Search Publications

Danussi C, Akavia UDavid, Niola F, Jovic A, Lasorella A, Pe'er D, Iavarone A.  2013.  RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation. Cancer Res. Go to Pubmed
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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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