Publications

2009

Abraham J, Kwong JA, Albariño CG, Lu JG, Radoshitzky SR, Salazar-Bravo J, Farzan M, Spiropoulou CF, Choe H.Host-species transferrin receptor 1 orthologs are cellular receptors for nonpathogenic new world clade B arenaviruses. PLoS Pathog. 2009 Apr;5(4):e1000358. Epub 2009 Apr 3. PMID: 19343214

Chen Y, Aguirre AD, Ruvinskaya L, Devor A, Boas DA, Fujimoto JG. Optical coherence tomography (OCT) reveals depth-resolved dynamics during functional brain activation. J Neurosci Methods. 2009 Mar 30;178(1):162-73. Epub 2008 Dec 11. PMID: 19121336

Noguchi Y, Young JD, Aleman JO, Hansen ME, Kelleher JK, Stephanopoulos G. Effect of anaplerotic fluxes and amino acid availability on hepatic lipoapoptosis. J Biol Chem. 2009 Sep 16. [Epub ahead of print] PMID: 19758988

Bajmoczi M, Gadjeva M, Alper SL, Pier GB, Golan DE. Cystic fibrosis transmembrane conductance regulator and caveolin-1 regulate epithelial cell internalization of Pseudomonas aeruginosa. Am J Physiol Cell Physiol. 2009 Aug;297(2):C263-77. Epub 2009 Apr 22. PMID: 19386787

Bryan AW Jr, Menke M, Cowen LJ, Lindquist SL, Berger B. BETASCAN: probable beta-amyloids identified by pairwise probabilistic analysis. PLoS Comput Biol. 2009 Mar;5(3):e1000333. Epub 2009 Mar 27. PMID: 19325876

Reish RG, Zuhaili B, Bergmann J, Aflaki P, Koyama T, Hackl F, Waisbren E, Canseco JA, Verma KD, Eriksson E, Yao F. Modulation of scarring in a liquid environment in the Yorkshire pig. Wound Repair Regen. 2009 Nov-Dec;17(6):806-16. PMID: 19903302

Brock A*, Chang H*, Huang S. Non-genetic heterogeneity--a mutation-independent driving force for the somatic evolution of tumours. Nat Rev Genet. 2009 May;10(5):336-42. PMID: 19337290 *Equal contribution.

Chen YE, Tsokos CG, Biondi EG, Perchuk BS, Laub MT. Dynamics of two phosphorelays controlling cell cycle progression in Caulobacter crescentus. J Bacteriol. 2009 Sep 25. [Epub ahead of print] PMID: 19783630

Cangul MZ, Chretien YR, Gutman R, Rubin DB. Testing treatment effects in unconfounded studies under model misspecification: logistic regression, discretization, and their combination. Stat Med. 2009 Sep 10;28(20):2531-51. PMID: 19572258

Artavanis-Tsakonas K, Weihofen WA, Antos JM, Coleman BI, Comeaux CA, Duraisingh MT, Gaudet R, Ploegh HL. Characterlization and structural studies of the Plasmodium falciparum ubiquitin and Nedd8 hydrolase UCHL3. J Biol Chem. 2009 Dec 30. [Epub ahead of print] PMID: 20042598
 
Desimone TM, Jennings CV, Bei AK, Comeaux C, Coleman BI, Refour P, Triglia T, Stubbs J, Cowman AF, Duraisingh MT. Cooperativity between Plasmodium falciparum adhesive proteins for invasion into erythrocytes. Mol Microbiol. 2009 Apr 14. [Epub ahead of print] PMID: 19400777

Liu Y, Peacey E, Dickson J, Donahue CP, Zheng S, Varani G, Wolfe MS. Mitoxantrone Analogues as Ligands for a Stem-Loop Structure of Tau Pre-mRNA. J Med Chem. 2009 Oct 19. [Epub ahead of print] PMID: 19839622

Dougan M, Dranoff G. The immune response to tumors. Curr Protoc Immunol. 2009 Apr;Chapter 20:Unit 20.11. PMID: 19347848

Lyssiotis CA, Foreman RK, Staerk J, Garcia M, Mathur D, Markoulaki S, Hanna J, Lairson LL, Charette BD, Bouchez LC, Bollong M, Kunick C, Brinker A, Cho CY, Schultz PG, Jaenisch R. Reprogramming of murine fibroblasts to induced pluripotent stem cells with chemical complementation of Klf4. Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8912-7. Epub 2009 May 15. PMID: 19447925

Hanna J, Markoulaki S, Mitalipova M, Cheng AW, Cassady JP, Staerk J, Carey BW, Lengner CJ, Foreman R, Love J, Gao Q, Kim J, Jaenisch R. Metastable pluripotent states in NOD-mouse-derived ESCs. Cell Stem Cell. 2009 Jun 5;4(6):513-24. Epub 2009 May 7. Erratum in: Cell Stem Cell. 2009 Jul 2;5(1):124. PMID: 19427283

Kaplow IM, Singh R, Friedman A, Bakal C, Perrimon N, Berger B. RNAiCut: automated detection of significant genes from functional genomic screens. Nat Methods. 2009 Jul;6(7):476-7. No abstract available. PMID: 19564846

Yang X, Friedman A, Nagpal S, Perrimon N, Asara JM. Use of a label-free quantitative platform based on MS/MS average TIC to calculate dynamics of protein complexes in insulin signaling. J Biomol Tech. 2009 Dec;20(5):272-7. PMID: 19949701

Veerapen N, Brigl M, Garg S, Cerundolo V, Cox LR, Brenner MB, Besra GS. Synthesis and biological activity of alpha-galactosyl ceramide KRN7000 and galactosyl (alpha1-->2) galactosyl ceramide. Bioorg Med Chem Lett. 2009 Aug 1;19(15):4288-91. Epub 2009 May 27. PMID: 19502056

Cohen NR, Garg S, Brenner MB. Antigen Presentation by CD1 Lipids, T Cells, and NKT Cells in Microbial Immunity. Adv Immunol. 2009;102:1-94. Review. PMID: 19477319

Lee JJ, Rauter I, Garibyan L, Ozcan E, Sannikova T, Dillon SR, Cruz AC, Siegel RM, Bram R, Jabara H, Geha RS. The murine equivalent of the A181E TACI mutation associated with common variable immunodeficiency severely impairs B-cell function. Blood. 2009 Sep 10;114(11):2254-62. Epub 2009 Jul 15. PMID: 19605846

Ozcan E*, Garibyan L*, Lee JJ, Bram RJ, Lam KP, Geha RS. Transmembrane activator, calcium modulator, and cyclophilin ligand interactor drives plasma cell differentiation in LPS-activated B cells. J Allergy Clin Immunol. 2009 Jun;123(6):1277-86.e5. Epub 2009 May 8. PMID: 19427685

George PM, Saigal R, Lawlor MW, Moore MJ, LaVan DA, Marini RP, Selig M, Makhni M, Burdick JA, Langer R, Kohane DS. Three-dimensional conductive constructs for nerve regeneration. J Biomed Mater Res A. 2009 Nov;91(2):519-27. PMID: 18985787

Shim JH, Greenblatt MB, Xie M, Schneider MD, Zou W, Zhai B, Gygi S, Glimcher LH. TAK1 is an essential regulator of BMP signalling in cartilage. EMBO J. 2009 Jul 22;28(14):2028-41. Epub 2009 Jun 18. PMID: 19536134

Geiben-Lynn R, Greenland JR, Frimpong-Boateng K, Letvin NL. Non-classical natural killer T cells modulate plasmid DNA vaccine antigen expression and vaccine-elicited immune responses by MCP-1 secretion after interaction with a beta-2-microglobulin-independent CD1d. J Biol Chem. 2009 Oct 15. [Epub ahead of print] PMID: 19833737

Scholz J, Mannion RJ, Hord DE, Griffin RS, Rawal B, Zheng H, Scoffings D, Phillips A, Guo J, Laing RJ, Abdi S, Decosterd I, Woolf CJ. A novel tool for the assessment of pain: validation in low back pain. PLoS Med. 2009 Apr 7;6(4):e1000047. Epub 2009 Apr 7. PMID: 19360087

Beltman JB, Henrickson SE, von Andrian UH, de Boer RJ, Marée AF. Towards estimating the true duration of dendritic cell interactions with T cells. J Immunol Methods. 2009 Aug 15;347(1-2):54-69. Epub 2009 Jun 9. PMID: 19520083

Johnson MD, He L, Herman D, Wakimoto H, Wallace CA, Zidek V, Mlejnek P, Musilova A, Simakova M, Vorlicek J, Kren V, Viklicky O, Qi NR, Wang J, Seidman CE, Seidman J, Kurtz TW, Aitman TJ, Pravenec M. Dissection of chromosome 18 blood pressure and salt-sensitivity quantitative trait loci in the spontaneously hypertensive rat. Hypertension. 2009 Sep;54(3):639-45. Epub 2009 Jul 20. PMID: 19620519

Body SC, Collard CD, Shernan SK, Fox AA, Liu KY, Ritchie MD, Perry TE, Muehlschlegel JD, Aranki S, Donahue BS, Pretorius M, Estrada JC, Ellinor PT, Newton-Cheh C, Seidman CE, Seidman JG, Herman DS, Lichtner P, Meitinger T, Pfeufer A, Kääb S, Brown NJ, Roden DM, Darbar D. Variation in the 4q25 chromosomal locus predicts atrial fibrillation after coronary artery bypass graft surgery. Circ Cardiovasc Genet. 2009 Oct;2(5):499-506. Epub 2009 Aug 2. PMID: 20031626

Fox AA, Collard CD, Shernan SK, Seidman CE, Seidman JG, Liu KY, Muehlschlegel JD, Perry TE, Aranki SF, Lange C, Herman DS, Meitinger T, Lichtner P, Body SC. Natriuretic peptide system gene variants are associated with ventricular dysfunction after coronary artery bypass grafting. Anesthesiology. 2009 Apr;110(4):738-47. PMID: 19326473

Herman DS, Hovingh GK, Iartchouk O, Rehm HL, Kucherlapati R, Seidman JG, Seidman CE. Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection. Nat Methods. 2009 Jul;6(7):507-10. Epub 2009 Jun 21. PMID: 19543287

Herrington TM, Masse NY, Hachmeh KJ, Smith JE, Assad JA, Cook EP. The effect of microsaccades on the correlation between neural activity and behavior in middle temporal, ventral intraparietal, and lateral intraparietal areas. J Neurosci. 2009 May 6;29(18):5793-805. PMID: 19420247

Herrington TM, Assad JA. Neural activity in the middle temporal area and lateral intraparietal area during endogenously cued shifts of attention. J Neurosci. 2009 Nov 11;29(45):14160-76. PMID: 19906965

Hollenhorst MA, Clardy J, Walsh CT. The ATP-Dependent Amide Ligases DdaG and DdaF Assemble the Fumaramoyl-Dipeptide Scaffold of the Dapdiamide Antibiotics. Biochemistry. 2009 Oct 6. [Epub ahead of print] PMID: 19807062

Horng S, Kreiman G, Ellsworth C, Page D, Blank M, Millen K, Sur M. Differential gene expression in the developing lateral geniculate nucleus and medial geniculate nucleus reveals novel roles for Zic4 and Foxp2 in visual and auditory pathway development. J Neurosci. 2009 Oct 28;29(43):13672-83. PMID: 19864579

Huffaker SJ, Chen J, Nicodemus KK, Sambataro F, Yang F, Mattay V, Lipska BK, Hyde TM, Song J, Rujescu D, Giegling I, Mayilyan K, Proust MJ, Soghoyan A, Caforio G, Callicott JH, Bertolino A, Meyer-Lindenberg A, Chang J, Ji Y, Egan MF, Goldberg TE, Kleinman JE, Lu B, Weinberger DR. A primate-specific, brain isoform of KCNH2 affects cortical physiology, cognition, neuronal repolarization and risk of schizophrenia. Nat Med. 2009 May;15(5):509-18. Epub 2009 May 3. PMID:19412172

Berg J, Hung YP, Yellen G. A genetically encoded fluorescent reporter of ATP:ADP ratio. Nature Methods 2009 Feb;6(2):161-6. PMID: 19122669.

LaFemina J, Roberts PA, Hung YP, Gusella JF, Sahani D, Fernández-del Castillo C, Warshaw AL, Thayer SP. Identification of a novel kindred with familial pancreatitis and pancreatic cancer. Pancreatology. 2009;9(3):273-9. Epub 2009 Apr 29. PMID: 19407482

Huynh MA, Stegmüller J, Litterman N, Bonni A. Regulation of Cdh1-APC function in axon growth by Cdh1 phosphorylation. J Neurosci. 2009 Apr 1;29(13):4322-7. PMID: 19339626

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

Iweala OI*, Smith DW*, Matharu KS, Sada-Ovalle I, Nguyen DD, Dekruyff RH, Umetsu DT, Behar SM, Nagler CR. Vaccine-Induced Antibody Isotypes Are Skewed by Impaired CD4 T Cell and Invariant NKT Cell Effector Responses in MyD88-Deficient Mice. J Immunol. 2009 Aug 15;183(4):2252-60. Epub 2009 Jul 20. PMID: 19620295 *Equal contribution.

Matharu KS, Mizoguchi E, Cotoner CA, Nguyen DD, Mingle B, Iweala OI, McBee ME, Stefka AT, Prioult G, Haigis KM, Bhan AK, Snapper SB, Murakami H, Schauer DB, Reinecker HC, Mizoguchi A, Nagler CR.. Toll-like receptor 4-mediated regulation of spontaneous Helicobacter-dependent colitis in IL-10-deficient mice. Gastroenterology. 2009 Oct;137(4):1380-90.e1-3. Epub 2009 Aug 3. PMID: 19596011

Jadhav AP, Roesch K, Cepko CL. Development and neurogenic potential of Müller glial cells in the vertebrate retina. Prog Retin Eye Res. 2009 Jul;28(4):249-62. Epub 2009 May 22. Review. PMID: 19465144

Lee YN, Alt FW, Reyes J, Gleason M, Zarrin AA, Jung D. Differential utilization of T cell receptor TCRalpha/TCRdelta locus variable region gene segments is mediated by accessibility. Proc Natl Acad Sci U S A. 2009 Oct 13;106(41):17487-92. Epub 2009 Sep 28. PMID: 19805067

Chen R, Khormaee S, Eccleston ME, Slater NK. Effect of L-leucine graft content on aqueous solution behavior and membrane-lytic activity of a pH-responsive pseudopeptide. Biomacromolecules. 2009 Sep 14;10(9):2601-8. PMID: 19642668

Chen R, Khormaee S, Eccleston ME, Slater NK.The role of hydrophobic amino acid grafts in the enhancement of membrane-disruptive activity of pH-responsive pseudo-peptides. Biomaterials. 2009 Apr;30(10):1954-61. Epub 2009 Jan 12. PMID: 19138797

Emery CM, Vijayendran KG, Zipser MC, Sawyer AM, Niu L, Kim JJ, Hatton C, Chopra R, Oberholzer PA, Karpova MB, Macconaill LE, Zhang J, Gray NS, Sellers WR, Dummer R, Garraway LA. MEK1 mutations confer resistance to MEK and B-RAF inhibition. Proc Natl Acad Sci U S A. 2009 Nov 13. [Epub ahead of print]PMID: 19915144

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

Roach KL, King KR, Uygun BE, Kohane IS, Yarmush ML, Toner M. High throughput single cell bioinformatics. Biotechnol Prog. 2009 Oct 14. [Epub ahead of print] PMID: 19830811

Patel SJ, King KR, Casali M, Yarmush ML. DNA-triggered innate immune responses are propagated by gap junction communication. Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12867-72. Epub 2009 Jul 17. PMID: 19617563

Yarmush ML, King KR. Living-cell microarrays. Annu Rev Biomed Eng. 2009;11:235-57. Review. PMID: 19413510

Roach KL, King KR, Uygun K, Hand SC, Kohane IS, Yarmush ML, Toner M. High-throughput single cell arrays as a novel tool in biopreservation. Cryobiology. 2009 Jun;58(3):315-21. Epub 2009 Mar 19. PMID: 19303403

Janorkar AV, King KR, Megeed Z, Yarmush ML. Development of an in vitro cell culture model of hepatic steatosis using hepatocyte-derived reporter cells. Biotechnol Bioeng. 2009 Apr 1;102(5):1466-74. PMID: 19061238

Koffie RM, Meyer-Luehmann M, Hashimoto T, Adams KW, Mielke ML, Garcia-Alloza M, Micheva KD, Smith SJ, Kim ML, Lee VM, Hyman BT, Spires-Jones TL. Oligomeric amyloid beta associates with postsynaptic densities and correlates with excitatory synapse loss near senile plaques. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):4012-7. Epub 2009 Feb 19.PMID: 19228947

Serluca FC, Xu B, Okabe N, Baker K, Lin SY, Sullivan-Brown J, Konieczkowski DJ, Jaffe KM, Bradner JM, Fishman MC, Burdine RD. Mutations in zebrafish leucine-rich repeat-containing six-like affect cilia motility and result in pronephric cysts, but have variable effects on left-right patterning. Development. 2009 May;136(10):1621-31.

Schwer B, Eckersdorff M, Li Y, Silva JC, Fermin D, Kurtev MV, Giallourakis C, Comb MJ, Alt FW, Lombard DB. Calorie restriction alters mitochondrial protein acetylation. Aging Cell. 2009 Sep;8(5):604-6. Epub 2009 Jul 9. PMID: 19594485

Hoyer KK, Kuswanto WF, Gallo E, Abbas AK. Distinct roles of helper T-cell subsets in a systemic autoimmune disease. Blood. 2009 Jan 8;113(2):389-95. Epub 2008 Sep 24. PMID: 18815283 PMC2615653

O’Gorman WE, Dooms H, Thorne SH, Kuswanto WF, Simonds EF, Krutzik PO, Nolan G, Abbas AK. The initial phase of an immune response functions to activate regulatory T cells. J Immunol. 2009 Jul 1;183(1):332-9. PMID: 19542444 PMCID: PMC2753472

Ladapo JA, Horwitz JR, Weinstein MC, Gazelle GS, Cutler DM. Adoption And Spread Of New Imaging Technology: A Case Study. Health Aff (Millwood). 2009 Oct 14. [Epub ahead of print] PMID: 19828487

Ladapo JA, Jaffer FA, Hoffmann U, Thomson CC, Bamberg F, Dec W, Cutler DM, Weinstein MC, Gazelle GS. Clinical outcomes and cost-effectiveness of coronary computed tomography angiography in the evaluation of patients with chest pain. J Am Coll Cardiol. 2009 Dec 15;54(25):2409-22. PMID: 20082932

Vakoc BJ*, Lanning RM*, Tyrrell JA, Padera TP, Bartlett LA, Stylianopoulos T, Munn LL, Tearney GJ, Fukumura D, Jain RK, Bouma BE. Three-dimensional microscopy of the tumor microenvironment in vivo using optical frequency domain imaging. Nat Med. 2009 Oct;15(10):1219-23. Epub 2009 Sep 13. PMID: 19749772

Chauhan VP, Lanning RM, Diop-Frimpong B, Mok W, Brown EB, Padera TP, Boucher Y, Jain RK. Multiscale measurements distinguish cellular and interstitial hindrances to diffusion in vivo. Biophys J. 2009 Jul 8;97(1):330-6. PMID: 19580771

Tzafriri AR, Levin AD, Edelman ER. Diffusion-limited binding explains binary dose response for local arterial and tumour drug delivery. Cell Prolif. 2009 Jun;42(3):348-63. Epub 2009 Mar 31. PMID: 19438899

Lu TK, Khalil AS, Collins JJ. Next-generation synthetic gene networks. Nat Biotechnol. 2009 Dec;27(12):1139-50. PMID: 20010597

Friedland AE, Lu TK, Wang X, Shi D, Church G, Collins JJ. Synthetic gene networks that count. Science. 2009 May 29;324(5931):1199-202.PMID: 19478183

Lu TK, Collins JJ. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4629-34. Epub 2009 Mar 2. PMID: 19255432

Walshe TE, Dole VS, Maharaj AS, Patten IS, Wagner DD, D'Amore PA. Inhibition of VEGF or TGF-{beta} signaling activates endothelium and increases leukocyte rolling. Arterioscler Thromb Vasc Biol. 2009 Aug;29(8):1185-92. Epub 2009 May 21. PMID: 19461051

Walshe TE, Saint-Geniez M, Maharaj AS, Sekiyama E, Maldonado AE, D'Amore PA. TGF-beta is required for vascular barrier function, endothelial survival and homeostasis of the adult microvasculature. PLoS One. 2009;4(4):e5149. Epub 2009 Apr 2. PMID: 19340291

Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, Dunn IF, Schinzel AC, Sandy P, Meylan E, Scholl C, Fröhling S, Chan EM, Sos ML, Michel K, Mermel C, Silver SJ, Weir BA, Reiling JH, Sheng Q, Gupta PB, Wadlow RC, Le H, Hoersch S, Wittner BS, Ramaswamy S, Livingston DM, Sabatini DM, Meyerson M, Thomas RK, Lander ES, Mesirov JP, Root DE, Gilliland DG, Jacks T, Hahn WC. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009 Oct 21. [Epub ahead of print] PMID: 19847166

Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, Kim SY, Wardwell L, Tamayo P, Gat-Viks I, Ramos AH, Woo MS, Weir BA, Getz G, Beroukhim R, O'Kelly M, Dutt A, Rozenblatt-Rosen O, Dziunycz P, Komisarof J, Chirieac LR, Lafargue CJ, Scheble V, Wilbertz T, Ma C, Rao S, Nakagawa H, Stairs DB, Lin L, Giordano TJ, Wagner P, Minna JD, Gazdar AF, Zhu CQ, Brose MS, Cecconello I, Jr UR, Marie SK, Dahl O, Shivdasani RA, Tsao MS, Rubin MA, Wong KK, Regev A, Hahn WC, Beer DG, Rustgi AK, Meyerson M. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet. 2009 Nov;41(11):1238-42. Epub 2009 Oct 4. PMID: 19801978

Ramos AH, Dutt A, Mermel C, Perner S, Cho J, Lafargue CJ, Johnson LA, Stiedl AC, Tanaka KE, Bass AJ, Barretina J, Weir BA, Beroukhim R, Thomas RK, Minna JD, Chirieac LR, Lindeman NI, Giordano T, Beer DG, Wagner P, Wistuba II, Rubin MA, Meyerson M. Amplification of chromosomal segment 4q12 in non-small cell lung cancer. Cancer Biol Ther. 2009 Nov 7;8(21). [Epub ahead of print] PMID: 19755855

Viswanathan SR, Mermel CH, Lu J, Lu CW, Golub TR, Daley GQ.microRNA expression during trophectoderm specification. PLoS One. 2009 Jul 3;4(7):e6143. PMID: 19582159

Viswanathan SR, Powers JT, Einhorn W, Hoshida Y, Ng TL, Toffanin S, O'Sullivan M, Lu J, Phillips LA, Lockhart VL, Shah SP, Tanwar PS, Mermel CH, Beroukhim R, Azam M, Teixeira J, Meyerson M, Hughes TP, Llovet JM, Radich J, Mullighan CG, Golub TR, Sorensen PH, Daley GQ.Lin28 promotes transformation and is associated with advanced human malignancies. Nat Genet. 2009 Jul;41(7):843-8. Epub 2009 May 31. PMID: 19483683

Sos ML, Michel K, Zander T, Weiss J, Frommolt P, Peifer M, Li D, Ullrich R, Koker M, Fischer F, Shimamura T, Rauh D, Mermel C, Fischer S, Stückrath I, Heynck S, Beroukhim R, Lin W, Winckler W, Shah K, LaFramboise T, Moriarty WF, Hanna M, Tolosi L, Rahnenführer J, Verhaak R, Chiang D, Getz G, Hellmich M, Wolf J, Girard L, Peyton M, Weir BA, Chen TH, Greulich H, Barretina J, Shapiro GI, Garraway LA, Gazdar AF, Minna JD, Meyerson M, Wong KK, Thomas RK.Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions. J Clin Invest. 2009 Jun;119(6):1727-40. doi: 10.1172/JCI37127. Epub 2009 May 18. PMID: 19451690

Sos ML, Koker M, Weir BA, Heynck S, Rabinovsky R, Zander T, Seeger JM, Weiss J, Fischer F, Frommolt P, Michel K, Peifer M, Mermel C, Girard L, Peyton M, Gazdar AF, Minna JD, Garraway LA, Kashkar H, Pao W, Meyerson M, Thomas RK. PTEN loss contributes to erlotinib resistance in EGFR-mutant lung cancer by activation of Akt and EGFR. Cancer Res. 2009 Apr 15;69(8):3256-61. Epub 2009 Apr 7. PMID: 19351834

Etemadmoghadam D, deFazio A, Beroukhim R, Mermel C, George J, Getz G, Tothill R, Okamoto A, Raeder MB, Harnett P, Lade S, Akslen LA, Tinker AV, Locandro B, Alsop K, Chiew YE, Traficante N, Fereday S, Johnson D, Fox S, Sellers W, Urashima M, Salvesen HB, Meyerson M, Bowtell D; AOCS Study Group. Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas. Clin Cancer Res. 2009 Feb 15;15(4):1417-27. Epub 2009 Feb 3. PMID: 19193619

Hofmann I, Stover EH, Cullen DE, Mao J, Morgan KJ, Lee BH, Kharas MG, Miller PG, Cornejo MG, Okabe R, Armstrong SA, Ghilardi N, Gould S, de Sauvage FJ, McMahon AP, Gilliland DG. Hedgehog signaling is dispensable for adult murine hematopoietic stem cell function and hematopoiesis. Cell Stem Cell. 2009 Jun 5;4(6):559-67.PMID: 19497284

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

Molyneaux BJ, Arlotta P, Fame RM, MacDonald JL, MacQuarrie KL, Macklis JD. Novel subtype-specific genes identify distinct subpopulations of callosal projection neurons. J Neurosci. 2009 Sep 30;29(39):12343-54. PMID: 19793993

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

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

Ng SY, Yoshida T, Zhang J, Georgopoulos K. Genome-wide lineage-specific transcriptional networks underscore Ikaros-dependent lymphoid priming in hematopoietic stem cells. Immunity. 2009 Apr 17;30(4):493-507. Epub 2009 Apr 2. PMID: 19345118

Lattanzi R, Grant AK, Polimeni JR, Ohliger MA, Wiggins GC, Wald LL, Sodickson DK. Performance evaluation of a 32-element head array with respect to the ultimate intrinsic SNR. NMR Biomed. 2009 Nov 10. [Epub ahead of print] PMID: 19904727

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML Diversity and complexity in DNA recognition by transcription factors. Science. 2009 Jun 26;324(5935):1720-3. Epub 2009 May 14. PMID: 19443739

Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML. High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 2009 Apr;19(4):556-66. Epub 2009 Jan 21. PMID: 19158363

Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR. Predicting the binding preference of transcription factors to individual DNA k-mers. Bioinformatics. 2009 Apr 15;25(8):1012-8. Epub 2008 Dec 16. PMID: 19088121

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

Kim AH, Puram SV, Bilimoria PM, Ikeuchi Y, Keough S, Wong M, Rowitch D, Bonni A. Centrosomal Cdc20-APC Pathway Controls Dendrite Morphogenesis in Postmitotic Neurons. Cell. 2009 Jan 23;136(2):322-36. PMID: 19167333

Eide PK, Rapoport RI, Gormley WB, Madsen JR. A dynamic nonlinear relationship between the static and pulsatile components of intracranial pressure in patients with subarachnoid hemorrhage. Journal of Neurosurgery (4 September 2009, E-publication ahead of print).

Rapoport BI, Wattanapanitch W, Penagos HL, Musallam S, Andersen RA, Sarpeshkar R. A biomimetic adaptive algorithm and low-power architecture for implantable neural decoders. Conf Proc IEEE Eng Med Biol Soc. 2009;1:4214-7. PMID: 19964345

Aptekar JW, Cassidy MC, Johnson AC, Barton RA, Lee M, Ogier AC, Vo C, Anahtar MN, Ren Y, Bhatia SN, Ramanathan C, Cory DG, Hill AL, Mair RW, Rosen MS, Walsworth RL, Marcus CM. Silicon nanoparticles as hyperpolarized magnetic resonance imaging agents. ACS Nano. 2009 Dec 22;3(12):4003-8. PMID: 19950973

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