Publications

Author ID

Mee MT, Collins JJ, Church GM, Wang HH. 2014. Syntrophic exchange in synthetic microbial communities.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed

Brown AAnand, Buil A, Viñuela A, Lappalainen T, Zheng H-F, J Richards B, Small KS, Spector TD, Dermitzakis ET, Durbin R. 2014. Genetic interactions affecting human gene expression identified by variance association mapping.. Elife. 3:e01381.▶ Go to Pubmed

Backenroth D, Homsy J, Murillo LR, Glessner J, Lin E, Brueckner M, Lifton R, Goldmuntz E, Chung WK, Shen Y. 2014. CANOES: detecting rare copy number variants from whole exome sequencing data.. Nucleic Acids Res. ▶ Go to Pubmed

Bendall SC, Davis KL, Amir E-ADavid, Tadmor MD, Simonds EF, Chen TJ, Shenfeld DK, Nolan GP, Pe'er D. 2014. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development.. Cell. 157(3):714-25.▶ Go to Pubmed

Miller CP, Thorpe JD, Kortum AN, Coy CM, Cheng W-Y, Yang T-HOu, Anastassiou D, J Beatty D, Urban ND, C Blau A. 2014. JAK2 expression is associated with tumor-infiltrating lymphocytes and improved breast cancer outcomes: implications for evaluating JAK2 inhibitors.. Cancer Immunol Res. 2(4):301-6.▶ Go to Pubmed

Matos MJoão, Vilar S, García-Morales V, Tatonetti N, Uriarte E, Santana L, Viña D. 2014. Insight into the Functional and Structural Properties of 3-Arylcoumarin as an Interesting Scaffold in Monoamine Oxidase B Inhibition.. ChemMedChem. ▶ Go to Pubmed

Lee E, de Ridder J, Kool J, Wessels LFA, Bussemaker H. 2014. Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis.. Proc Natl Acad Sci U S A. 111(15):5747-52.▶ Go to Pubmed

Mann RS. 2014. Neuroscience. The Michael Jackson fly.. Science. 344(6179):48-9.▶ Go to Pubmed

Kermany AR, Segurel L, Oliver TR, Przeworski M. 2014. TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception.. Bioinformatics. ▶ Go to Pubmed

Oikonomou P, Goodarzi H, Tavazoie S. 2014. Systematic Identification of Regulatory Elements in Conserved 3' UTRs of Human Transcripts.. Cell Rep. ▶ Go to Pubmed

van de Meent J-W, Bronson JE, Wiggins C, Gonzalez RL. 2014. Empirical Bayes Methods Enable Advanced Population-Level Analyses of Single-Molecule FRET Experiments.. Biophys J. 106(6):1327-37.▶ Go to Pubmed

Hoffman KB, Dimbil M, Erdman CB, Tatonetti N, Overstreet BM. 2014. The Weber Effect and the United States Food and Drug Administration's Adverse Event Reporting System (FAERS): Analysis of Sixty-Two Drugs Approved from 2006 to 2010.. Drug Saf. ▶ Go to Pubmed

Sonabend AM, Carminucci A, Amendolara B, Bansal M, Leung R, Lei L, Realubit R, Li H, Karan C, Yun J, Showers C, Rothcock R, O J, Califano A, Canoll P, Bruce JN. 2014. Convection-enhanced delivery of etoposide is effective against murine proneural glioblastoma.. Neuro Oncol. ▶ Go to Pubmed

Llobet-Navas D, Rodriguez-Barrueco R, Castro V, Ugalde AP, Sumazin P, Jacob-Sendler D, Demircan B, Castillo-Martin M, Putcha P, Marshall N, Villagrasa P, Chan JMinhow, Sanchez-Garcia F, Pe'er D, Rabadan R, Iavarone A, Cordon-Cardo C, Califano A, López-Otín C, Ezhkova E, Silva J. 2014. The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.. Genes Dev. ▶ Go to Pubmed

Matos MJoão, Janeiro P, Franco RMaría Gon, Vilar S, Tatonetti N, Santana L, Uriarte E, Borges F, Fontenla JAngel, Viña D. 2014. Synthesis, pharmacological study and docking calculations of new benzo[f]coumarin derivatives as dual inhibitors of enzymatic systems involved in neurodegenerative diseases.. Future Med Chem. 6(4):371-83.▶ Go to Pubmed

Sundling C, Zhang Z, Phad GE, Sheng Z, Wang Y, Mascola JR, Li Y, Wyatt RT, Shapiro L, Hedestam GBKarlsson. 2014. Single-Cell and Deep Sequencing of IgG-Switched Macaque B Cells Reveal a Diverse Ig Repertoire following Immunization.. J Immunol. ▶ Go to Pubmed

Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, Krainer AR, Darnell RB, Zhang C. 2014. HITS-CLIP and Integrative Modeling Define the Rbfox Splicing-Regulatory Network Linked to Brain Development and Autism.. Cell Rep. ▶ Go to Pubmed

Skouta R, Dixon SJ, Wang J, Dunn DE, Orman M, Shimada K, Rosenberg P, Lo D, Weinberg J, Linkermann A, Stockwell BR. 2014. Ferrostatins inhibit oxidative lipid damage and cell death in diverse disease models.. J Am Chem Soc. ▶ Go to Pubmed

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

Messina M, Del Giudice I, Khiabanian H, Rossi D, Chiaretti S, Rasi S, Spina V, Holmes A, Marinelli M, Fabbri G, Piciocchi A, Mauro FR, Guarini A, Gaidano G, Dalla-Favera R, Pasqualucci L, Rabadan R, Foá R. 2014. Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness.. Blood. ▶ Go to Pubmed

Song F, Del Pozo CHurtado, Rosario R, Zou YShan, Ananthakrishnan R, Xu X, Patel PR, Benoit VM, Yan SFang, Li H, Friedman R, Kim JK, Ramasamy R, Ferrante AW, Schmidt AMarie. 2014. RAGE Regulates the Metabolic and Inflammatory Response to High Fat Feeding in Mice.. Diabetes. ▶ Go to Pubmed

Karczewski KJ, Snyder M, Altman R, Tatonetti N. 2014. Coherent functional modules improve transcription factor target identification, cooperativity prediction, and disease association.. PLoS Genet. 10(2):e1004122.▶ 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

Rossi D, Khiabanian H, Spina V, Ciardullo C, Bruscaggin A, Famà R, Rasi S, Monti S, Deambrogi C, De Paoli L, Wang J, Gattei V, Guarini A, Foá R, Rabadan R, Gaidano G. 2014. Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia.. Blood. ▶ Go to Pubmed

Kurki MI, Gaál EIlona, Kettunen J, Lappalainen T, Menelaou A, Anttila V, Hof FNG van 't, Fraunberg Mvon Und Zu, Helisalmi S, Hiltunen M, Lehto H, Laakso A, Kivisaari R, Koivisto T, Ronkainen A, Rinne J, Kiemeney LAL, Vermeulen SH, Kaunisto MA, Eriksson JG, Aromaa A, Perola M, Lehtimäki T, Raitakari OT, Salomaa V, Gunel M, Dermitzakis ET, Ruigrok YM, Rinkel GJE, Niemelä M, Hernesniemi J, Ripatti S, de Bakker PIW, Palotie A, Jääskeläinen JE. 2014. High risk population isolate reveals low frequency variants predisposing to intracranial aneurysms.. PLoS Genet. 10(1):e1004134.▶ Go to Pubmed

Piana S, Klepeis JL, Shaw DE. 2014. Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations.. Curr Opin Struct Biol. 24C:98-105.▶ Go to Pubmed

Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray M-A, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RGW, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG. 2014. ZFHX4 Interacts with the NuRD Core Member CHD4 and Regulates the Glioblastoma Tumor-Initiating Cell State.. Cell Rep. ▶ Go to Pubmed

Yang WSeok, Sriramaratnam R, Welsch ME, Shimada K, Skouta R, Viswanathan VS, Cheah JH, Clemons PA, Shamji AF, Clish CB, Brown LM, Girotti AW, Cornish VW, Schreiber SL, Stockwell BR. 2014. Regulation of Ferroptotic Cancer Cell Death by GPX4.. Cell. 156(1-2):317-31.▶ Go to Pubmed

Kode A, Manavalan JS, Mosialou I, Bhagat G, Rathinam CV, Luo N, Khiabanian H, Lee A, Murty VV, Friedman R, Brum A, Park D, Galili N, Mukherjee S, Teruya-Feldstein J, Raza A, Rabadan R, Berman E, Kousteni S. 2014. Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts.. Nature. ▶ Go to Pubmed

Palomero T, Couronné L, Khiabanian H, Kim M-Y, Ambesi-Impiombato A, Perez-Garcia A, Carpenter Z, Abate F, Allegretta M, J Haydu E, Jiang X, Lossos IS, Nicolas C, Balbin M, Bastard C, Bhagat G, Piris MA, Campo E, Bernard OA, Rabadan R, Ferrando A. 2014. Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas.. Nat Genet. ▶ Go to Pubmed

Moore MJ, Zhang C, Gantman EConn, Mele A, Darnell JC, Darnell RB. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis.. Nat Protoc. 9(2):263-93.▶ Go to Pubmed

Tepper RG, Murphy CT, Bussemaker H. 2014. DAF-16 and PQM-1: Partners in longevity.. Aging (Albany NY). ▶ Go to Pubmed

Sonabend AM, Bansal M, Guarnieri P, Lei L, Amendolara B, Soderquist C, Leung R, Yun J, Kennedy B, Sisti J, Bruce S, Bruce R, Shakya R, Ludwig T, Rosenfeld S, Sims PA, Bruce JN, Califano A, Canoll P. 2014. The Transcriptional Regulatory Network of Proneural Glioma Determines the Genetic Alterations Selected During Tumor Progression.. Cancer Res. ▶ Go to Pubmed

Pasqualucci L, Khiabanian H, Fangazio M, Vasishtha M, Messina M, Holmes A, Ouillette P, Trifonov V, Rossi D, Tabbò F, Ponzoni M, Chadburn A, Murty VV, Bhagat G, Gaidano G, Inghirami G, Malek SN, Rabadan R, Dalla-Favera R. 2014. Genetics of follicular lymphoma transformation.. Cell Rep. 6(1):130-40.▶ Go to Pubmed

Yu L, Bennett JT, Wynn J, Carvill GL, Cheung YHim, Shen Y, Mychaliska GB, Azarow KS, Crombleholme TM, Chung DH, Potoka D, Warner BW, Bucher B, Lim F-Y, Pietsch J, Stolar C, Aspelund G, Arkovitz MS, Mefford H, Chung WK. 2014. Whole exome sequencing identifies de novo mutations in GATA6 associated with congenital diaphragmatic hernia.. J Med Genet. ▶ 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, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink J, Cordon-Cardo C, Califano A, Ferrando A. 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

Shazman S, Lee H, Socol Y, Mann RS, Honig B. 2014. OnTheFly: a Database of Drosophila melanogaster Transcription Factors and Their Binding Sites.. Nucleic Acids Res. 42(1):D167-71.▶ Go to Pubmed

Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. 2014. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.. Bioinformatics. 30(2):165-71.▶ Go to Pubmed

Lencz T, Guha S, Liu C, Rosenfeld J, Mukherjee S, Derosse P, John M, Cheng L, Zhang C, Badner JA, Ikeda M, Iwata N, Cichon S, Rietschel M, Nöthen MM, Cheng ATA, Hodgkinson C, Yuan Q, Kane JM, Lee AT, Pisanté A, Gregersen PK, Pe'er I, Malhotra AK, Goldman D, Darvasi A. 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, Bezzina CR, Schulze-Bahr E, Zumhagen S, Guicheney P, Bishopric NH, Marshall V, Shakir S, Dalageorgou C, Bevan S, Jamshidi Y, Bastiaenen R, Myerburg RJ, Schott J-J, A Camm J, Steinbeck G, Norris K, Altman R, Tatonetti N, Jeffery S, Kubo M, Nakamura Y, Shen Y, George AL, Roden DM. 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, Peitsch M, Poussin C, Pratt D, Rhrissorrakrai K, Schlage WK, Stolovitzky G, Talikka M. 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, Baell JB, Sexton PM, Christopoulos A, Shaw DE. 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, Jensen LJuhl, Nicolae D, Shah NH, Grossman RL, Cox NJ, White KP, Rzhetsky A. 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, Kandel JJ, Yamashiro DJ. 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, Mardis ER, Neumann PJ, Pardoll DM, Prendergast GC, Reed JC, Weiner GJ. 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, Sharan R, Kupiec M. 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, Shen MM, Califano A, Abate-Shen C. 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, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu S-Y, Bateman A, Blumenthal RM, J Bollinger M, Chang W-S, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, Delisi C, Roberts RJ, Steffen M, Kasif S. 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, Bracha AL, Liefeld T, Wawer M, Gilbert JC, Wilson AJ, Stransky N, Kryukov GV, Dancik V, Barretina J, Garraway LA, C Hon S-Y, Munoz B, Bittker JA, Stockwell BR, Khabele D, Stern AM, Clemons PA, Shamji AF, Schreiber SL. 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, Nandy P, Norel R, Peitsch M, J Rice J, Romero R, Stolovitzky G, Talikka M, Xiang Y, Zechner C. 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, Shen MM, Abate-Shen C. 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, Danussi C, Dolgalev I, Porrati P, Pellegatta S, Heguy A, Gupta G, Pisapia DJ, Canoll P, Bruce JN, McLendon RE, Yan H, Aldape K, Finocchiaro G, Mikkelsen T, Privé GG, Bigner DD, Lasorella A, Rabadan R, Iavarone A. 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, Tallman MS, Paganin M, Basso G, Tong W, Chung WK, Ferrando A. 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, Myers RM, Maniatis T. 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, Tector M, Limdi NA, Cavallari LH, Perera M, Johnson JA, Klein TE, Altman R. 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, 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

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