Search Publications

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