Publications

Author ID

Chen Z, Cornish VW, Min W. 2013. Chemical tags: inspiration for advanced imaging techniques.. Curr Opin Chem Biol. ▶ Go to Pubmed

Jing C, Cornish VW. 2013. A fluorogenic TMP-tag for high signal-to-background intracellular live cell imaging.. ACS Chem Biol. ▶ Go to Pubmed

Chen J, Repunte-Canonigo V, Kawamura T, Lefebvre C, Shin W, Howell LL, Hemby SE, Harvey BK, Califano A, Morales M, Koob GF, Sanna PPaolo. 2013. Hypothalamic proteoglycan syndecan-3 is a novel cocaine addiction resilience factor.. Nat Commun. 4:1955.▶ Go to Pubmed

Tosello V, Ferrando A. 2013. The NOTCH signaling pathway: role in the pathogenesis of T-cell acute lymphoblastic leukemia and implication for therapy.. Ther Adv Hematol. 4(3):199-210.▶ Go to Pubmed

Kim THun, Chung KYoung, Manglik A, Hansen AL, Dror RO, Mildorf TJ, Shaw DE, Kobilka BK, R Prosser S. 2013. The role of ligands on the equilibria between functional states of a G protein-coupled receptor.. J Am Chem Soc. 135(25):9465-74.▶ Go to Pubmed

J Haydu E, Ferrando A. 2013. Early T-cell precursor acute lymphoblastic leukaemia.. Curr Opin Hematol. 20(4):369-73.▶ Go to Pubmed

Van Vlierberghe P, Ambesi-Impiombato A, De Keersmaecker K, Hadler M, Paietta E, Tallman MS, Rowe JM, Forne C, Rue M, Ferrando A. 2013. Prognostic relevance of integrated genetic profiling in adult T-cell acute lymphoblastic leukemia.. Blood. 122(1):74-82.▶ Go to Pubmed

Zhang C, Lee K-Y, Swanson MS, Darnell RB. 2013. Prediction of clustered RNA-binding protein motif sites in the mammalian genome.. Nucleic Acids Res. ▶ Go to Pubmed

Amir E-ADavid, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D. 2013. viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.. Nat Biotechnol. ▶ Go to Pubmed

Shen MM. 2013. Chromoplexy: a new category of complex rearrangements in the cancer genome.. Cancer Cell. 23(5):567-9.▶ Go to Pubmed

Bardot ES, Valdes VJ, Zhang J, Perdigoto CN, Nicolis S, Hearn SA, Silva J, Ezhkova E. 2013. Polycomb subunits Ezh1 and Ezh2 regulate the Merkel cell differentiation program in skin stem cells.. EMBO J. ▶ Go to Pubmed

Tabbò F, Ponzoni M, Rabadan R, Bertoni F, Inghirami G. 2013. Beyond NPM-anaplastic lymphoma kinase driven lymphomagenesis: alternative drivers in anaplastic large cell lymphoma.. Curr Opin Hematol. ▶ Go to Pubmed

Bilal E, Dutkowski J, Guinney J, Jang ISock, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Vollan HKristian M, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez M, Kristensen VN, Aparicio S, Børresen-Dale A-L, Caldas C, Califano A, Friend S, Ideker T, Schadt E, Stolovitzky G, Margolin A. 2013. Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling.. PLoS Comput Biol. 9(5):e1003047.▶ Go to Pubmed

Zaidi S, Choi M, Wakimoto H, Ma L, Jiang J, Overton JD, Romano-Adesman A, Bjornson RD, Breitbart RE, Brown KK, Carriero NJ, Cheung YHim, Deanfield J, Depalma S, Fakhro KA, Glessner J, Hakonarson H, Italia MJ, Kaltman JR, Kaski J, Kim R, Kline JK, Lee T, Leipzig J, Lopez A, Mane SM, Mitchell LE, Newburger JW, Parfenov M, Pe'er I, Porter G, Roberts AE, Sachidanandam R, Sanders SJ, Seiden HS, State MW, Subramanian S, Tikhonova IR, Wang W, Warburton D, White PS, Williams IA, Zhao H, Seidman JG, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Seidman CE, Lifton RP. 2013. De novo mutations in histone-modifying genes in congenital heart disease.. Nature. ▶ Go to Pubmed

Califano A, Kellis M, Stolovitzky G. 2013. Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue.. J Comput Biol. 20(5):373-4.▶ Go to Pubmed

Keniry M, Pires MM, Mense S, Lefebvre C, Gan B, Justiano K, Lau Y-KIngar, Hopkins B, Hodakoski C, Koujak S, Toole J, Fenton F, Calahan A, Califano A, Depinho RA, Maurer M, Parsons R. 2013. Survival factor NFIL3 restricts FOXO-induced gene expression in cancer.. Genes Dev. 27(8):916-27.▶ Go to Pubmed

Gill R, Cheung YHim, Shen Y, Lanzano P, Mirza NM, Ten S, Maclaren NK, Motaghedi R, Han JC, Yanovski JA, Leibel RL, Chung WK. 2013. Whole-exome sequencing identifies novel LEPR mutations in individuals with severe early onset obesity.. Obesity (Silver Spring). ▶ Go to Pubmed

Zhang W, Hui KY, Gusev A, Warner N, Ng SMeng, Ferguson J, Choi M, Burberry A, Abraham C, Mayer L, Desnick R, Cardinale CJ, Hakonarson H, Waterman M, Chowers Y, Karban A, Brant S, Silverberg MS, Gregersen PK, Katz S, Lifton RP, Zhao H, Nuñez G, Pe'er I, Peter I, Cho J. 2013. Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3.. Genes Immun. ▶ Go to Pubmed

Taylor S, Wang J, Kostic N, Stojanovic MN. 2013. Monovalent streptavidin that senses oligonucleotides.. Angew Chem Int Ed Engl. 52(21):5509-12.▶ Go to Pubmed

Hu J, Locasale JW, Bielas JH, O'Sullivan J, Sheahan K, Cantley LC, Heiden MGVander, Vitkup D. 2013. Heterogeneity of tumor-induced gene expression changes in the human metabolic network.. Nat Biotechnol. ▶ Go to Pubmed

Destefano GM, Fantauzzo KA, Petukhova L, Kurban M, Tadin-Strapps M, Levy B, Warburton D, Cirulli ET, Han Y, Sun X, Shen Y, Shirazi M, Jobanputra V, Cepeda-Valdes R, Salas-Alanis JCesar, Christiano AM. 2013. Position effect on FGF13 associated with X-linked congenital generalized hypertrichosis.. Proc Natl Acad Sci U S A. 110(19):7790-5.▶ Go to Pubmed

Cheng W-Y, Yang T-HOu, Anastassiou D. 2013. Development of a prognostic model for breast cancer survival in an open challenge environment.. Sci Transl Med. 5(181):181ra50.▶ Go to Pubmed

Jensen MØ, Jogini V, Eastwood MP, Shaw DE. 2013. Atomic-level simulation of current-voltage relationships in single-file ion channels.. J Gen Physiol. 141(5):619-32.▶ Go to Pubmed

Ferino G, Cadoni E, Matos MJoão, Quezada E, Uriarte E, Santana L, Vilar S, Tatonetti N, Yáñez M, Viña D, Picciau C, Serra S, Delogu G. 2013. MAO Inhibitory Activity of 2-Arylbenzofurans versus 3-Arylcoumarins: Synthesis, in vitro Study, and Docking Calculations.. ChemMedChem. 8(6):956-66.▶ Go to Pubmed

Varma H, Gangadhar NM, Letso R, Wolpaw AJ, Sriramaratnam R, Stockwell BR. 2013. Identification of a small molecule that induces ATG5-and-cathepsin-l-dependent cell death and modulates polyglutamine toxicity.. Exp Cell Res. ▶ Go to Pubmed

Shan Y, Arkhipov A, Kim ET, Pan AC, Shaw DE. 2013. Transitions to catalytically inactive conformations in EGFR kinase.. Proc Natl Acad Sci U S A. 110(18):7270-5.▶ Go to Pubmed

Lazarovici A, Zhou T, Shafer A, Machado ACarolina D, Riley T, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker H. 2013. Probing DNA shape and methylation state on a genomic scale with DNase I.. Proc Natl Acad Sci U S A. 110(16):6376-81.▶ Go to Pubmed

Wu J, Anczuków O, Krainer AR, Zhang MQ, Zhang C. 2013. OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.. Nucleic Acids Res. 41(10):5149-5163.▶ Go to Pubmed

Delto JC, Kobayashi T, Benson M, McKiernan J, Abate-Shen C. 2013. Preclinical analyses of intravesical chemotherapy for prevention of bladder cancer progression.. Oncotarget. 4(2):269-76.▶ Go to Pubmed

Jin F, Irshad S, Yu W, Belakavadi M, Chekmareva M, Ittmann MM, Abate-Shen C, Fondell JD. 2013. ERK and AKT signaling pathways promote MED1 overexpression in prostate cancer cells in association with elevated proliferation and tumorigenicity.. Mol Cancer Res. ▶ Go to Pubmed

Trifonov V, Pasqualucci L, Dalla-Favera R, Rabadan R. 2013. MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples.. BMC Syst Biol. 7(1):25.▶ Go to Pubmed

Wu Y, Honig B, Ben-Shaul A. 2013. Theory and simulations of adhesion receptor dimerization on membrane surfaces.. Biophys J. 104(6):1221-9.▶ Go to Pubmed

Vilar S, Uriarte E, Santana L, Tatonetti N, Friedman C. 2013. Detection of drug-drug interactions by modeling interaction profile fingerprints.. PLoS One. 8(3):e58321.▶ Go to Pubmed

Finck R, Simonds EF, Jager A, Krishnaswamy S, Sachs K, Fantl W, Pe'er D, Nolan GP, Bendall SC. 2013. Normalization of mass cytometry data with bead standards.. Cytometry A. ▶ Go to Pubmed

Sonabend AM, Yun J, Lei L, Leung R, Soderquist C, Crisman C, Gill BJ, Carminucci A, Sisti J, Castelli M, Sims PA, Bruce JN, Canoll P. 2013. Murine cell line model of proneural glioma for evaluation of anti-tumor therapies.. J Neurooncol. 112(3):375-82.▶ Go to Pubmed

Piana S, Lindorff-Larsen K, Shaw DE. 2013. Atomic-level description of ubiquitin folding.. Proc Natl Acad Sci U S A. 110(15):5915-20.▶ Go to Pubmed

Letso R, Bauer AJ, Lunn MR, Yang WSeok, Stockwell BR. 2013. Small Molecule Screen Reveals Regulation of Survival Motor Neuron Protein Abundance by Ras Proteins.. ACS Chem Biol. ▶ Go to Pubmed

Matos MJoão, Vilar S, Gonzalez-Franco RM, Uriarte E, Santana L, Friedman C, Tatonetti N, Viña D, Fontenla JAngel. 2013. Novel (coumarin-3-yl)carbamates as selective MAO-B inhibitors: Synthesis, in vitro and in vivo assays, theoretical evaluation of ADME properties and docking study.. Eur J Med Chem. 63C:151-161.▶ Go to Pubmed

Cheng W-Y, Yang T-HOu, Anastassiou D. 2013. Biomolecular events in cancer revealed by attractor metagenes.. PLoS Comput Biol. 9(2):e1002920.▶ Go to Pubmed

White RW, Tatonetti N, Shah NH, Altman R, Horvitz E. 2013. Web-scale pharmacovigilance: listening to signals from the crowd.. J Am Med Inform Assoc. 20(3):404-8.▶ Go to Pubmed

Pan AC, Borhani DW, Dror RO, Shaw DE. 2013. Molecular determinants of drug-receptor binding kinetics.. Drug Discov Today. ▶ Go to Pubmed

Wang ZA, Mitrofanova A, Bergren SK, Abate-Shen C, Cardiff RD, Califano A, Shen MM. 2013. Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity.. Nat Cell Biol. 15(3):274-83.▶ Go to Pubmed

Singh APal, Zafer S, Pe'er I. 2013. Metaseq: privacy preserving meta-analysis of sequencing-based association studies.. Pac Symp Biocomput. :356-67.▶ Go to Pubmed

Ostrov N, Wingler LM, Cornish VW. 2013. Gene assembly and combinatorial libraries in S. cerevisiae via reiterative recombination.. Methods Mol Biol. 978:187-203.▶ Go to Pubmed

Romanini DW, Peralta-Yahya P, Mondol V, Cornish VW. 2012. A Heritable Recombination System for Synthetic Darwinian Evolution in Yeast.. ACS Synth Biol. 1(12):602-609.▶ Go to Pubmed

Jia AY, Castillo-Martin M, Domingo-Domenech J, Bonal DM, Sánchez-Carbayo M, Silva J, Cordon-Cardo C. 2013. A Common MicroRNA Signature Consisting of miR-133a, miR-139-3p, and miR-142-3p Clusters Bladder Carcinoma in Situ with Normal Umbrella Cells.. Am J Pathol. 182(4):1171-9.▶ Go to Pubmed

Eydgahi H, Chen WW, Muhlich JL, Vitkup D, Tsitsiklis JN, Sorger PK. 2013. Properties of cell death models calibrated and compared using Bayesian approaches.. Mol Syst Biol. 9:644.▶ Go to Pubmed

Tzoneva G, Perez-Garcia A, Carpenter Z, Khiabanian H, Tosello V, Allegretta M, Paietta E, Racevskis J, Rowe JM, Tallman MS, Paganin M, Basso G, Hof J, Kirschner-Schwabe R, Palomero T, Rabadan R, Ferrando A. 2013. Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL.. Nat Med. 19(3):368-71.▶ Go to Pubmed

Li Q, Seo J-H, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML. 2013. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.. Cell. 152(3):633-41.▶ Go to Pubmed

Arkhipov A, Shan Y, Das R, Endres NF, Eastwood MP, Wemmer DE, Kuriyan J, Shaw DE. 2013. Architecture and membrane interactions of the EGF receptor.. Cell. 152(3):557-69.▶ Go to Pubmed

Endres NF, Das R, Smith AW, Arkhipov A, Kovacs E, Huang Y, Pelton JG, Shan Y, Shaw DE, Wemmer DE, Groves JT, Kuriyan J. 2013. Conformational coupling across the plasma membrane in activation of the EGF receptor.. Cell. 152(3):543-56.▶ Go to Pubmed

Nygaard R, Zou Y, Dror RO, Mildorf TJ, Arlow DH, Manglik A, Pan AC, Liu CW, Fung JJosé, Bokoch MP, Thian FSun, Kobilka TSun, Shaw DE, Mueller L, R Prosser S, Kobilka BK. 2013. The dynamic process of β(2)-adrenergic receptor activation.. Cell. 152(3):532-42.▶ Go to Pubmed

Chan JMinhow, Rabadan R. 2013. Quantifying pathogen surveillance using temporal genomic data.. MBio. 4(1):e00524-12.▶ Go to Pubmed

Eom T, Zhang C, Wang H, Lay K, Fak J, Noebels JL, Darnell RB. 2013. NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure.. Elife. 2:e00178.▶ Go to Pubmed

Yu J, Putcha P, Califano A, Silva J. 2013. Pooled shRNA screenings: computational analysis.. Methods Mol Biol. 980:371-84.▶ Go to Pubmed

Rodriguez-Barrueco R, Marshall N, Silva J. 2013. Pooled shRNA screenings: experimental approach.. Methods Mol Biol. 980:353-70.▶ Go to Pubmed

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley T, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, Bussemaker H, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR. 2013. Evaluation of methods for modeling transcription factor sequence specificity.. Nat Biotechnol. 31(2):126-34.▶ Go to Pubmed

Dey F, Zhang QCliff, Petrey D, Honig B. 2013. Toward a "Structural BLAST": Using structural relationships to infer function.. Protein Sci. 22(4):359-66.▶ Go to Pubmed

Yang X, Li H, Regan K, Li J, Huang Y, Lussier YA. 2012. Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients.. AMIA Annu Symp Proc. 2012:1040-9.▶ Go to Pubmed

Contreras JL, Floratos A, Holden AL. 2013. The International Serious Adverse Events Consortium's data sharing model.. Nat Biotechnol. 31(1):17-9.▶ Go to Pubmed

Maute RL, Schneider C, Sumazin P, Holmes A, Califano A, Basso K, Dalla-Favera R. 2013. tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma.. Proc Natl Acad Sci U S A. 110(4):1404-9.▶ Go to Pubmed

Carmi S, Palamara PFrancesco, Vacic V, Lencz T, Darvasi A, Pe'er I. 2013. The variance of identity-by-descent sharing in the Wright-Fisher model.. Genetics. 193(3):911-28.▶ Go to Pubmed

Rossi D, Rasi S, Spina V, Bruscaggin A, Monti S, Ciardullo C, Deambrogi C, Khiabanian H, Serra R, Bertoni F, Forconi F, Laurenti L, Marasca R, Dal-Bo M, Rossi FMaria, Bulian P, Nomdedeu J, Del Poeta G, Gattei V, Pasqualucci L, Rabadan R, Foá R, Dalla-Favera R, Gaidano G. 2013. Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia.. Blood. 121(8):1403-12.▶ Go to Pubmed

Zhang C, Srinivasan Y, Arlow DH, Fung JJosé, Palmer D, Zheng Y, Green HF, Pandey A, Dror RO, Shaw DE, Weis WI, Coughlin SR, Kobilka BK. 2012. High-resolution crystal structure of human protease-activated receptor 1.. Nature. 492(7429):387-92.▶ Go to Pubmed

Zhang QCliff, Petrey D, Garzón JIgnacio, Deng L, Honig B. 2013. PrePPI: a structure-informed database of protein-protein interactions.. Nucleic Acids Res. 41(Database issue):D828-33.▶ Go to Pubmed

Bisikirska B, Adam SJ, Alvarez M, Rajbhandari P, Cox R, Lefebvre C, Wang K, Rieckhof G, Felsher DW, Califano A. 2012. STK38 is a critical upstream regulator of MYC's oncogenic activity in human B-cell lymphoma.. Oncogene. ▶ Go to Pubmed

Schmidt AG, Xu H, Khan AR, O'Donnell T, Khurana S, King LR, Manischewitz J, Golding H, Suphaphiphat P, Carfi A, Settembre EC, Dormitzer PR, Kepler TB, Zhang R, M Moody A, Haynes BF, Liao H-X, Shaw DE, Harrison SC. 2013. Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody.. Proc Natl Acad Sci U S A. 110(1):264-9.▶ Go to Pubmed

Gilman SR, Chang J, Xu B, Bawa TS, Gogos JA, Karayiorgou M, Vitkup D. 2012. Diverse types of genetic variation converge on functional gene networks involved in schizophrenia.. Nat Neurosci. 15(12):1723-8.▶ Go to Pubmed

Yu L, Wynn J, Cheung YHim, Shen Y, Mychaliska GB, Crombleholme TM, Azarow KS, Lim F-Y, Chung DH, Potoka D, Warner BW, Bucher B, Stolar C, Aspelund G, Arkovitz MS, Chung WK. 2013. Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia.. Hum Genet. 132(3):285-92.▶ Go to Pubmed

Iliadis A, Anastassiou D, Wang X. 2012. Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data.. BMC Genet. 13:94.▶ Go to Pubmed

Palamara PFrancesco, Lencz T, Darvasi A, Pe'er I. 2012. Length distributions of identity by descent reveal fine-scale demographic history.. Am J Hum Genet. 91(5):809-22.▶ Go to Pubmed

Singer S, Zhao R, Barsotti AM, Ouwehand A, Fazlollahi M, Coutavas E, Breuhahn K, Neumann O, Longerich T, Pusterla T, Powers MA, Giles KM, Leedman PJ, Hess J, Grunwald D, Bussemaker H, Singer RH, Schirmacher P, Prives C. 2012. Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes.. Mol Cell. 48(5):799-810.▶ Go to Pubmed

Zhuang Z, Gusev A, Cho J, Pe'er I. 2012. Detecting identity by descent and homozygosity mapping in whole-exome sequencing data.. PLoS One. 7(10):e47618.▶ Go to Pubmed

Shibata M, Shen MM. 2013. The roots of cancer: stem cells and the basis for tumor heterogeneity.. Bioessays. 35(3):253-60.▶ Go to Pubmed

Zhang QCliff, Petrey D, Deng L, Qiang L, Shi Y, Thu CAye, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. 2012. Structure-based prediction of protein-protein interactions on a genome-wide scale.. Nature. 490(7421):556-60.▶ Go to Pubmed

Urban TJ, Shen Y, Stolz A, Chalasani N, Fontana RJ, Rochon J, Ge D, Shianna KV, Daly AK, M Lucena I, Nelson MR, Molokhia M, Aithal GP, Floratos A, Pe'er I, Serrano J, Bonkovsky H, Davern TJ, Lee WM, Navarro VJ, Talwalkar JA, Goldstein DB, Watkins PB. 2012. Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs.. Pharmacogenet Genomics. 22(11):784-95.▶ Go to Pubmed

Plata G, Fuhrer T, Hsiao T-L, Sauer U, Vitkup D. 2012. Global probabilistic annotation of metabolic networks enables enzyme discovery.. Nat Chem Biol. 8(10):848-54.▶ Go to Pubmed

Yang Y, Wu J, Demir A, Castillo-Martin M, Melamed R, Zhang G, Fukunaga-Kanabis M, Perez-Lorenzo R, Zheng B, Silvers DN, Brunner G, Wang S, Rabadan R, Cordon-Cardo C, Celebi JT. 2012. GAB2 induces tumor angiogenesis in NRAS-driven melanoma.. Oncogene. ▶ Go to Pubmed

Harrison O, Vendome J, Brasch J, Jin X, Hong S, Katsamba PS, Ahlsen G, Troyanovsky RB, Troyanovsky SM, Honig B, Shapiro L. 2012. Nectin ectodomain structures reveal a canonical adhesive interface.. Nat Struct Mol Biol. 19(9):906-15.▶ Go to Pubmed

Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PPaolo, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foá R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. 2012. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development.. J Exp Med. 209(9):1537-51.▶ Go to Pubmed

Campbell CL, Palamara PFrancesco, Dubrovsky M, Botigué LR, Fellous M, Atzmon G, Oddoux C, Pearlman A, Hao L, Henn BM, Burns E, Bustamante CD, Comas D, Friedman E, Pe'er I, Ostrer H. 2012. North African Jewish and non-Jewish populations form distinctive, orthogonal clusters.. Proc Natl Acad Sci U S A. 109(34):13865-70.▶ Go to Pubmed

Anthony SJ, St Leger JA, Pugliares K, Ip HS, Chan JMinhow, Carpenter Z, Navarrete-Macias I, Sanchez-Leon M, Saliki JT, Pedersen J, Karesh W, Daszak P, Rabadan R, Rowles T, Lipkin WI. 2012. Emergence of fatal avian influenza in New England harbor seals.. MBio. 3(4):e00166-12.▶ Go to Pubmed

Singh D, Chan JMinhow, Zoppoli P, Niola F, Sullivan R, Castano A, Liu EMinwei, Reichel J, Porrati P, Pellegatta S, Qiu K, Gao Z, Ceccarelli M, Riccardi R, Brat DJ, Guha A, Aldape K, Golfinos JG, Zagzag D, Mikkelsen T, Finocchiaro G, Lasorella A, Rabadan R, Iavarone A. 2012. Transforming fusions of FGFR and TACC genes in human glioblastoma.. Science. 337(6099):1231-5.▶ Go to Pubmed

Wang J, Kobayashi T, Floc'h N, Kinkade CWaugh, Aytes A, Dankort D, Lefebvre C, Mitrofanova A, Cardiff RD, McMahon M, Califano A, Shen MM, Abate-Shen C. 2012. B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer.. Cancer Res. 72(18):4765-76.▶ Go to Pubmed

Califano A, Butte AJ, Friend S, Ideker T, Schadt E. 2012. Leveraging models of cell regulation and GWAS data in integrative network-based association studies.. Nat Genet. 44(8):841-7.▶ Go to Pubmed

Silverstein SC, Rabadan R. 2012. How many neutrophils are enough (redux, redux)? J Clin Invest. 122(8):2776-9.▶ Go to Pubmed

Freddolino PL, Tavazoie S. 2012. The dawn of virtual cell biology.. Cell. 150(2):248-50.▶ Go to Pubmed

Floc'h N, Kinkade CWaugh, Kobayashi T, Aytes A, Lefebvre C, Mitrofanova A, Cardiff RD, Califano A, Shen MM, Abate-Shen C. 2012. Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model.. Cancer Res. 72(17):4483-93.▶ Go to Pubmed

Girgis HS, Harris K, Tavazoie S. 2012. Large mutational target size for rapid emergence of bacterial persistence.. Proc Natl Acad Sci U S A. 109(31):12740-5.▶ Go to Pubmed

Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G. 2012. Wisdom of crowds for robust gene network inference.. Nat Methods. 9(8):796-804.▶ Go to Pubmed

Prabhu S, Pe'er I. 2012. Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease.. Genome Res. 22(11):2230-40.▶ Go to Pubmed

R McIsaac S, Petti AA, Bussemaker H, Botstein D. 2012. Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.. Mol Biol Cell. 23(15):2993-3007.▶ Go to Pubmed

Petti AA, R McIsaac S, Ho-Shing O, Bussemaker H, Botstein D. 2012. Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.. Mol Biol Cell. 23(15):3008-24.▶ Go to Pubmed

Freddolino PL, Goodarzi H, Tavazoie S. 2012. Fitness landscape transformation through a single amino acid change in the rho terminator.. PLoS Genet. 8(5):e1002744.▶ Go to Pubmed

Vilar S, Harpaz R, Uriarte E, Santana L, Rabadan R, Friedman C. 2012. Drug-drug interaction through molecular structure similarity analysis.. J Am Med Inform Assoc. 19(6):1066-74.▶ Go to Pubmed

Iliadis A, Anastassiou D, Wang X. 2012. A unified framework for haplotype inference in nuclear families.. Ann Hum Genet. 76(4):312-25.▶ Go to Pubmed

Herman AG, Hayano M, Poyurovsky MV, Shimada K, Skouta R, Prives C, Stockwell BR. 2011. Discovery of Mdm2-MdmX E3 ligase inhibitors using a cell-based ubiquitination assay.. Cancer Discov. 1(4):312-25.▶ Go to Pubmed

Shan Y, Eastwood MP, Zhang X, Kim ET, Arkhipov A, Dror RO, Jumper J, Kuriyan J, Shaw DE. 2012. Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization.. Cell. 149(4):860-70.▶ Go to Pubmed

Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE. 2012. Biomolecular simulation: a computational microscope for molecular biology.. Annu Rev Biophys. 41:429-52.▶ Go to Pubmed

Andreopoulos B, Anastassiou D. 2012. Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature.. Cancer Inform. 11:61-75.▶ Go to Pubmed

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