Search Publications

2013 Publications

Trifonov V, Pasqualucci L, Tiacci E, Falini B, Rabadan R.  2013.  SAVI: a statistical algorithm for variant frequency identification. BMC Syst Biol. 7 Suppl 2:S2. Go to Pubmed
Jang ISock, Margolin A, Califano A.  2013.  hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests. Interface Focus. 3(4):20130011. Go to Pubmed
Dixon SJ, Stockwell BR.  2013.  The Role of Iron and Reactive Oxygen Secies in Cell Death. Nat Chem Biol. 10(1):9-17. Go to Pubmed
Liu L, Kim H, Casta A, Kobayashi Y, Shapiro L, Christiano AM.  2013.  Hairless Is a Histone H3K9 Demethylase. FASEB J. Go to Pubmed
Harton MD, Wingler LM, Cornish VW.  2013.  Transcriptional regulation improves the throughput of three-hybrid counter selections in Saccharomyces cerevisiae. Biotechnol J. 8(12):1485-91. Go to Pubmed
Freddolino PL, Goodarzi H, Tavazoie S.  2013.  Revealing the Genetic Basis of Natural Bacterial Phenotypic Divergence. J Bacteriol. Go to Pubmed
Piovan E, Yu J, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva ACarolina, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo-Martin M et al.  2013.  Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia. Cancer Cell. 24(6):766-76. Go to Pubmed
Plata G, Vitkup D.  2013.  Genetic Robustness and Functional Evolution of Gene Duplicates. Nucleic Acids Res. Go to Pubmed
Lencz T, Guha S, Liu C, Rosenfeld J, Mukherjee S, Derosse P, John M, Cheng L, Zhang C, Badner JA et al.  2013.  Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder. Nat Commun. 4:2739. Go to Pubmed
Becker-Weimann S, Xiong G, Furuta S, Han J, Kuhn I, Akavia UDavid, Pe'er D, Bissell MJ, Xu R.  2013.  NFkB disrupts tissue polarity in 3D by preventing integration of microenvironmental signals. Oncotarget. Go to Pubmed
Behr ER, Ritchie MD, Tanaka T, Kääb S, Crawford DC, Nicoletti P, Floratos A, Sinner MF, Kannankeril PJ, Wilde AAM et al.  2013.  Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes. PLoS One. 8(11):e78511. Go to Pubmed
Lippert RA, Predescu C, Ierardi DJ, Mackenzie KM, Eastwood MP, Dror RO, Shaw DE.  2013.  Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure. J Chem Phys. 139(16):164106. Go to Pubmed
Abate-Shen C, Pandolfi PP.  2013.  Effective utilization and appropriate selection of genetically engineered mouse models for translational integration of mouse and human trials. Cold Spring Harb Protoc. 2013(11) Go to Pubmed
Chan JMinhow, Carlsson G, Rabadan R.  2013.  Topology of viral evolution. Proc Natl Acad Sci U S A. 110(46):18566-71. Go to Pubmed
Ansari S, Binder J, Boue S, Di Fabio A, Hayes W, Hoeng J, Iskandar A, Kleiman R, Norel R, O'Neel B et al.  2013.  On crowd-verification of biological networks. Bioinform Biol Insights. 7:307-25. Go to Pubmed
Fabbri G, Khiabanian H, Holmes A, Wang J, Messina M, Mullighan CG, Pasqualucci L, Rabadan R, Dalla-Favera R.  2013.  Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome. J Exp Med. 210(11):2273-88. Go to Pubmed
Dror RO, Green HF, Valant C, Borhani DW, Valcourt JR, Pan AC, Arlow DH, Canals M, J Lane R, Rahmani R et al.  2013.  Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature. 503(7475):295-9. Go to Pubmed
Leduc CA, Crouch EE, Wilson A, Lefkowitch J, Wamelink MMC, Jakobs C, Salomons GS, Sun X, Shen Y, Chung WK.  2013.  Novel association of early onset hepatocellular carcinoma with transaldolase deficiency. JIMD Rep. Go to Pubmed
Sun X, Vilar S, Tatonetti N.  2013.  High-throughput methods for combinatorial drug discovery. Sci Transl Med. 5(205):205rv1. Go to Pubmed
Blair DR, Lyttle CS, Mortensen JM, Bearden CF, Jensen ABoeck, Khiabanian H, Melamed R, Rabadan R, Bernstam EV, Brunak S et al.  2013.  A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell. 155(1):70-80. Go to Pubmed
Weinstein JN, Collisson EA, Mills GB, Shaw KRMills, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM.  2013.  The Cancer Genome Atlas Pan-Cancer Analysis Project. Nat Genet. 45(10):1113-20. Go to Pubmed
Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon A-K, Pe'er D, Steinmetz LM.  2013.  Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype. PLoS Genet. 9(9):e1003803. Go to Pubmed
Li Y, Altorelli NL, Bahna F, Honig B, Shapiro L, Palmer AG.  2013.  Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion. Proc Natl Acad Sci U S A. 110(41):16462-7. Go to Pubmed
Hernandez SL, Banerjee D, Garcia A, Kangsamaksin T, Cheng W-Y, Anastassiou D, Funahashi Y, Kadenhe-Chiweshe A, Shawber CJ, Kitajewski JK et al.  2013.  Notch and VEGF pathways play distinct but complementary roles in tumor angiogenesis. Vasc Cell. 5(1):17. Go to Pubmed
Sawyers CL, Abate-Shen C, Anderson KC, Barker A, Baselga J, Berger NA, Foti M, Jemal A, Lawrence TS, Li CI et al.  2013.  AACR Cancer Progress Report 2013. Clin Cancer Res. 19(20 Suppl):S1-S98. Go to Pubmed
Romano GHagit, Harari, iv Y, Yehuda T, Podhorzer A, Rubinstein L, Shamir R, Gottlieb A, Silberberg Y, Pe'er D, Ruppin E et al.  2013.  Environmental stresses disrupt telomere length homeostasis. PLoS Genet. 9(9):e1003721. Go to Pubmed
Mancini F, Wiggins C, Marsili M, Walczak AM.  2013.  Time-dependent information transmission in a model regulatory circuit. Phys Rev E Stat Nonlin Soft Matter Phys. 88(2):022708. Go to Pubmed
Barlow LJ, Shen MM.  2013.  SnapShot: Prostate cancer. Cancer Cell. 24(3):400.e1. Go to Pubmed
Irshad S, Bansal M, Castillo-Martin M, Zheng T, Aytes A, Wenske S, Le Magnen C, Guarnieri P, Sumazin P, Benson M et al.  2013.  A molecular signature predictive of indolent prostate cancer. Sci Transl Med. 5(202):202ra122. Go to Pubmed
Anton BP, Chang Y-C, Brown P, Choi H-P, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A et al.  2013.  The COMBREX project: design, methodology, and initial results. PLoS Biol. 11(8):e1001638. Go to Pubmed
Jajamovich GH, Iliadis A, Anastassiou D, Wang X.  2013.  Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA. BMC Bioinformatics. 14(1):270. Go to Pubmed
Jacunski A, Tatonetti N.  2013.  Connecting the dots: applications of network medicine in pharmacology and disease. Clin Pharmacol Ther. 94(6):659-69. Go to Pubmed
Basu A, Bodycombe NE, Cheah JH, Price EV, Liu K, Schaefer GI, Ebright RY, Stewart ML, Ito D, Wang S et al.  2013.  An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules. Cell. 154(5):1151-61. Go to Pubmed
Tavazoie S.  2013.  Synaptic state matching: a dynamical architecture for predictive internal representation and feature detection. PLoS One. 8(8):e72865. Go to Pubmed
Ying CY, Dominguez-Sola D, Fabi M, Lorenz IC, Hussein S, Bansal M, Califano A, Pasqualucci L, Basso K, Dalla-Favera R.  2013.  MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma. Nat Immunol. Go to Pubmed
Tarca AL, Lauria M, Unger M, Bilal E, Boue S, Dey KKumar, Hoeng J, Koeppl H, Martin F, Meyer P et al.  2013.  Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. Bioinformatics. 29(22):2892-9. Go to Pubmed
Sun J, Keim CD, Wang J, Kazadi D, Oliver PM, Rabadan R, Basu U.  2013.  E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells. Genes Dev. 27(16):1821-33. Go to Pubmed
Meyer P, Siwo G, Zeevi D, Sharon E, Norel R, Segal E, Stolovitzky G.  2013.  Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome Res. 23(11):1928-37. Go to Pubmed
Antebi YE, Reich-Zeliger S, Hart Y, Mayo A, Eizenberg I, Rimer J, Putheti P, Pe'er D, Friedman N.  2013.  Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates. PLoS Biol. 11(7):e1001616. Go to Pubmed
Aytes A, Mitrofanova A, Kinkade CWaugh, Lefebvre C, Lei M, Phelan V, H Lekaye C, Koutcher JA, Cardiff RD, Califano A et al.  2013.  ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer. Proc Natl Acad Sci U S A. Go to Pubmed
Frattini V, Trifonov V, Chan JMinhow, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F et al.  2013.  The integrated landscape of driver genomic alterations in glioblastoma. Nat Genet. Go to Pubmed
Tepper RG, Ashraf J, Kaletsky R, Kleemann G, Murphy CT, Bussemaker H.  2013.  PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity. Cell. 154(3):676-90. Go to Pubmed
Perez-Garcia A, Ambesi-Impiombato A, Hadler M, Rigo I, Leduc CA, Kelly K, Jalas C, Paietta E, Racevskis J, Rowe JM et al.  2013.  Genetic loss of SH2B3 in acute lymphoblastic leukemia. Blood. Go to Pubmed
Rudchenko M, Taylor S, Pallavi P, Dechkovskaia A, Khan S, Butler VP, Rudchenko S, Stojanovic MN.  2013.  Autonomous molecular cascades for evaluation of cell surfaces. Nat Nanotechnol. 8(8):580-6. Go to Pubmed
Piana S, Lindorff-Larsen K, Shaw DE.  2013.  Atomistic description of the folding of a dimeric protein. J Phys Chem B. Go to Pubmed
Arkhipov A, Shan Y, Kim ET, Dror RO, Shaw DE.  2013.  Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family. Elife. 2:e00708. Go to Pubmed
Tatonetti N, Denny JC, Altman R.  2013.  Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden et al. J Am Med Inform Assoc. 20(3):591. Go to Pubmed
Hottes AK, Freddolino PL, Khare A, Donnell ZN, Liu JC, Tavazoie S.  2013.  Bacterial adaptation through loss of function. PLoS Genet. 9(7):e1003617. Go to Pubmed
Chiu IM, Morimoto ETA, Goodarzi H, Liao JT, O'Keeffe S, Phatnani HP, Muratet M, Carroll MC, Levy S, Tavazoie S et al.  2013.  A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model. Cell Rep. 4(2):385-401. Go to Pubmed
Kreimer A, Pe'er I.  2013.  Variants in exons and in transcription factors affect gene expression in trans. Genome Biol. 14(7):R71. Go to Pubmed
Eastwood MP, Chitra T, Jumper J, Palmo K, Pan AC, Shaw DE.  2013.  Rotational relaxation in ortho-terphenyl: using atomistic simulations to bridge theory and experiment. J Phys Chem B. Go to Pubmed
Jing C, Cornish VW.  2013.  Design, synthesis, and application of the trimethoprim-based chemical tag for live-cell imaging. Curr Protoc Chem Biol. 5(2):131-55. Go to Pubmed
Daneshjou R, Tatonetti N, Karczewski KJ, Sagreiya H, Bourgeois S, Drozda K, Burmester JK, Tsunoda T, Nakamura Y, Kubo M et al.  2013.  Pathway analysis of genome-wide data improves warfarin dose prediction. BMC Genomics. 14 Suppl 3:S11. Go to Pubmed
Kobayashi T, Wang J, Al-Ahmadie HA, Abate-Shen C.  2013.  ARF regulates the stability of p16 protein via REGγ-dependent proteasome degradation. Mol Cancer Res. Go to Pubmed
de Julio MKruithof-, Shibata M, Desai N, Reynon M, M Halili V, Hu Y-P, Price SM, Abate-Shen C, Shen MM.  2013.  Canonical Wnt signaling regulates Nkx3.1 expression and luminal epithelial differentiation during prostate organogenesis. Dev Dyn. Go to Pubmed
Palamara PFrancesco, Pe'er I.  2013.  Inference of historical migration rates via haplotype sharing. Bioinformatics. 29(13):i180-i188. Go to Pubmed
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
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
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
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