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2010

2010 Publications

Huning Dai, Christian Murphy, Gail Kaiser .  2010.   Configuration Fuzzing for Software Vulnerability Detection.. Proc Int Conf Availab Reliab Secur. :525-530 ▶ Go to Pubmed
Younghee Lee, Jianrong Li, Eric Gamazon, James Chen, Anna Tikhomirov, Nancy Cox, Yves Lussier .  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
Tara Borlawsky, Jianrong Li, Lyudmila Shagina, Matthew Crowson, Yang Liu, Carol Friedman, Yves Lussier .  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
Xinan Yang, Younghee Lee, Hong Fan, Xiao Sun, Yves Lussier .  2010.   Identification of common microRNA-mRNA regulatory biomodules in human epithelial cancers.. Chin Sci Bull. 55 (31) :3576-3589 ▶ Go to Pubmed
Xiaoyuan Xie, Joshua Ho, Christian Murphy, Gail Kaiser, Baowen Xu, Tsong Chen .  2010.   Application of Metamorphic Testing to Supervised Classifiers.. Proc Int Conf Qual Softw. 2009 (2009) :135-144 ▶ Go to Pubmed
Christian Murphy, Moses Vaughan, Waseem Ilahi, Gail Kaiser .  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
Uri Akavia, Oren Litvin, Jessica Kim, Felix Sanchez-Garcia, Dylan Kotliar, Helen Causton, Panisa Pochanard, Eyal Mozes, Levi Garraway, Dana Pe'er .  2010.   An integrated approach to uncover drivers of cancer.. Cell. 143 (6) :1005-17 ▶ Go to Pubmed
Benjamin Hoffstrom, Anna Kaplan, Reka Letso, Ralf Schmid, Gregory Turmel, Donald Lo, Brent Stockwell .  2010.   Inhibitors of protein disulfide isomerase suppress apoptosis induced by misfolded proteins.. Nat Chem Biol. 6 (12) :900-6 ▶ Go to Pubmed
Hoon Kim, John Watkinson, Vinay Varadan, Dimitris Anastassiou .  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
Xinan Yang, Younghee Lee, Yong Huang, James Chen, Rosie Xing, Yves Lussier .  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
Huning Dai, Christian Murphy, Gail Kaiser .  2010.   CONFU: Configuration Fuzzing Testing Framework for Software Vulnerability Detection.. Int J Secur Softw Eng. 1 (3) :41-55 ▶ Go to Pubmed
Eric Gamazon, Hae-Kyung Im, Shiwei Duan, Yves Lussier, Nancy Cox, Eileen Dolan, Wei Zhang .  2010.   Exprtarget: an integrative approach to predicting human microRNA targets.. PLoS One. 5 (10) :e13534 ▶ Go to Pubmed
Germán Plata, Max Gottesman, Dennis Vitkup .  2010.   The rate of the molecular clock and the cost of gratuitous protein synthesis.. Genome Biol. 11 (9) :R98 ▶ Go to Pubmed
Guillaume Filion, Joke van Bemmel, Ulrich Braunschweig, Wendy Talhout, Jop Kind, Lucas Ward, Wim Brugman, Inês de Castro, Ron Kerkhoven, Harmen Bussemaker, Bas van Steensel .  2010.   Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.. Cell. 143 (2) :212-24 ▶ Go to Pubmed
Yinghao Wu, Xiangshu Jin, Oliver Harrison, Lawrence Shapiro, Barry Honig, Avinoam Ben-Shaul .  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
Andrew Mugler, Aleksandra Walczak, Chris Wiggins .  2010.   Information-optimal transcriptional response to oscillatory driving.. Phys Rev Lett. 105 (5) :058101 ▶ Go to Pubmed
Eunjee Lee, Harmen Bussemaker .  2010.   Identifying the genetic determinants of transcription factor activity.. Mol Syst Biol. 6 :412 ▶ Go to Pubmed
Hossein Khiabanian, Antony Holmes, Brendan Kelly, Mrinalini Gururaj, George Hripcsak, Raul Rabadan .  2010.   Signs of the 2009 influenza pandemic in the New York-Presbyterian Hospital electronic health records.. PLoS One. 5 (9) ▶ Go to Pubmed
Michiel de Hoon, Patrick Eichenberger, Dennis Vitkup .  2010.   Hierarchical evolution of the bacterial sporulation network.. Curr Biol. 20 (17) :R735-45 ▶ Go to Pubmed
Thomas Laframboise, Ninad Dewal, Katherine Wilkins, Itsik Pe'er, Matthew Freedman .  2010.   Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis.. PLoS Genet. 6 (9) :e1001086 ▶ Go to Pubmed
Germán Plata, Tzu-Lin Hsiao, Kellen Olszewski, Manuel Llinás, Dennis Vitkup .  2010.   Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network.. Mol Syst Biol. 6 :408 ▶ Go to Pubmed
Richard Wombacher, Meike Heidbreder, Sebastian van de Linde, Michael Sheetz, Mike Heilemann, Virginia Cornish, Markus Sauer .  2010.   Live-cell super-resolution imaging with trimethoprim conjugates.. Nat Methods. 7 (9) :717-9 ▶ Go to Pubmed
James Love, Filippo Mancia, Lawrence Shapiro, Marco Punta, Burkhard Rost, Mark Girvin, Da-Neng Wang, Ming Zhou, John Hunt, Thomas Szyperski, Eric Gouaux, Roderick MacKinnon, Ann McDermott, Barry Honig, Masayori Inouye, Gaetano Montelione, Wayne Hendrickson .  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
Jesko Koehnke, Phinikoula Katsamba, Goran Ahlsen, Fabiana Bahna, Jeremie Vendome, Barry Honig, Lawrence Shapiro, Xiangshu Jin .  2010.   Splice form dependence of beta-neurexin/neuroligin binding interactions.. Neuron. 67 (1) :61-74 ▶ Go to Pubmed
Gil Atzmon, Li Hao, Itsik Pe'er, Christopher Velez, Alexander Pearlman, Pier Palamara, Bernice Morrow, Eitan Friedman, Carole Oddoux, Edward Burns, Harry Ostrer .  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
Qiangfeng Zhang, Donald Petrey, Raquel Norel, Barry Honig .  2010.   Protein interface conservation across structure space.. Proc Natl Acad Sci U S A. 107 (24) :10896-901 ▶ Go to Pubmed
Celine Lefebvre, Presha Rajbhandari, Mariano Alvarez, Pradeep Bandaru, Wei Lim, Mai Sato, Kai Wang, Pavel Sumazin, Manjunath Kustagi, Brygida Bisikirska, Katia Basso, Pedro Beltrao, Nevan Krogan, Jean Gautier, Riccardo Dalla-Favera, Andrea Califano .  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
Raquel Norel, Donald Petrey, Barry Honig .  2010.   PUDGE: a flexible, interactive server for protein structure prediction.. Nucleic Acids Res. 38 (Web Server issue) :W550-4 ▶ Go to Pubmed
Aris Floratos, Kenneth Smith, Zhou Ji, John Watkinson, Andrea Califano .  2010.   geWorkbench: an open source platform for integrative genomics.. Bioinformatics (Oxford, England). 26 (14) :1779-80 ▶ Go to Pubmed
Aris Floratos, Kenneth Smith, Zhou Ji, John Watkinson, Andrea Califano .  2010.   geWorkbench: an open source platform for integrative genomics.. Bioinformatics. 26 (14) :1779-80 ▶ Go to Pubmed
Hossein Khiabanian, Pieter Van Vlierberghe, Teresa Palomero, Adolfo Ferrando, Raul Rabadan .  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
Yves Lussier, Atul Butte, Lawrence Hunter .  2010.   Current methodologies for translational bioinformatics.. J Biomed Inform. 43 (3) :355-7 ▶ Go to Pubmed
Xuejing Li, Casandra Panea, Chris Wiggins, Valerie Reinke, Christina Leslie .  2010.   Learning "graph-mer" motifs that predict gene expression trajectories in development.. PLoS Comput Biol. 6 (4) :e1000761 ▶ Go to Pubmed
Xinan Yang, Yong Huang, Matthew Crowson, Jianrong Li, Michael Maitland, Yves Lussier .  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
Anil Raj, Chris Wiggins .  2010.   An information-theoretic derivation of min-cut-based clustering.. IEEE Trans Pattern Anal Mach Intell. 32 (6) :988-95 ▶ Go to Pubmed
Arnaud Chastanet, Dennis Vitkup, Guo-Cheng Yuan, Thomas Norman, Jun Liu, Richard Losick .  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
Felix Sanchez-Garcia, Uri Akavia, Eyal Mozes, Dana Pe'er .  2010.   JISTIC: identification of significant targets in cancer.. BMC Bioinformatics. 11 :189 ▶ Go to Pubmed
Hunjoong Lee, Zhaohui Li, Antonina Silkov, Markus Fischer, Donald Petrey, Barry Honig, Diana Murray .  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
Younghee Lee, Xinan Yang, Yong Huang, Hanli Fan, Qingbei Zhang, Youngfei Wu, Jianrong Li, Rifat Hasina, Chao Cheng, Mark Lingen, Mark Gerstein, Ralph Weichselbaum, Rosie Xing, Yves Lussier .  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
Malka Kitayner, Haim Rozenberg, Remo Rohs, Oded Suad, Dov Rabinovich, Barry Honig, Zippora Shakked .  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
Xiang Zhou, Pavel Sumazin, Presha Rajbhandari, Andrea Califano .  2010.   A systems biology approach to transcription factor binding site prediction.. PLoS One. 5 (3) :e9878 ▶ Go to Pubmed
James Chen, Lee Sam, Yong Huang, Younghee Lee, Jianrong Li, Yang Liu, Rosie Xing, Yves Lussier .  2010.   Protein interaction network underpins concordant prognosis among heterogeneous breast cancer signatures.. J Biomed Inform. 43 (3) :385-96 ▶ Go to Pubmed
Lixia Yao, James Evans, Andrey Rzhetsky .  2010.   Novel opportunities for computational biology and sociology in drug discovery.. Trends Biotechnol. 28 (4) :161-70 ▶ Go to Pubmed
Remo Rohs, Xiangshu Jin, Sean West, Rohit Joshi, Barry Honig, Richard Mann .  2010.   Origins of specificity in protein-DNA recognition.. Annu Rev Biochem. 79 :233-69 ▶ Go to Pubmed
Sean West, Remo Rohs, Richard Mann, Barry Honig .  2010.   Electrostatic interactions between arginines and the minor groove in the nucleosome.. J Biomol Struct Dyn. 27 (6) :861-6 ▶ Go to Pubmed
Pieter Van Vlierberghe, Teresa Palomero, Hossein Khiabanian, Joni Van der Meulen, Mireia Castillo-Martin, Nadine Van Roy, Barbara De Moerloose, Jan Philippé, Sara González-García, María Toribio, Tom Taghon, Linda Zuurbier, Barbara Cauwelier, Christine Harrison, Claire Schwab, Markus Pisecker, Sabine Strehl, Anton Langerak, Jozef Gecz, Edwin Sonneveld, Rob Pieters, Elisabeth Paietta, Jacob Rowe, Peter Wiernik, Yves Benoit, Jean Soulier, Bruce Poppe, Xiaopan Yao, Carlos Cordon-Cardo, Jules Meijerink, Raul Rabadan, Frank Speleman, Adolfo Ferrando .  2010.   PHF6 mutations in T-cell acute lymphoblastic leukemia.. Nat Genet. 42 (4) :338-42 ▶ Go to Pubmed
Xiang-Jun Lu, Wilma Olson, Harmen Bussemaker .  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
Carlo Ciatto, Fabiana Bahna, Niccolò Zampieri, Harper VanSteenhouse, Phinikoula Katsamba, Goran Ahlsen, Oliver Harrison, Julia Brasch, Xiangshu Jin, Shoshana Posy, Jeremie Vendome, Barbara Ranscht, Thomas Jessell, Barry Honig, Lawrence Shapiro .  2010.   T-cadherin structures reveal a novel adhesive binding mechanism.. Nat Struct Mol Biol. 17 (3) :339-47 ▶ Go to Pubmed
Oliver Harrison, Fabiana Bahna, Phinikoula Katsamba, Xiangshu Jin, Julia Brasch, Jeremie Vendome, Goran Ahlsen, Kilpatrick Carroll, Stephen Price, Barry Honig, Lawrence Shapiro .  2010.   Two-step adhesive binding by classical cadherins.. Nat Struct Mol Biol. 17 (3) :348-57 ▶ Go to Pubmed
De-xiu Bu, Vivek Rai, Xiaoping Shen, Rosa Rosario, Yan Lu, Vivette D'Agati, Shi Yan, Richard Friedman, Edem Nuglozeh, Ann Schmidt .  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
Jiang Zhu, Lingpeng Cheng, Qin Fang, Hong Zhou, Barry Honig .  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
Marinus van Batenburg, Hualing Li, Annelies Polman, Servane Lachize, Nicole Datson, Harmen Bussemaker, Onno Meijer .  2010.   Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene.. PLoS One. 5 (1) :e8839 ▶ Go to Pubmed
Ulf Klein, Marie Lia, Marta Crespo, Rachael Siegel, Qiong Shen, Tongwei Mo, Alberto Ambesi-Impiombato, Andrea Califano, Anna Migliazza, Govind Bhagat, Riccardo Dalla-Favera .  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
Maria Carro, Wei Lim, Mariano Alvarez, Robert Bollo, Xudong Zhao, Evan Snyder, Erik Sulman, Sandrine Anne, Fiona Doetsch, Howard Colman, Anna Lasorella, Ken Aldape, Andrea Califano, Antonio Iavarone .  2010.   The transcriptional network for mesenchymal transformation of brain tumours.. Nature. 463 (7279) :318-25 ▶ Go to Pubmed
Katia Basso, Masumichi Saito, Pavel Sumazin, Adam Margolin, Kai Wang, Wei-Keat Lim, Yukiko Kitagawa, Christof Schneider, Mariano Alvarez, Andrea Califano, Riccardo Dalla-Favera .  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
Tzu-Lin Hsiao, Olga Revelles, Lifeng Chen, Uwe Sauer, Dennis Vitkup .  2010.   Automatic policing of biochemical annotations using genomic correlations.. Nat Chem Biol. 6 (1) :34-40 ▶ Go to Pubmed
Kiran Singarapu, Jeffrey Mills, Rong Xiao, Thomas Acton, Marco Punta, Markus Fischer, Barry Honig, Burkhard Rost, Gaetano Montelione, Thomas Szyperski .  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
Penelope Bonnen, Jennifer Lowe, David Altshuler, Jan Breslow, Markus Stoffel, Jeffrey Friedman, Itsik Pe'er .  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