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2008

2008 Publications

Yufeng Shen, Sumeet Sarin, Ye Liu, Oliver Hobert, Itsik Pe'er .  2008.   Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing.. PLoS One. 3 (12) :e4012 ▶ Go to Pubmed
Ting Wang, Liliana Moreno-Vinasco, Yong Huang, Gabriel Lang, Jered Linares, Sascha Goonewardena, Alayna Grabavoy, Jonathan Samet, Alison Geyh, Patrick Breysse, Yves Lussier, Viswanathan Natarajan, Joe Garcia .  2008.   Murine lung responses to ambient particulate matter: genomic analysis and influence on airway hyperresponsiveness.. Environ Health Perspect. 116 (11) :1500-8 ▶ Go to Pubmed
Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, Christina Leslie .  2008.   A predictive model of the oxygen and heme regulatory network in yeast.. PLoS Comput Biol. 4 (11) :e1000224 ▶ Go to Pubmed
Iain Melvin, Jason Weston, Christina Leslie, William Noble .  2008.   Combining classifiers for improved classification of proteins from sequence or structure.. BMC Bioinformatics. 9 :389 ▶ Go to Pubmed
André Boorsma, Xiang-Jun Lu, Anna Zakrzewska, Frans Klis, Harmen Bussemaker .  2008.   Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.. PLoS One. 3 (9) :e3112 ▶ Go to Pubmed
Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky, John Wilbur .  2008.   Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users.. Bioinformatics. 24 (18) :2086-93 ▶ Go to Pubmed
Vesselin Miloushev, Fabiana Bahna, Carlo Ciatto, Goran Ahlsen, Barry Honig, Lawrence Shapiro, Arthur Palmer .  2008.   Dynamic properties of a type II cadherin adhesive domain: implications for the mechanism of strand-swapping of classical cadherins.. Structure. 16 (8) :1195-205 ▶ Go to Pubmed
Sumeet Sarin, Snehit Prabhu, Maggie O'Meara, Itsik Pe'er, Oliver Hobert .  2008.   Caenorhabditis elegans mutant allele identification by whole-genome sequencing.. Nat Methods. 5 (10) :865-7 ▶ Go to Pubmed
Sang-Bum Hong, Yong Huang, Liliana Moreno-Vinasco, Saad Sammani, Jaideep Moitra, Joseph Barnard, Shwu-Fan Ma, Tamara Mirzapoiazova, Carrie Evenoski, Ryan Reeves, Eddie Chiang, Gabriel Lang, Aliya Husain, Steven Dudek, Jeffrey Jacobson, Shui Ye, Yves Lussier, Joe Garcia .  2008.   Essential role of pre-B-cell colony enhancing factor in ventilator-induced lung injury.. Am J Respir Crit Care Med. 178 (6) :605-17 ▶ Go to Pubmed
Martin Cadeiras, Manuel Bayern, Elizabeth Burke, Russell Dedrick, Anatasia Gangadin, Farhana Latif, Farhana Latif, Khurram Shahzad, Khurram Shazad, Anshu Sinha, Esteban Tabak, Charles Marboe, Andrea Califano, Mario Deng .  2008.   Gene expression profiles of patients with antibody-mediated rejection after cardiac transplantation.. J Heart Lung Transplant. 27 (8) :932-4 ▶ Go to Pubmed
Jake Hofman, Chris Wiggins .  2008.   Bayesian approach to network modularity.. Phys Rev Lett. 100 (25) :258701 ▶ Go to Pubmed
Andrey Rzhetsky, Michael Seringhaus, Mark Gerstein .  2008.   Seeking a new biology through text mining.. Cell. 134 (1) :9-13 ▶ Go to Pubmed
Lucas Ward, Harmen Bussemaker .  2008.   Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.. Bioinformatics. 24 (13) :i165-71 ▶ Go to Pubmed
Ivo Dinov, Daniel Rubin, William Lorensen, Jonathan Dugan, Jeff Ma, Shawn Murphy, Beth Kirschner, William Bug, Michael Sherman, Aris Floratos, David Kennedy, H Jagadish V, Jeanette Schmidt, Brian Athey, Andrea Califano, Mark Musen, Russ Altman, Ron Kikinis, Isaac Kohane, Scott Delp, Stott Parker, Arthur Toga .  2008.   iTools: a framework for classification, categorization and integration of computational biology resources.. PLoS One. 3 (5) :e2265 ▶ Go to Pubmed
Pier Piccaluga, Andrea Califano, Ulf Klein, Claudio Agostinelli, Beatriz Bellosillo, Eva Gimeno, Sergi Serrano, Francisco Solè, Yonghui Zang, Brunangelo Falini, Pier Zinzani, Stefano Pileri .  2008.   Gene expression analysis provides a potential rationale for revising the histological grading of follicular lymphomas.. Haematologica. 93 (7) :1033-8 ▶ Go to Pubmed
Ivan Iossifov, Tian Zheng, Miron Baron, Conrad Gilliam, Andrey Rzhetsky .  2008.   Genetic-linkage mapping of complex hereditary disorders to a whole-genome molecular-interaction network.. Genome Res. 18 (7) :1150-62 ▶ Go to Pubmed
Shoshana Posy, Lawrence Shapiro, Barry Honig .  2008.   Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?. J Mol Biol. 378 (4) :954-68 ▶ Go to Pubmed
Susan Christian, Camille Brune, Jyotsna Sudi, Ravinesh Kumar, Shaung Liu, Samer Karamohamed, Judith Badner, Seiichi Matsui, Jeffrey Conroy, Devin McQuaid, James Gergel, Eli Hatchwell, Conrad Gilliam, Elliot Gershon, Norma Nowak, William Dobyns, Edwin Cook .  2008.   Novel submicroscopic chromosomal abnormalities detected in autism spectrum disorder.. Biol Psychiatry. 63 (12) :1111-7 ▶ Go to Pubmed
Elzo de Wit, Ulrich Braunschweig, Frauke Greil, Harmen Bussemaker, Bas van Steensel .  2008.   Global chromatin domain organization of the Drosophila genome.. PLoS Genet. 4 (3) :e1000045 ▶ Go to Pubmed
Itsik Pe'er, Roman Yelensky, David Altshuler, Mark Daly .  2008.   Estimation of the multiple testing burden for genomewide association studies of nearly all common variants.. Genet Epidemiol. 32 (4) :381-5 ▶ Go to Pubmed
Jesko Koehnke, Xiangshu Jin, Nikola Trbovic, Phinikoula Katsamba, Julia Brasch, Goran Ahlsen, Peter Scheiffele, Barry Honig, Arthur Palmer, Lawrence Shapiro .  2008.   Crystal structures of beta-neurexin 1 and beta-neurexin 2 ectodomains and dynamics of splice insertion sequence 4.. Structure. 16 (3) :410-21 ▶ Go to Pubmed
Igor Feldman, Andrey Rzhetsky, Dennis Vitkup .  2008.   Network properties of genes harboring inherited disease mutations.. Proc Natl Acad Sci U S A. 105 (11) :4323-8 ▶ Go to Pubmed
Raul Rodriguez-Esteban, Andrey Rzhetsky .  2008.   Six senses in the literature. The bleak sensory landscape of biomedical texts.. EMBO Rep. 9 (3) :212-5 ▶ Go to Pubmed
Liliana Moreno-Vinasco, Mardi Gomberg-Maitland, Michael Maitland, Ankit Desai, Patrick Singleton, Saad Sammani, Lee Sam, Yang Liu, Aliya Husain, Roberto Lang, Mark Ratain, Yves Lussier, Joe Garcia .  2008.   Genomic assessment of a multikinase inhibitor, sorafenib, in a rodent model of pulmonary hypertension.. Physiol Genomics. 33 (2) :278-91 ▶ Go to Pubmed
Kartik Mani, Celine Lefebvre, Kai Wang, Wei Lim, Katia Basso, Riccardo Dalla-Favera, Andrea Califano .  2008.   A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas.. Mol Syst Biol. 4 :169 ▶ Go to Pubmed
Jesko Koehnke, Xiangshu Jin, Elaine Budreck, Shoshana Posy, Peter Scheiffele, Barry Honig, Lawrence Shapiro .  2008.   Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2.. Proc Natl Acad Sci U S A. 105 (6) :1873-8 ▶ Go to Pubmed
Ravinesh Kumar, Samer Karamohamed, Jyotsna Sudi, Donald Conrad, Camille Brune, Judith Badner, Conrad Gilliam, Norma Nowak, Edwin Cook, William Dobyns, Susan Christian .  2008.   Recurrent 16p11.2 microdeletions in autism.. Hum Mol Genet. 17 (4) :628-38 ▶ Go to Pubmed
Lixia Yao, Andrey Rzhetsky .  2008.   Quantitative systems-level determinants of human genes targeted by successful drugs.. Genome Res. 18 (2) :206-13 ▶ Go to Pubmed
Omar Jabado, Yang Liu, Sean Conlan, Lan Quan, Hédi Hegyi, Yves Lussier, Thomas Briese, Gustavo Palacios, W Lipkin .  2008.   Comprehensive viral oligonucleotide probe design using conserved protein regions.. Nucleic Acids Res. 36 (1) :e3 ▶ Go to Pubmed
Julia Stoyanovich, Itsik Pe'er .  2008.   MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data.. Bioinformatics. 24 (3) :440-2 ▶ Go to Pubmed
Barrett Foat, Ronald Tepper, Harmen Bussemaker .  2008.   TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors.. Nucleic Acids Res. 36 (Database issue) :D125-31 ▶ Go to Pubmed