub 2014 May 11. PMID: 24813252 PMCID: PMC4172922 read article


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 read article


Yang L, Yang JL, Byrne S, Pan J, Church GM. CRISPR/Cas9-Directed Genome Editing of Cultured Cells. Curr Protoc Mol Biol. 2014 Jul 1;107:31.1.1-17. doi: 10.1002/0471142727.mb3101s107. PMID: 24984853 read article


Xiang M, Birkbak NJ, Vafaizadeh V, Walker SR, Yeh JE, Liu S, Kroll Y, Boldin M, Taganov K, Groner B, Richardson AL, Frank DA. STAT3 induction of miR-146b forms a feedback loop to inhibit the NF-κB to IL-6 signaling axis and STAT3-driven cancer phenotypes. Sci Signal. 2014 Jan 28;7(310):ra11. doi: 10.1126/scisignal.2004497. PMID: 24473196 PMCID: PMC4233120 read article


Xiang M, Birkbak NJ, Vafaizadeh V, Walker SR, Yeh JE, Liu S, Kroll Y, Boldin M, Taganov K, Groner B, Richardson AL, Frank DA. STAT3 induction of miR-146b forms a feedback loop to inhibit the NF-κB to IL-6 signaling axis and STAT3-driven cancer phenotypes. Sci Signal. 2014 Jan 28;7(310):ra11. doi: 10.1126/scisignal.2004497. PMID: 24473196 PMCID: PMC4233120 read article


Yu R, Jih G, Iglesias N, Moazed D. Determinants of heterochromatic siRNA biogenesis and function. Mol Cell. 2014 Jan 23;53(2):262-76. doi: 10.1016/j.molcel.2013.11.014. Epub 2013 Dec 26. PMID: 24374313 PMCID: PMC4357591 read article


Bandopadhayay P, Bergthold G, Nguyen B, Schubert S, Gholamin S, Tang Y, Bolin S, Schumacher SE, Zeid R, Masoud S, Yu F, Vue N, Gibson WJ, Paolella BR, Mitra SS, Cheshier SH, Qi J, Liu KW, Wechsler-Reya R, Weiss WA, Swartling FJ, Kieran MW, Bradner JE, Beroukhim R, Cho YJ. BET bromodomain inhibition of MYC-amplified medulloblastoma. Clin Cancer Res. 2014 Feb 15;20(4):912-25. doi: 10.1158/1078-0432.CCR-13-2281. Epub 2013 Dec 2. PMID 24297863 PMCID: PMC4198154 read article


Sackton KL, Dimova N, Zeng X, Tian W, Zhang M, Sackton TB, Meaders J, Pfaff KL, Sigoillot F, Yu H, Luo X, King RW. Synergistic blockade of mitotic exit by two chemical inhibitors of the APC/C. Nature. 2014 Oct 30;514(7524):646-9. doi: 10.1038/nature13660. Epub 2014 Aug 24. PMID: 25156254 PMCID: PMC4214887 read article


Zhou W, Yuan J. Necroptosis in health and diseases. Semin Cell Dev Biol. 2014 Nov;35:14-23. doi: 10.1016/j.semcdb.2014.07.013. Epub 2014 Aug 1. PMID: 25087983 read article


Degterev A, Zhou W, Maki JL, Yuan J. Assays for necroptosis and activity of RIP kinases. Methods Enzymol. 2014;545:1-33. doi: 10.1016/B978-0-12-801430-1.00001-9. PMID: 25065884 read article


Zhou W, Yuan J. SnapShot: Necroptosis. Cell. 2014 Jul 17;158(2):464-464.e1. doi: 10.1016/j.cell.2014.06.041. PMID: 25036639 read article


top

2013


Albacker CE, Storer NY, Langdon EM, Dibiase A, Zhou Y, Langenau DM, Zon LI. The histone methyltransferase SUV39H1 suppresses embryonal rhabdomyosarcoma formation in zebrafish. PLoS One. 2013 May 21;8(5):e64969. doi: 10.1371/journal.pone.0064969. Print 2013. PMID: 23705022 PMCID: PMC3660348 read article


Kim PG, Albacker CE, Lu YF, Jang IH, Lim Y, Heffner GC, Arora N, Bowman TV, Lin MI, Lensch MW, De Los Angeles A, Zon LI, Loewer S, Daley GQ. Signaling axis involving Hedgehog, Notch, and Scl promotes the embryonic endothelial-to-hematopoietic transition. Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):E141-50. doi: 10.1073/pnas.1214361110. Epub 2012 Dec 12. PMID: 23236128 PMCID: PMC3545793 read article


Amamoto R, Arlotta P. Reshaping the Brain: Direct Lineage Conversion in the Nervous System. F1000Prime Rep. 2013 Sep 2;5:33. doi: 10.12703/P5-33. 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


Hubbard BP, Loh C, Gomes AP, Li J, Lu Q, Doyle TL, Disch JS, Armour SM, Ellis JL, Vlasuk GP, Sinclair DA. Carboxamide SIRT1 inhibitors block DBC1 binding via an acetylation-independent mechanism. Cell Cycle. 2013 Jul 15;12(14):2233-40. doi: 10.4161/cc.25268. PMID: 23892437 PMCID: PMC3755073 read article


Armour SM, Bennett EJ, Braun CR, Zhang XY, McMahon SB, Gygi SP, Harper JW, Sinclair DA. A high-confidence interaction map identifies SIRT1 as a mediator of acetylation of USP22 and the SAGA coactivator complex. Mol Cell Biol. 2013 Apr;33(8):1487-502. doi: 10.1128/MCB.00971-12. Epub 2013 Feb 4. PMID: 23382074 PMCID: PMC3624249 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


Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA. Punctuated evolution of prostate cancer genomes. Cell. 2013 Apr 25;153(3):666-77. doi: 10.1016/j.cell.2013.03.021. PMID: 23622249 PMCID: PMC3690918 read article


Bagchi M, Kim LA, Boucher J, Walshe TE, Kahn CR, D'Amore PA. Vascular endothelial growth factor is important for brown adipose tissue development and maintenance. FASEB J. 2013 Aug;27(8):3257-71. doi: 10.1096/fj.12-221812. Epub 2013 May 16. PMID: 23682123 PMCID: PMC3714576 read article


Long JB, Bagonis M, Lowery LA, Lee H, Danuser G, Van Vactor D. Multiparametric analysis of CLASP-interacting protein functions during interphase microtubule dynamics. Mol Cell Biol. 2013 Apr;33(8):1528-45. doi: 10.1128/MCB.01442-12. PMID: 23382075  read article


Whited JL, Tsai SL, Beier KT, White JN, Piekarski N, Hanken J, Cepko CL, Tabin CJ. Pseudotyped retroviruses for infecting axolotl in vivo and in vitro. Development. 2013 Mar;140(5):1137-46. doi: 10.1242/dev.087734. Epub 2013 Jan 23. PMID: 23344705 PMCID: PMC3583047 read article


Beier KT, Saunders AB, Oldenburg IA, Sabatini BL, Cepko CL. Vesicular stomatitis virus with the rabies virus glycoprotein directs retrograde transsynaptic transport among neurons in vivo. Front Neural Circuits. 2013 Feb 7;7:11. doi: 10.3389/fncir.2013.00011. eCollection 2013. PMID: 23403489 PMCID: PMC3566411 read article


Beier KT, Borghuis BG, El-Danaf RN, Huberman AD, Demb JB, Cepko CL. Transsynaptic tracing with vesicular stomatitis virus reveals novel retinal circuitry. J Neurosci. 2013 Jan 2;33(1):35-51. doi: 10.1523/JNEUROSCI.0245-12.2013. PMID: 23283320 PMCID: PMC3711516 read article


Jiang H, Wang L, Beier KT, Cepko CL, Fekete DM, Brigande JV. Lineage analysis of the late otocyst stage mouse inner ear by transuterine microinjection of a retroviral vector encoding alkaline phosphatase and an oligonucleotide library. PLoS One. 2013 Jul 25;8(7):e69314. doi: 10.1371/journal.pone.0069314. Print 2013. PMID: 23935981 PMCID: PMC3723842 read article


Joyce EF, Apostolopoulos N, Beliveau BJ, Wu CT. Germline progenitors escape the widespread phenomenon of homolog pairing during Drosophila development. PLoS Genet. 2013;9(12):e1004013. doi: 10.1371/journal.pgen.1004013. Epub 2013 Dec 19.PMID: 24385920 PMCID: PMC3868550 read article


Zhang S, Zhang N, Blain JC, Szostak JW. Synthesis of N3'-P5'-linked phosphoramidate DNA by nonenzymatic template-directed primer extension. J Am Chem Soc. 2013 Jan 16;135(2):924-32. doi: 10.1021/ja311164j. Epub 2013 Jan 7. PMID: 23252395 PMCID: PMC3548433 read article


Zhang S, Blain JC, Zielinska D, Gryaznov SM, Szostak JW. Fast and accurate nonenzymatic copying of an RNA-like synthetic genetic polymer. Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17732-7. doi: 10.1073/pnas.1312329110. Epub 2013 Oct 7. PMID: 24101473 PMCID: PMC3816440  read article


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Storer NY, White RM, Uong A, Price E, Nielsen GP, Langenau DM, Zon LI. Zebrafish rhabdomyosarcoma reflects the developmental stage of oncogene expression during myogenesis. Development. 2013 Jul;140(14):3040-50. doi: 10.1242/dev.087858. PMID: 23821038 PMCID: PMC3699286 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


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 read article


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 read article


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 PMCID: PMC4058317 read article


Tajonar A, Maehr R, Hu G, Sneddon JB, Rivera-Feliciano J, Cohen DE, Elledge SJ, Melton DA. Brief report: VGLL4 is a novel regulator of survival in human embryonic stem cells. Stem Cells. 2013 Dec;31(12):2833-41. doi: 10.1002/stem.1445. PMID: 23765749 PMCID: PMC4617635  read article


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 read article


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 PMCID: PMC3983654 read article


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 read article


Schlehe JS, Journel MS, Taylor KP, Amodeo KD, LaVoie MJ. The mitochondrial disease associated protein Ndufaf2 is dispensable for Complex-1 assembly but critical for the regulation of oxidative stress. Neurobiol Dis. 2013 Oct;58:57-67. doi: 10.1016/j.nbd.2013.05.007. Epub 2013 May 20. PMID: 23702311 PMCID: PMC3748239 read article


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 read article


Chung WS, Clarke LE, Wang GX, Stafford BK, Sher A, Chakraborty C, Joung J, Foo LC, Thompson A, Chen C, Smith SJ, Barres BA. Astrocytes mediate synapse elimination through MEGF10 and MERTK pathways. Nature. 2013 Dec 19;504(7480):394-400. doi: 10.1038/nature12776. Epub 2013 Nov 24. PMID: 24270812 PMCID: PMC3969024 read article


Conforti P, Camnasio S, Mutti C, Valenza M, Thompson M, Fossale E, Zeitlin S, MacDonald ME, Zuccato C, Cattaneo E. Lack of huntingtin promotes neural stem cells differentiation into glial cells while neurons expressing huntingtin with expanded polyglutamine tracts undergo cell death. Neurobiol Dis. 2013 Feb;50:160-70. doi: 10.1016/j.nbd.2012.10.015. Epub 2012 Oct 23. PMID: 23089356 read article


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 JH5, Steensma DP, Munoz B, Bittker JA, Shamji AF, Clemons PA, Tolliday NJ, Carpenter AE, Gilliland DG, Stern AM, Moore MAS, 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):840-848. doi: 10.1038/nchembio.1367. Epub 2013 Oct 27. PMID: 24161946 PMCID: PMC4009363 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 read article


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


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 read article


Kelley JM, Tulpule A, Daley GQ. Proteolytic autodigestion: common tissue pathology in Shwachman-Diamond syndrome? Cell Cycle. 2013;12(22):3457-8. doi: 10.4161/cc.26698. Epub 2013 Oct 8. PMID: 24107623 PMCID: PMC3906327  read article


Tulpule A, Kelley JM, Lensch MW, McPherson J, Park IH, Hartung O, Nakamura T, Schlaeger TM, Shimamura A, Daley GQ. Pluripotent stem cell models of Shwachman-Diamond syndrome reveal a common mechanism for pancreatic and hematopoietic dysfunction. Cell Stem Cell. 2013 Jun 6;12(6):727-36. doi: 10.1016/j.stem.2013.04.002. Epub 2013 Apr 18. PMID: 23602541 PMCID: PMC3755012  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


Doulatov S, Vo LT, Chou SS, Kim PG, Arora N, Li H, Hadland BK, Bernstein ID, Collins JJ, Zon LI, Daley GQ. Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. Cell Stem Cell. 2013 Oct 3;13(4):459-70. doi: 10.1016/j.stem.2013.09.002. PMID: 24094326 PMCID: PMC3888026 read article


Tolstorukov MY, Sansam CG, Lu P, Koellhoffer EC, Helming KC, Alver BH, Tillman EJ, Evans JA, Wilson BG, Park PJ, Roberts CW. Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):10165-70. doi: 10.1073/pnas.1302209110. Epub 2013 May 30. PMID: 23723349 PMCID: PMC3690861 read article


Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell. 2013 Jun 6;12(6):699-712. doi: 10.1016/j.stem.2013.04.013. Epub 2013 May 9. PMID: 23665121 PMCID: PMC3725985 read article


Walsh RM, Hochedlinger K. A variant CRISPR-Cas9 system adds versatility to genome engineering. Proc Natl Acad Sci U S A. 2013 Sep 24;110(39):15514-5. doi: 10.1073/pnas.1314697110. Epub 2013 Sep 6. PMID: 24014593 PMCID: PMC3785752 read article


Traag BA, Ramirez-Peralta A, Wang Erickson AF, Setlow P, Losick R. A novel RNA polymerase-binding protein controlling genes involved in spore germination in Bacillus subtilis. Mol Microbiol. 2013 Jul;89(1):113-22. doi: 10.1111/mmi.12262. Epub 2013 Jun 5. PMID: 23678950 PMCID: PMC3694343 read article


Wang CI, Alekseyenko AA, LeRoy G, Elia AE, Gorchakov AA, Britton LM, Elledge SJ, Kharchenko PV, Garcia BA, Kuroda MI. Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol. 2013 Feb;20(2):202-9. doi: 10.1038/nsmb.2477. Epub 2013 Jan 6. PMID: 23295261 PMCID: PMC3674866 read article


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 read article


Eguchi J, Kong X, Tenta M, Wang X, Kang S, Rosen ED. Interferon regulatory factor 4 regulates obesity-induced inflammation through regulation of adipose tissue macrophage polarization. Diabetes. 2013 Oct;62(10):3394-403. doi: 10.2337/db12-1327. Epub 2013 Jul 8. PMID: 23835343 PMCID: PMC3781469 read article


Liu Q, Xu C, Kirubakaran S, Zhang X, Hur W, Liu Y, Kwiatkowski NP, Wang J, Westover KD, Gao P, Ercan D, Niepel M, Thoreen CC, Kang SA, Patricelli MP, Wang Y, Tupper T, Altabef A, Kawamura H, Held KD, Chou DM, Elledge SJ, Janne PA, Wong KK, Sabatini DM, Gray NS. Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM, and ATR. Cancer Res. 2013 Apr 15;73(8):2574-86. doi: 10.1158/0008-5472.CAN-12-1702. Epub 2013 Feb 22. PMID: 23436801 PMCID: PMC3760004 read article


Greig LC, Woodworth MB, Galazo MJ, Padmanabhan H, Macklis JD. Molecular logic of neocortical projection neuron specification, development and diversity. Nat Rev Neurosci. 2013 Nov;14(11):755-69. doi: 10.1038/nrn3586. Epub 2013 Oct 9. PMID: 24105342 PMCID: PMC3876965 read article


Wu MP, Doyle JR, Barry B, Beauvais A, Rozkalne A, Piao X, Lawlor MW, Kopin AS, Walsh CA, Gussoni E. G-protein coupled receptor 56 promotes myoblast fusion through serum response factor- and nuclear factor of activated T-cell-mediated signalling but is not essential for muscle development in vivo. FEBS J. 2013 Dec;280(23):6097-113. doi: 10.1111/febs.12529. Epub 2013 Oct 8. PMID: 24102982 PMCID: PMC3877849 read article


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):909-921. doi: 10.1016/j.cell.2013.10.023. PMID: 24209627 PMCID: PMC3902670  read article


Peters NT, Morlot C, Yang DC, Uehara T, Vernet T, Bernhardt TG. Structure-function analysis of the LytM domain of EnvC, an activator of cell wall remodelling at the Escherichia coli division site. Mol Microbiol. 2013 Aug;89(4):690-701. doi: 10.1111/mmi.12304. Epub 2013 Jul 23. PMID: 23796240 PMCID: PMC3923381 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. Nucleic Acids Res. 2013 Oct;41(19):9049-61. doi: 10.1093/nar/gkt555. Epub 2013 Jul 31. PMID: 23907390 PMCID: PMC3799423 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 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. Nucleic Acids Res. 2013 Oct;41(19):9049-61. doi: 10.1093/nar/gkt555. Epub 2013 Jul 31. PMID: 23907390 PMCID: PMC3799423 read article


Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol. 2013 Sep;31(9):833-8. doi: 10.1038/nbt.2675. Epub 2013 Aug 1. PMID: 23907171 PMCID: PMC3818127 read article


Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. RNA-guided human genome engineering via Cas9. Science. 2013 Feb 15;339(6121):823-6. doi: 10.1126/science.1232033. Epub 2013 Jan 3. PMID: 23287722 PMCID: PMC3712628 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 P, 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 read article


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 read article


Zappaterra MW, LaMantia AS, Walsh CA, Lehtinen MK. Isolation of cerebrospinal fluid from rodent embryos for use with dissected cerebral cortical explants. J Vis Exp. 2013 Mar 11;(73):e50333. doi: 10.3791/50333. PMID: 23524481 PMCID: PMC3635544  read article


Puissant A, Frumm SM, Alexe G, Bassil CF, Qi J, Chanthery YH, Nekritz EA, Zeid R, Gustafson WC, Greninger P, Garnett MJ, McDermott U, Benes CH, Kung AL, Weiss WA, Bradner JE, Stegmaier K. Targeting MYCN in neuroblastoma by BET bromodomain inhibition. Cancer Discov. 2013 Mar;3(3):308-23. doi: 10.1158/2159-8290.CD-12-0418. Epub 2013 Feb 21. PMID: 23430699 PMCID: PMC3672953 read article


Shen RR, Zhou AY, Kim E, O'Connell JT, Hagerstrand D, Beroukhim R, Hahn WC. TRAF2 is an NF-κB-activating oncogene in epithelial cancers. Oncogene. 2015 Jan 8;34(2):209-16. doi: 10.1038/onc.2013.543. Epub 2013 Dec 23. PMID: 24362534 PMCID: PMC4067463 read article


Tu D, Zhu Z, Zhou AY, Yun CH, Lee KE, Toms AV, Li Y, Dunn GP, Chan E, Thai T, Yang S, Ficarro SB, Marto JA, Jeon H, Hahn WC, Barbie DA, Eck MJ. Structure and ubiquitination-dependent activation of TANK-binding kinase 1. Cell Rep. 2013 Mar 28;3(3):747-58. doi: 10.1016/j.celrep.2013.01.033. Epub 2013 Feb 28. PMID: 23453972 PMCID: PMC3863638 read article


Zhou AY, Shen RR, Kim E, Lock YJ, Xu M, Chen ZJ, Hahn WC. IKKε-mediated tumorigenesis requires K63-linked polyubiquitination by a cIAP1/cIAP2/TRAF2 E3 ubiquitin ligase complex. Cell Rep. 2013 Mar 28;3(3):724-33. doi: 10.1016/j.celrep.2013.01.031. Epub 2013 Feb 28. PMID: 23453969 PMCID: PMC4135466 read article


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


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 read article


Ahn S, Spatt D, Winston F. The Schizosaccharomyces pombe inv1+ regulatory region is unusually large and contains redundant cis-acting elements that function in a SAGA- and Swi/Snf-dependent fashion. Eukaryot Cell. 2012 Aug;11(8):1067-74. doi: 10.1128/EC.00141-12. Epub 2012 Jun 15. PMID: 22707486 PMCID: PMC3416058 read article


Pai VP, Aw S, Shomrat T, Lemire JM, Levin M. Transmembrane voltage potential controls embryonic eye patterning in Xenopus laevis. Development. 2012 Jan;139(2):313-23. doi: 10.1242/dev.073759. Epub 2011 Dec 7. PMID: 22159581 PMCID: PMC3243095 read article


Alenghat FJ, Baca QJ, Rubin NT, Pao LI, Matozaki T, Lowell CA, Golan DE, Neel BG, Swanson KD. Macrophages require Skap2 and Sirpα for integrin-stimulated cytoskeletal rearrangement. J Cell Sci. 2012 Nov 15;125(Pt 22):5535-45. doi: 10.1242/jcs.111260. Epub 2012 Sep 12. PMID: 22976304 PMCID: PMC3561861 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


Barbieri CE, Baca SC, Lawrence MS, Demichelis F, Blattner M, Theurillat JP, White TA, Stojanov P, Van Allen E, Stransky N, Nickerson E, Chae SS, Boysen G, Auclair D, Onofrio RC, Park K, Kitabayashi N, MacDonald TY, Sheikh K, Vuong T, Guiducci C, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Hussain WM, Ramos AH, Winckler W, Redman MC, Ardlie K, Tewari AK, Mosquera JM, Rupp N, Wild PJ, Moch H, Morrissey C, Nelson PS, Kantoff PW, Gabriel SB, Golub TR, Meyerson M, Lander ES, Getz G, Rubin MA, Garraway LA. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet. 2012 May 20;44(6):685-9. doi: 10.1038/ng.2279. PMID: 22610119 PMCID: PMC3673022  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. doi: 10.1073/pnas.1203138109. Epub 2012 Apr 27. PMID: 22543161 PMCID: PMC3356608 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. doi: 10.1073/pnas.1203138109. Epub 2012 Apr 27. PMID: 22543161 PMCID: PMC3356608 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


Bick AG, Flannick J, Ito K, Cheng S, Vasan RS, Parfenov MG, Herman DS, DePalma SR, Gupta N, Gabriel SB, Funke BH, Rehm HL, Benjamin EJ, Aragam J, Taylor HA Jr, Fox ER, Newton-Cheh C, Kathiresan S, O'Donnell CJ, Wilson JG, Altshuler DM, Hirschhorn JN, Seidman JG, Seidman C. Burden of rare sarcomere gene variants in the Framingham and Jackson Heart Study cohorts. Am J Hum Genet. 2012 Sep 7;91(3):513-9. doi: 10.1016/j.ajhg.2012.07.017. PMID: 22958901 PMCID: PMC3511985 read article


Bick AG, Calvo SE, Mootha VK. Evolutionary diversity of the mitochondrial calcium uniporter. Science. 2012 May 18;336(6083):886. doi: 10.1126/science.1214977. PMID: 22605770 PMCID: PMC3518847 read article


Bick AG, Calvo SE, Mootha VK. Evolutionary diversity of the mitochondrial calcium uniporter. Science. 2012 May 18;336(6083):886. doi: 10.1126/science.1214977. PMID: 22605770 PMCID: PMC3518847  read article


Boettger LM, Handsaker RE, Zody MC, McCarroll SA. Structural haplotypes and recent evolution of the human 17q21.31 region. Nat Genet. 2012 Jul 1;44(8):881-5. doi: 10.1038/ng.2334. PMID: 22751096 PMCID: PMC4020351 read article


Bowen ME, Henke K, Siegfried KR, Warman ML, Harris MP. Efficient mapping and cloning of mutations in zebrafish by low-coverage whole-genome sequencing. Genetics. 2012 Mar;190(3):1017-24. doi: 10.1534/genetics.111.136069. Epub 2011 Dec 14. PMID: 22174069 PMCID: PMC3296239 read article


Adams A, McBratney-Owen B, Newby B, Bowen ME, Olsen BR, Warman ML. Presphenoidal synchondrosis fusion in DBA/2J mice. Mamm Genome. 2013 Feb;24(1-2):54-62. doi: 10.1007/s00335-012-9437-8. Epub 2012 Nov 21. PMID: 23179633 PMCID: PMC3560942  read article


Kurek KC, Luks VL, Ayturk UM, Alomari AI, Fishman SJ, Spencer SA, Mulliken JB, Bowen ME, Yamamoto GL, Kozakewich HP, Warman ML. Somatic mosaic activating mutations in PIK3CA cause CLOVES syndrome. Am J Hum Genet. 2012 Jun 8;90(6):1108-15. doi: 10.1016/j.ajhg.2012.05.006. Epub 2012 May 31. PMID: 22658544 PMCID: PMC3370283 read article


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Kim TH, Escudero S, Shivdasani RA. Intact function of Lgr5 receptor-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


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