Publications

Author ID

2010 Publications

Dai H, Murphy C, Kaiser G. 2010. Configuration Fuzzing for Software Vulnerability Detection.. Proc Int Conf Availab Reliab Secur. :525-530.▶ Go to Pubmed

Lee Y, Li J, Gamazon E, Chen JL, Tikhomirov A, Cox NJ, Lussier YA. 2010. Biomolecular Systems of Disease Buried Across Multiple GWAS Unveiled by Information Theory and Ontology.. AMIA Jt Summits Transl Sci Proc. 2010:31-5.▶ Go to Pubmed

Borlawsky TB, Li J, Shagina L, Crowson MG, Liu Y, Friedman C, Lussier YA. 2010. Evaluation of an Ontology-anchored Natural Language-based Approach for Asserting Multi-scale Biomolecular Networks for Systems Medicine.. AMIA Jt Summits Transl Sci Proc. 2010:6-10.▶ Go to Pubmed

Yang X, Lee Y, Fan H, Sun X, Lussier YA. 2010. Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancers.. Chin Sci Bull. 55(31):3576-3589.▶ Go to Pubmed

Xie X, Ho J, Murphy C, Kaiser G, Xu B, Chen TYueh. 2010. Application of Metamorphic Testing to Supervised Classifiers.. Proc Int Conf Qual Softw. 2009(2009):135-144.▶ Go to Pubmed

Murphy C, Vaughan M, Ilahi W, Kaiser G. 2010. Automatic Detection of Previously-Unseen Application States for Deployment Environment Testing and Analysis.. Proc Int Workshop Autom Softw Test. 2010:16-23.▶ Go to Pubmed

Akavia UDavid, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe'er D. 2010. An integrated approach to uncover drivers of cancer.. Cell. 143(6):1005-17.▶ Go to Pubmed

Hoffstrom BG, Kaplan A, Letso R, Schmid RS, Turmel GJ, Lo D, Stockwell BR. 2010. Inhibitors of protein disulfide isomerase suppress apoptosis induced by misfolded proteins.. Nat Chem Biol. 6(12):900-6.▶ Go to Pubmed

Kim H, Watkinson J, Varadan V, Anastassiou D. 2010. Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1.. BMC Med Genomics. 3:51.▶ Go to Pubmed

Yang X, Lee Y, Huang Y, Chen JL, Xing RH, Lussier YA. 2010. Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models.. BMC Bioinformatics. 11 Suppl 9:S11.▶ Go to Pubmed

Dai H, Murphy C, Kaiser G. 2010. CONFU: Configuration Fuzzing Testing Framework for Software Vulnerability Detection.. Int J Secur Softw Eng. 1(3):41-55.▶ Go to Pubmed

Gamazon ER, Im H-K, Duan S, Lussier YA, Cox NJ, M Dolan E, Zhang W. 2010. Exprtarget: an integrative approach to predicting human microRNA targets.. PLoS One. 5(10):e13534.▶ Go to Pubmed

Plata G, Gottesman ME, Vitkup D. 2010. The rate of the molecular clock and the cost of gratuitous protein synthesis.. Genome Biol. 11(9):R98.▶ Go to Pubmed

Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B. 2010. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.. Cell. 143(2):212-24.▶ Go to Pubmed

Wu Y, Jin X, Harrison O, Shapiro L, Honig B, Ben-Shaul A. 2010. Cooperativity between trans and cis interactions in cadherin-mediated junction formation.. Proc Natl Acad Sci U S A. 107(41):17592-7.▶ Go to Pubmed

Mugler A, Walczak AM, Wiggins C. 2010. Information-optimal transcriptional response to oscillatory driving.. Phys Rev Lett. 105(5):058101.▶ Go to Pubmed

Lee E, Bussemaker HJ. 2010. Identifying the genetic determinants of transcription factor activity.. Mol Syst Biol. 6:412.▶ Go to Pubmed

Khiabanian H, Holmes AB, Kelly BJ, Gururaj M, Hripcsak G, Rabadan R. 2010. Signs of the 2009 influenza pandemic in the New York-Presbyterian Hospital electronic health records.. PLoS One. 5(9)▶ Go to Pubmed

de Hoon MJL, Eichenberger P, Vitkup D. 2010. Hierarchical evolution of the bacterial sporulation network.. Curr Biol. 20(17):R735-45.▶ Go to Pubmed

Laframboise T, Dewal N, Wilkins K, Pe'er I, Freedman ML. 2010. Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis.. PLoS Genet. 6(9):e1001086.▶ Go to Pubmed

Plata G, Hsiao T-L, Olszewski KL, Llinás M, Vitkup D. 2010. Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network.. Mol Syst Biol. 6:408.▶ Go to Pubmed

Wombacher R, Heidbreder M, van de Linde S, Sheetz MP, Heilemann M, Cornish VW, Sauer M. 2010. Live-cell super-resolution imaging with trimethoprim conjugates.. Nat Methods. 7(9):717-9.▶ Go to Pubmed

Love J, Mancia F, Shapiro L, Punta M, Rost B, Girvin M, Wang D-N, Zhou M, Hunt J, Szyperski T, Gouaux E, MacKinnon R, McDermott A, Honig B, Inouye M, Montelione G, Hendrickson WA. 2010. The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins.. J Struct Funct Genomics. 11(3):191-9.▶ Go to Pubmed

Koehnke J, Katsamba PS, Ahlsen G, Bahna F, Vendome J, Honig B, Shapiro L, Jin X. 2010. Splice form dependence of beta-neurexin/neuroligin binding interactions.. Neuron. 67(1):61-74.▶ Go to Pubmed

Atzmon G, Hao L, Pe'er I, Velez C, Pearlman A, Palamara PFrancesco, Morrow B, Friedman E, Oddoux C, Burns E, Ostrer H. 2010. Abraham's children in the genome era: major Jewish diaspora populations comprise distinct genetic clusters with shared Middle Eastern Ancestry.. Am J Hum Genet. 86(6):850-9.▶ Go to Pubmed

Zhang QCliff, Petrey D, Norel R, Honig B. 2010. Protein interface conservation across structure space.. Proc Natl Acad Sci U S A. 107(24):10896-901.▶ Go to Pubmed

Lefebvre C, Rajbhandari P, Alvarez M, Bandaru P, Lim WKeat, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska B, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A. 2010. A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers.. Mol Syst Biol. 6:377.▶ Go to Pubmed

Norel R, Petrey D, Honig B. 2010. PUDGE: a flexible, interactive server for protein structure prediction.. Nucleic Acids Res. 38(Web Server issue):W550-4.▶ Go to Pubmed

Floratos A, Smith K, Ji Z, Watkinson J, Califano A. 2010. geWorkbench: an open source platform for integrative genomics.. Bioinformatics. 26(14):1779-80.▶ Go to Pubmed

Khiabanian H, Van Vlierberghe P, Palomero T, Ferrando AA, Rabadan R. 2010. ParMap, an algorithm for the identification of small genomic insertions and deletions in nextgen sequencing data.. BMC Res Notes. 3:147.▶ Go to Pubmed

Lussier YA, Butte AJ, Hunter L. 2010. Current methodologies for translational bioinformatics.. J Biomed Inform. 43(3):355-7.▶ Go to Pubmed

Li X, Panea C, Wiggins C, Reinke V, Leslie C. 2010. Learning "graph-mer" motifs that predict gene expression trajectories in development.. PLoS Comput Biol. 6(4):e1000761.▶ Go to Pubmed

Yang X, Huang Y, Crowson M, Li J, Maitland ML, Lussier Y. 2010. Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data.. J Biomed Inform. 43(3):376-84.▶ Go to Pubmed

Raj A, Wiggins CH. 2010. An information-theoretic derivation of min-cut-based clustering.. IEEE Trans Pattern Anal Mach Intell. 32(6):988-95.▶ Go to Pubmed

Chastanet A, Vitkup D, Yuan G-C, Norman TM, Liu JS, Losick RM. 2010. Broadly heterogeneous activation of the master regulator for sporulation in Bacillus subtilis.. Proc Natl Acad Sci U S A. 107(18):8486-91.▶ Go to Pubmed

Sanchez-Garcia F, Akavia UDavid, Mozes E, Pe'er D. 2010. JISTIC: identification of significant targets in cancer.. BMC Bioinformatics. 11:189.▶ Go to Pubmed

Lee H, Li Z, Silkov A, Fischer M, Petrey D, Honig B, Murray D. 2010. High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics.. J Struct Funct Genomics. 11(1):51-9.▶ Go to Pubmed

Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Wu Y, Li J, Hasina R, Cheng C, Lingen MW, Gerstein M, Weichselbaum RR, H Xing R, Lussier Y. 2010. Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis.. PLoS Comput Biol. 6(4):e1000730.▶ Go to Pubmed

Kitayner M, Rozenberg H, Rohs R, Suad O, Rabinovich D, Honig B, Shakked Z. 2010. Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs.. Nat Struct Mol Biol. 17(4):423-9.▶ Go to Pubmed

Zhou X, Sumazin P, Rajbhandari P, Califano A. 2010. A systems biology approach to transcription factor binding site prediction.. PLoS One. 5(3):e9878.▶ Go to Pubmed

Chen J, Sam L, Huang Y, Lee Y, Li J, Liu Y, H Xing R, Lussier Y. 2010. Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures.. J Biomed Inform. 43(3):385-96.▶ Go to Pubmed

Yao L, Evans JA, Rzhetsky A. 2010. Novel opportunities for computational biology and sociology in drug discovery.. Trends Biotechnol. 28(4):161-70.▶ Go to Pubmed

Rohs R, Jin X, West SM, Joshi R, Honig B, Mann RS. 2010. Origins of specificity in protein-DNA recognition.. Annu Rev Biochem. 79:233-69.▶ Go to Pubmed

West SM, Rohs R, Mann RS, Honig B. 2010. Electrostatic interactions between arginines and the minor groove in the nucleosome.. J Biomol Struct Dyn. 27(6):861-6.▶ Go to Pubmed

Van Vlierberghe P, Palomero T, Khiabanian H, Van der Meulen J, Castillo-Martin M, Van Roy N, De Moerloose B, Philippé J, González-García S, Toribio ML, Taghon T, Zuurbier L, Cauwelier B, Harrison CJ, Schwab C, Pisecker M, Strehl S, Langerak AW, Gecz J, Sonneveld E, Pieters R, Paietta E, Rowe JM, Wiernik PH, Benoit Y, Soulier J, Poppe B, Yao X, Cordon-Cardo C, Meijerink J, Rabadan R, Speleman F, Ferrando A. 2010. PHF6 mutations in T-cell acute lymphoblastic leukemia.. Nat Genet. 42(4):338-42.▶ Go to Pubmed

Lu X-J, Olson WK, Bussemaker H. 2010. The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.. Nucleic Acids Res. 38(14):4868-76.▶ Go to Pubmed

Ciatto C, Bahna F, Zampieri N, VanSteenhouse HC, Katsamba PS, Ahlsen G, Harrison O, Brasch J, Jin X, Posy S, Vendome J, Ranscht B, Jessell T, Honig B, Shapiro L. 2010. T-cadherin structures reveal a novel adhesive binding mechanism.. Nat Struct Mol Biol. 17(3):339-47.▶ Go to Pubmed

Harrison O, Bahna F, Katsamba PS, Jin X, Brasch J, Vendome J, Ahlsen G, Carroll K, Price SR, Honig B, Shapiro L. 2010. Two-step adhesive binding by classical cadherins.. Nat Struct Mol Biol. 17(3):348-57.▶ Go to Pubmed

Bu D-xiu, Rai V, Shen X, Rosario R, Lu Y, D'Agati V, Yan SFang, Friedman R, Nuglozeh E, Schmidt AMarie. 2010. Activation of the ROCK1 branch of the transforming growth factor-beta pathway contributes to RAGE-dependent acceleration of atherosclerosis in diabetic ApoE-null mice.. Circ Res. 106(6):1040-51.▶ Go to Pubmed

Zhu J, Cheng L, Fang Q, Z Zhou H, Honig B. 2010. Building and refining protein models within cryo-electron microscopy density maps based on homology modeling and multiscale structure refinement.. J Mol Biol. 397(3):835-51.▶ Go to Pubmed

van Batenburg MF, Li H, J Polman A, Lachize S, Datson NA, Bussemaker H, Meijer OC. 2010. Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene.. PLoS One. 5(1):e8839.▶ Go to Pubmed

Klein U, Lia M, Crespo M, Siegel R, Shen Q, Mo T, Ambesi-Impiombato A, Califano A, Migliazza A, Bhagat G, Dalla-Favera R. 2010. The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia.. Cancer Cell. 17(1):28-40.▶ Go to Pubmed

Carro MStella, Lim WKeat, Alvarez M, Bollo RJ, Zhao X, Snyder EY, Sulman EP, Anne SL, Doetsch F, Colman H, Lasorella A, Aldape K, Califano A, Iavarone A. 2010. The transcriptional network for mesenchymal transformation of brain tumours.. Nature. 463(7279):318-25.▶ Go to Pubmed

Basso K, Saito M, Sumazin P, Margolin AA, Wang K, Lim W-K, Kitagawa Y, Schneider C, Alvarez MJ, Califano A, Dalla-Favera R. 2010. Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells.. Blood. 115(5):975-84.▶ Go to Pubmed

Hsiao T-L, Revelles O, Chen L, Sauer U, Vitkup D. 2010. Automatic policing of biochemical annotations using genomic correlations.. Nat Chem Biol. 6(1):34-40.▶ Go to Pubmed

Singarapu KKumar, Mills JL, Xiao R, Acton T, Punta M, Fischer M, Honig B, Rost B, Montelione G, Szyperski T. 2010. Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175.. Proteins. 78(3):779-84.▶ Go to Pubmed

Bonnen PE, Lowe JK, Altshuler DM, Breslow JL, Stoffel M, Friedman JM, Pe'er I. 2010. European admixture on the Micronesian island of Kosrae: lessons from complete genetic information.. Eur J Hum Genet. 18(3):309-16.▶ Go to Pubmed

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