Search Publications

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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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 et al.  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