Publications

Author ID

2011 Publications

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

Trifonov V, Pasqualucci L, Dalla-Favera R, Rabadan R. 2011. Fractal-like distributions over the rational numbers in high-throughput biological and clinical data.. Sci Rep. 1:191.▶ Go to Pubmed

Anastassiou D, Rumjantseva V, Cheng W-Y, Huang J, Canoll P, Yamashiro DJ, Kandel JJ. 2011. Human cancer cells express Slug-based epithelial-mesenchymal transition gene expression signature obtained in vivo.. BMC Cancer. 11:529.▶ Go to Pubmed

Chard K, Russell M, Lussier YA, Mendonça EA, Silverstein JC. 2011. A cloud-based approach to medical NLP.. AMIA Annu Symp Proc. 2011:207-16.▶ Go to Pubmed

Lussier YA, H Xing R, Salama JK, Khodarev NN, Huang Y, Zhang Q, Khan SA, Yang X, Hasselle MD, Darga TE, Malik R, Fan H, Perakis S, Filippo M, Corbin K, Lee Y, Posner MC, Chmura SJ, Hellman S, Weichselbaum RR. 2011. MicroRNA expression characterizes oligometastasis(es).. PLoS One. 6(12):e28650.▶ Go to Pubmed

Raj A, Dewar M, Palacios G, Rabadan R, Wiggins CH. 2011. Identifying hosts of families of viruses: a machine learning approach.. PLoS One. 6(12):e27631.▶ Go to Pubmed

Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker H, Mann RS. 2011. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.. Cell. 147(6):1270-82.▶ Go to Pubmed

Luan B, Martyna G, Stolovitzky G. 2011. Characterizing and controlling the motion of ssDNA in a solid-state nanopore.. Biophys J. 101(9):2214-22.▶ Go to Pubmed

Rossi D, Bruscaggin A, Spina V, Rasi S, Khiabanian H, Messina M, Fangazio M, Vaisitti T, Monti S, Chiaretti S, Guarini A, Del Giudice I, Cerri M, Cresta S, Deambrogi C, Gargiulo E, Gattei V, Forconi F, Bertoni F, Deaglio S, Rabadan R, Pasqualucci L, Foá R, Dalla-Favera R, Gaidano G. 2011. Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness.. Blood. 118(26):6904-8.▶ Go to Pubmed

Amini S, Hottes AK, Smith LE, Tavazoie S. 2011. Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms.. PLoS Pathog. 7(10):e1002298.▶ Go to Pubmed

Sumazin P, Yang X, Chiu H-S, Chung W-J, Iyer A, Llobet-Navas D, Rajbhandari P, Bansal M, Guarnieri P, Silva J, Califano A. 2011. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma.. Cell. 147(2):370-81.▶ Go to Pubmed

Kuziemko A, Honig B, Petrey D. 2011. Using structure to explore the sequence alignment space of remote homologs.. PLoS Comput Biol. 7(10):e1002175.▶ Go to Pubmed

Birsoy K, Berry R, Wang T, Ceyhan O, Tavazoie S, Friedman JM, Rodeheffer MS. 2011. Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis.. Development. 138(21):4709-19.▶ Go to Pubmed

Shen Y, Gu Y, Pe'er I. 2011. A hidden Markov model for copy number variant prediction from whole genome resequencing data.. BMC Bioinformatics. 12 Suppl 6:S4.▶ Go to Pubmed

Basso K, Mussolin L, Lettieri A, Brahmachary M, Lim WKeat, Califano A, Basso G, Biondi A, Cazzaniga G, Rosolen A. 2011. T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses.. Genes Chromosomes Cancer. 50(12):1063-75.▶ Go to Pubmed

Califano A. 2011. Striking a balance between feasible and realistic biological models.. Sci Transl Med. 3(103):103ps39.▶ Go to Pubmed

Bishop EP, Rohs R, Parker SCJ, West SM, Liu P, Mann RS, Honig B, Tullius TD. 2011. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.. ACS Chem Biol. 6(12):1314-20.▶ Go to Pubmed

Vilar S, Harpaz R, Chase H, Costanzi S, Rabadan R, Friedman C. 2011. Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis.. J Am Med Inform Assoc. 18 Suppl 1:i73-80.▶ Go to Pubmed

Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch M, J Rice J, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G. 2011. Verification of systems biology research in the age of collaborative competition.. Nat Biotechnol. 29(9):811-5.▶ Go to Pubmed

Prill RJ, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Stolovitzky G. 2011. Crowdsourcing network inference: the DREAM predictive signaling network challenge.. Sci Signal. 4(189):mr7.▶ Go to Pubmed

Wolpaw AJ, Shimada K, Skouta R, Welsch ME, Akavia UDavid, Pe'er D, Shaik F, J Bulinski C, Stockwell BR. 2011. Modulatory profiling identifies mechanisms of small molecule-induced cell death.. Proc Natl Acad Sci U S A. 108(39):E771-80.▶ Go to Pubmed

Wingler LM, Cornish VW. 2011. Reiterative Recombination for the in vivo assembly of libraries of multigene pathways.. Proc Natl Acad Sci U S A. 108(37):15135-40.▶ Go to Pubmed

de Julio MKruithof-, Alvarez M, Galli A, Chu J, Price SM, Califano A, Shen MM. 2011. Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling.. Development. 138(18):3885-95.▶ Go to Pubmed

Amini S, Tavazoie S. 2011. Antibiotics and the post-genome revolution.. Curr Opin Microbiol. 14(5):513-8.▶ Go to Pubmed

Hottes AK, Tavazoie S. 2011. Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries.. Methods Mol Biol. 765:83-97.▶ Go to Pubmed

Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O, Chan JMinhow, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R. 2011. Analysis of the coding genome of diffuse large B-cell lymphoma.. Nat Genet. 43(9):830-7.▶ Go to Pubmed

Wu Y, Vendome J, Shapiro L, Ben-Shaul A, Honig B. 2011. Transforming binding affinities from three dimensions to two with application to cadherin clustering.. Nature. 475(7357):510-3.▶ Go to Pubmed

Holmes A, Hawson A, Liu F, Friedman C, Khiabanian H, Rabadan R. 2011. Discovering disease associations by integrating electronic clinical data and medical literature.. PLoS One. 6(6):e21132.▶ Go to Pubmed

Patwa LG, Fan T-J, Tchaptchet S, Liu Y, Lussier YA, R Sartor B, Hansen JJ. 2011. Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli.. Gastroenterology. 141(5):1842-51.e1-10.▶ Go to Pubmed

Mathew B, Jacobson JR, Berdyshev E, Huang Y, Sun X, Zhao Y, Gerhold LM, Siegler J, Evenoski C, Wang T, Zhou T, Zaidi R, Moreno-Vinasco L, Bittman R, Chen CTu, LaRiviere PJ, Sammani S, Lussier YA, Dudek SM, Natarajan V, Weichselbaum RR, Garcia JGN. 2011. Role of sphingolipids in murine radiation-induced lung injury: protection by sphingosine 1-phosphate analogs.. FASEB J. 25(10):3388-400.▶ Go to Pubmed

Fischer M, Zhang QCliff, Dey F, Chen BY, Honig B, Petrey D. 2011. MarkUs: a server to navigate sequence-structure-function space.. Nucleic Acids Res. 39(Web Server issue):W357-61.▶ Go to Pubmed

Chen JL, Li J, Stadler WM, Lussier YA. 2011. Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence.. J Am Med Inform Assoc. 18(4):392-402.▶ Go to Pubmed

Fabbri G, Rasi S, Rossi D, Trifonov V, Khiabanian H, Ma J, Grunn A, Fangazio M, Capello D, Monti S, Cresta S, Gargiulo E, Forconi F, Guarini A, Arcaini L, Paulli M, Laurenti L, Larocca LM, Marasca R, Gattei V, Oscier D, Bertoni F, Mullighan CG, Foá R, Pasqualucci L, Rabadan R, Dalla-Favera R, Gaidano G. 2011. Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation.. J Exp Med. 208(7):1389-401.▶ Go to Pubmed

Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MPaola, Pucciarini A, Bigerna B, Pacini R, Wells VA, Sportoletti P, Pettirossi V, Mannucci R, Elliott O, Liso A, Ambrosetti A, Pulsoni A, Forconi F, Trentin L, Semenzato G, Inghirami G, Capponi M, Di Raimondo F, Patti C, Arcaini L, Musto P, Pileri S, Haferlach C, Schnittger S, Pizzolo G, Foá R, Farinelli L, Haferlach T, Pasqualucci L, Rabadan R, Falini B. 2011. BRAF mutations in hairy-cell leukemia.. N Engl J Med. 364(24):2305-15.▶ Go to Pubmed

Gilman SR, Iossifov I, Levy D, Ronemus M, Wigler M, Vitkup D. 2011. Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses.. Neuron. 70(5):898-907.▶ Go to Pubmed

Zhu J, Yu Y, Ulbrich MH, Li M-hui, Isacoff EY, Honig B, Yang J. 2011. Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach.. Proc Natl Acad Sci U S A. 108(25):10133-8.▶ Go to Pubmed

Shen Y, Song R, Pe'er I. 2011. Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association.. Bioinformatics. 27(14):1995-7.▶ Go to Pubmed

Gusev A, Kenny EE, Lowe JK, Salit J, Saxena R, Kathiresan S, Altshuler D, Friedman JM, Breslow J, Pe'er I. 2011. DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation.. Am J Hum Genet. 88(6):706-17.▶ Go to Pubmed

Zhang QCliff, Deng L, Fisher M, Guan J, Honig B, Petrey D. 2011. PredUs: a web server for predicting protein interfaces using structural neighbors.. Nucleic Acids Res. 39(Web Server issue):W283-7.▶ Go to Pubmed

Harrer S, Waggoner PS, Luan B, Afzali-Ardakani A, Goldfarb DL, Peng H, Martyna G, Rossnagel SM, Stolovitzky G. 2011. Electrochemical protection of thin film electrodes in solid state nanopores.. Nanotechnology. 22(27):275304.▶ Go to Pubmed

Vendome J, Posy S, Jin X, Bahna F, Ahlsen G, Shapiro L, Honig B. 2011. Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins.. Nat Struct Mol Biol. 18(6):693-700.▶ Go to Pubmed

Xie X, Ho JWK, Murphy C, Kaiser G, Xu B, Chen TYueh. 2011. Testing and Validating Machine Learning Classifiers by Metamorphic Testing.. J Syst Softw. 84(4):544-558.▶ Go to Pubmed

Kim H, Watkinson J, Anastassiou D. 2011. Biomarker discovery using statistically significant gene sets.. J Comput Biol. 18(10):1329-38.▶ Go to Pubmed

Yang X, Li J, Lee Y, Lussier YA. 2011. GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns.. Bioinformatics. 27(10):1444-6.▶ Go to Pubmed

Pe'er D, Hacohen N. 2011. Principles and strategies for developing network models in cancer.. Cell. 144(6):864-73.▶ Go to Pubmed

Hoskins AA, Friedman LJ, Gallagher SS, Crawford DJ, Anderson EG, Wombacher R, Ramirez N, Cornish VW, Gelles J, Moore MJ. 2011. Ordered and dynamic assembly of single spliceosomes.. Science. 331(6022):1289-95.▶ Go to Pubmed

Pasqualucci L, Dominguez-Sola D, Chiarenza A, Fabbri G, Grunn A, Trifonov V, Kasper LH, Lerach S, Tang H, Ma J, Rossi D, Chadburn A, Murty VV, Mullighan CG, Gaidano G, Rabadan R, Brindle PK, Dalla-Favera R. 2011. Inactivating mutations of acetyltransferase genes in B-cell lymphoma.. Nature. 471(7337):189-95.▶ Go to Pubmed

Harrison O, Jin X, Hong S, Bahna F, Ahlsen G, Brasch J, Wu Y, Vendome J, Felsovalyi K, Hampton CM, Troyanovsky RB, Ben-Shaul A, Frank J, Troyanovsky SM, Shapiro L, Honig B. 2011. The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins.. Structure. 19(2):244-56.▶ Go to Pubmed

Ross KAndrew. 2011. Evidence for somatic gene conversion and deletion in bipolar disorder, Crohn's disease, coronary artery disease, hypertension, rheumatoid arthritis, type-1 diabetes, and type-2 diabetes.. BMC Med. 9:12.▶ Go to Pubmed

Brasch J, Harrison O, Ahlsen G, Carnally SM, Henderson RM, Honig B, Shapiro L. 2011. Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin.. J Mol Biol. 408(1):57-73.▶ Go to Pubmed

Shechtman CF, Henneberry AL, Seimon TA, Tinkelenberg AH, Wilcox LJ, Lee E, Fazlollahi M, Munkacsi AB, Bussemaker H, Tabas I, Sturley SL. 2011. Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response.. J Biol Chem. 286(14):11951-9.▶ Go to Pubmed

Yao L, Divoli A, Mayzus I, Evans JA, Rzhetsky A. 2011. Benchmarking ontologies: bigger or better? PLoS Comput Biol. 7(1):e1001055.▶ Go to Pubmed

Harpaz R, Perez H, Chase H, Rabadan R, Hripcsak G, Friedman C. 2011. Biclustering of adverse drug events in the FDA's spontaneous reporting system.. Clin Pharmacol Ther. 89(2):243-50.▶ Go to Pubmed

Mugler A, Grinshpun B, Franks R, Wiggins C. 2011. Statistical method for revealing form-function relations in biological networks.. Proc Natl Acad Sci U S A. 108(2):446-51.▶ Go to Pubmed

Behnke-Parks WM, Vendome J, Honig B, Maliga Z, Moores C, Rosenfeld S. 2011. Loop L5 acts as a conformational latch in the mitotic kinesin Eg5.. J Biol Chem. 286(7):5242-53.▶ Go to Pubmed

Kenny EE, Kim M, Gusev A, Lowe JK, Salit J, J Smith G, Kovvali S, Kang HMin, Newton-Cheh C, Daly MJ, Stoffel M, Altshuler D, Friedman JM, Eskin E, Breslow J, Pe'er I. 2011. Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population.. Hum Mol Genet. 20(4):827-39.▶ Go to Pubmed

Roberts RJ, Chang Y-C, Hu Z, Rachlin J, Anton BP, Pokrzywa R, Choi H-P, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick M, Osmani L, Swaminathan R, Tao K, Letovsky S, Vitkup D, Segrè D, Salzberg SL, Delisi C, Steffen M, Kasif S. 2011. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.. Nucleic Acids Res. 39(Database issue):D11-4.▶ Go to Pubmed

Cheung YHim, Watkinson J, Anastassiou D. 2011. Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC.. Hum Genet. 129(2):161-76.▶ Go to Pubmed

Cadeiras M, von Bayern M, Sinha A, Shahzad K, Latif F, Lim WKeat, Grenett H, Tabak E, Klingler T, Califano A, Deng MC. 2011. Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation.. J Cell Mol Med. 15(4):949-56.▶ Go to Pubmed

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