Search Publications

Filter Publications

By Year
Andrew Mugler, Aleksandra Walczak, Chris Wiggins .  2009.   Spectral solutions to stochastic models of gene expression with bursts and regulation.. Phys Rev E Stat Nonlin Soft Matter Phys. 80 (4 Pt 1) :041921 ▶ Go to Pubmed
Ivan Iossifov, Raul Rodriguez-Esteban, Ilya Mayzus, Kathleen Millen, Andrey Rzhetsky .  2009.   Looking at cerebellar malformations through text-mined interactomes of mice and humans.. PLoS Comput Biol. 5 (11) :e1000559 ▶ Go to Pubmed
Bo-Juen Chen, Helen Causton, Denesy Mancenido, Noel Goddard, Ethan Perlstein, Dana Pe'er .  2009.   Harnessing gene expression to identify the genetic basis of drug resistance.. Mol Syst Biol. 5 :310 ▶ Go to Pubmed
Remo Rohs, Sean West, Alona Sosinsky, Peng Liu, Richard Mann, Barry Honig .  2009.   The role of DNA shape in protein-DNA recognition.. Nature. 461 (7268) :1248-53 ▶ 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
Hossein Khiabanian, Vladimir Trifonov, Raul Rabadan .  2009.   Reassortment patterns in Swine influenza viruses.. PLoS One. 4 (10) :e7366 ▶ Go to Pubmed
Donald Petrey, Markus Fischer, Barry Honig .  2009.   Structural relationships among proteins with different global topologies and their implications for function annotation strategies.. Proc Natl Acad Sci U S A. 106 (41) :17377-82 ▶ Go to Pubmed
Kai Wang, Masumichi Saito, Brygida Bisikirska, Mariano Alvarez, Wei Lim, Presha Rajbhandari, Qiong Shen, Ilya Nemenman, Katia Basso, Adam Margolin, Ulf Klein, Riccardo Dalla-Favera, Andrea Califano .  2009.   Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.. Nat Biotechnol. 27 (9) :829-39 ▶ Go to Pubmed
Hossein Khiabanian, Gregory Farrell, Kirsten St George, Raul Rabadan .  2009.   Differences in patient age distribution between influenza A subtypes.. PLoS One. 4 (8) :e6832 ▶ Go to Pubmed
Xudong Zhao, Domenico Arca, Wei Lim, Manisha Brahmachary, Maria Carro, Thomas Ludwig, Carlos Cardo, Francois Guillemot, Ken Aldape, Andrea Califano, Antonio Iavarone, Anna Lasorella .  2009.   The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain.. Dev Cell. 17 (2) :210-21 ▶ Go to Pubmed
Harris Wang, Farren Isaacs, Peter Carr, Zachary Sun, George Xu, Craig Forest, George Church .  2009.   Programming cells by multiplex genome engineering and accelerated evolution.. Nature. 460 (7257) :894-898 ▶ Go to Pubmed
Phinikoula Katsamba, Kilpatrick Carroll, Goran Ahlsen, Fabiana Bahna, Jeremie Vendome, Shoshana Posy, M Rajebhosale, Stephen Price, Thomas Jessell, Avinoam Ben-Shaul, Lawrence Shapiro, Barry Honig .  2009.   Linking molecular affinity and cellular specificity in cadherin-mediated adhesion.. Proc Natl Acad Sci U S A. 106 (28) :11594-9 ▶ Go to Pubmed
Masumichi Saito, Urban Novak, Erich Piovan, Katia Basso, Pavel Sumazin, Christof Schneider, Marta Crespo, Qiong Shen, Govind Bhagat, Andrea Califano, Amy Chadburn, Laura Pasqualucci, Riccardo Dalla-Favera .  2009.   BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma.. Proc Natl Acad Sci U S A. 106 (27) :11294-9 ▶ Go to Pubmed
Ann Daly, Peter Donaldson, Pallav Bhatnagar, Yufeng Shen, Itsik Pe'er, Aris Floratos, Mark Daly, David Goldstein, Sally John, Matthew Nelson, Julia Graham, Kevin Park, John Dillon, William Bernal, Heather Cordell, Munir Pirmohamed, Guruprasad Aithal, Christopher Day, DILIGEN Study, International Consortium .  2009.   HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin.. Nat Genet. 41 (7) :816-9 ▶ Go to Pubmed
Ann Daly, Peter Donaldson, Pallav Bhatnagar, Yufeng Shen, Itsik Pe'er, Aris Floratos, Mark Daly, David Goldstein, Sally John, Matthew Nelson, Julia Graham, Kevin Park, John Dillon, William Bernal, Heather Cordell, Munir Pirmohamed, Guruprasad Aithal, Christopher Day, DILIGEN Study, International Consortium .  2009.   HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin.. Nature genetics. 41 (7) :816-9 ▶ Go to Pubmed
Vladimir Trifonov, Hossein Khiabanian, Raul Rabadan .  2009.   Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus.. N Engl J Med. 361 (2) :115-9 ▶ Go to Pubmed
Aly Khan, Doron Betel, Martin Miller, Chris Sander, Christina Leslie, Debora Marks .  2009.   Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs.. Nat Biotechnol. 27 (6) :549-55 ▶ Go to Pubmed
Snehit Prabhu, Itsik Pe'er .  2009.   Overlapping pools for high-throughput targeted resequencing.. Genome Res. 19 (7) :1254-61 ▶ Go to Pubmed
Katia Basso, Pavel Sumazin, Pavel Morozov, Christof Schneider, Roy Maute, Yukiko Kitagawa, Jonathan Mandelbaum, Joseph Haddad, Chang-Zheng Chen, Andrea Califano, Riccardo Dalla-Favera .  2009.   Identification of the human mature B cell miRNome.. Immunity. 30 (5) :744-52 ▶ Go to Pubmed
Trifonov V, Hossein Khiabanian, B Greenbaum, Raul Rabadan .  2009.   The origin of the recent swine influenza A(H1N1) virus infecting humans.. Euro Surveill. 14 (17) ▶ Go to Pubmed
Mara Compagno, Wei Lim, Adina Grunn, Subhadra Nandula V, Manisha Brahmachary, Qiong Shen, Francesco Bertoni, Maurilio Ponzoni, Marta Scandurra, Andrea Califano, Govind Bhagat, Amy Chadburn, Riccardo Dalla-Favera, Laura Pasqualucci .  2009.   Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma.. Nature. 459 (7247) :717-21 ▶ Go to Pubmed
Remo Rohs, Sean West, Peng Liu, Barry Honig .  2009.   Nuance in the double-helix and its role in protein-DNA recognition.. Curr Opin Struct Biol. 19 (2) :171-7 ▶ Go to Pubmed
Aleksandra Walczak, Andrew Mugler, Chris Wiggins .  2009.   A stochastic spectral analysis of transcriptional regulatory cascades.. Proc Natl Acad Sci U S A. 106 (16) :6529-34 ▶ Go to Pubmed
David Waltz, Bruce Buchanan .  2009.   Computer science. Automating science.. Science. 324 (5923) :43-4 ▶ Go to Pubmed
Donald Petrey, Barry Honig .  2009.   Is protein classification necessary? Toward alternative approaches to function annotation.. Curr Opin Struct Biol. 19 (3) :363-8 ▶ Go to Pubmed
Guy Nimrod, András Szilágyi, Christina Leslie, Nir Ben-Tal .  2009.   Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.. J Mol Biol. 387 (4) :1040-53 ▶ Go to Pubmed
Oren Litvin, Helen Causton, Bo-Juen Chen, Dana Pe'er .  2009.   Modularity and interactions in the genetics of gene expression.. Proc Natl Acad Sci U S A. 106 (16) :6441-6 ▶ Go to Pubmed
Wei Lim, Eugenia Lyashenko, Andrea Califano .  2009.   Master regulators used as breast cancer metastasis classifier.. Pac Symp Biocomput. :504-15 ▶ Go to Pubmed
Kai Wang, Mariano Alvarez, Brygida Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla-Favera, Andrea Califano .  2009.   Dissecting the interface between signaling and transcriptional regulation in human B cells.. Pac Symp Biocomput. :264-75 ▶ Go to Pubmed
Lee Sam, Eneida Mendonça, Jianrong Li, Judith Blake, Carol Friedman, Yves Lussier .  2009.   PhenoGO: an integrated resource for the multiscale mining of clinical and biological data.. BMC Bioinformatics. 10 Suppl 2 :S8 ▶ Go to Pubmed
Yang Liu, Lee Sam, Jianrong Li, Yves Lussier .  2009.   Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays.. BMC Bioinformatics. 10 Suppl 2 :S11 ▶ Go to Pubmed
Jennifer Lowe, Julian Maller, Itsik Pe'er, Benjamin Neale, Jacqueline Salit, Eimear Kenny, Jessica Shea, Ralph Burkhardt, Gustav Smith, Weizhen Ji, Martha Noel, Jia Foo, Maude Blundell, Vita Skilling, Laura Garcia, Marcia Sullivan, Heather Lee, Anna Labek, Hope Ferdowsian, Steven Auerbach, Richard Lifton, Christopher Newton-Cheh, Jan Breslow, Markus Stoffel, Mark Daly, David Altshuler, Jeffrey Friedman .  2009.   Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.. PLoS Genet. 5 (2) :e1000365 ▶ Go to Pubmed
Karen Sachs, Solomon Itani, Jennifer Carlisle, Garry Nolan, Dana Pe'er, Douglas Lauffenburger .  2009.   Learning signaling network structures with sparsely distributed data.. J Comput Biol. 16 (2) :201-12 ▶ Go to Pubmed
Su-In Lee, Aimée Dudley, David Drubin, Pamela Silver, Nevan Krogan, Dana Pe'er, Daphne Koller .  2009.   Learning a prior on regulatory potential from eQTL data.. PLoS Genet. 5 (1) :e1000358 ▶ Go to Pubmed
Jiang Liu, Murad Ghanim, Lei Xue, Christopher Brown, Ivan Iossifov, Cesar Angeletti, Sujun Hua, Nicolas Nègre, Michael Ludwig, Thomas Stricker, Hikmat Al-Ahmadie, Maria Tretiakova, Robert Camp, Montse Perera-Alberto, David Rimm, Tian Xu, Andrey Rzhetsky, Kevin White .  2009.   Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer.. Science. 323 (5918) :1218-22 ▶ Go to Pubmed
Nuala Meyer, Yong Huang, Patrick Singleton, Saad Sammani, Jaideep Moitra, Carrie Evenoski, Aliya Husain, Sumegha Mitra, Liliana Moreno-Vinasco, Jeffrey Jacobson, Yves Lussier, Joe Garcia .  2009.   GADD45a is a novel candidate gene in inflammatory lung injury via influences on Akt signaling.. FASEB J. 23 (5) :1325-37 ▶ Go to Pubmed
Adam Margolin, Teresa Palomero, Pavel Sumazin, Andrea Califano, Adolfo Ferrando, Gustavo Stolovitzky .  2009.   ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.. Proc Natl Acad Sci U S A. 106 (1) :244-9 ▶ Go to Pubmed
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 .  2009.   RANKPROP: a web server for protein remote homology detection.. Bioinformatics. 25 (1) :121-2 ▶ Go to Pubmed
Alexander Gusev, Jennifer Lowe, Markus Stoffel, Mark Daly, David Altshuler, Jan Breslow, Jeffrey Friedman, Itsik Pe'er .  2009.   Whole population, genome-wide mapping of hidden relatedness.. Genome Res. 19 (2) :318-26 ▶ 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
Lee Sam, Yang Liu, Jianrong Li, Carol Friedman, Yves Lussier .  2007.   Discovery of protein interaction networks shared by diseases.. Pac Symp Biocomput. :76-87 ▶ Go to Pubmed
Rohit Joshi, Jonathan Passner, Remo Rohs, Rinku Jain, Alona Sosinsky, Michael Crickmore, Vinitha Jacob, Aneel Aggarwal, Barry Honig, Richard Mann .  2007.   Functional specificity of a Hox protein mediated by the recognition of minor groove structure.. Cell. 131 (3) :530-43 ▶ Go to Pubmed
Etay Ziv, Ilya Nemenman, Chris Wiggins .  2007.   Optimal signal processing in small stochastic biochemical networks.. PLoS One. 2 (10) :e1077 ▶ 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
Anshul Kundaje, Steve Lianoglou, Xuejing Li, David Quigley, Marta Arias, Chris Wiggins, Li Zhang, Christina Leslie .  2007.   Learning regulatory programs that accurately predict differential expression with MEDUSA.. Ann N Y Acad Sci. 1115 :178-202 ▶ Go to Pubmed
Adam Margolin, Andrea Califano .  2007.   Theory and limitations of genetic network inference from microarray data.. Ann N Y Acad Sci. 1115 :51-72 ▶ Go to Pubmed
Lawrence David, Chris Wiggins .  2007.   Benchmarking of dynamic Bayesian networks inferred from stochastic time-series data.. Ann N Y Acad Sci. 1115 :90-101 ▶ Go to Pubmed
Harmen Bussemaker, Lucas Ward, André Boorsma .  2007.   Dissecting complex transcriptional responses using pathway-level scores based on prior information.. BMC Bioinformatics. 8 Suppl 6 :S6 ▶ Go to Pubmed
Michael Bales, Yves Lussier, Stephen Johnson .  2007.   Topological analysis of large-scale biomedical terminology structures.. J Am Med Inform Assoc. 14 (6) :788-97 ▶ Go to Pubmed
Ying Tao, Lee Sam, Jianrong Li, Carol Friedman, Yves Lussier .  2007.   Information theory applied to the sparse gene ontology annotation network to predict novel gene function.. Bioinformatics. 23 (13) :i529-38 ▶ Go to Pubmed
Wei Lim, Kai Wang, Celine Lefebvre, Andrea Califano .  2007.   Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks.. Bioinformatics. 23 (13) :i282-8 ▶ Go to Pubmed
Andrey Rzhetsky, David Wajngurt, Naeun Park, Tian Zheng .  2007.   Probing genetic overlap among complex human phenotypes.. Proc Natl Acad Sci U S A. 104 (28) :11694-9 ▶ Go to Pubmed
Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford, Christina Leslie .  2007.   SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.. BMC Bioinformatics. 8 Suppl 4 :S2 ▶ Go to Pubmed
Nicholas Yagoda, Moritz von Rechenberg, Elma Zaganjor, Andras Bauer, Wan Yang, Daniel Fridman, Adam Wolpaw, Inese Smukste, John Peltier, Jay Boniface, Richard Smith, Stephen Lessnick, Sudhir Sahasrabudhe, Brent Stockwell .  2007.   RAS-RAF-MEK-dependent oxidative cell death involving voltage-dependent anion channels.. Nature. 447 (7146) :864-8 ▶ Go to Pubmed
Murat Cokol, Raul Rodriguez-Esteban, Andrey Rzhetsky .  2007.   A recipe for high impact.. Genome Biol. 8 (5) :406 ▶ Go to Pubmed
James Chen, Yang Liu, Lee Sam, Jianrong Li, Yves Lussier .  2007.   Evaluation of high-throughput functional categorization of human disease genes.. BMC Bioinformatics. 8 Suppl 3 :S7 ▶ Go to Pubmed
Murat Cokol, Ivan Iossifov, Raul Rodriguez-Esteban, Andrey Rzhetsky .  2007.   How many scientific papers should be retracted?. EMBO Rep. 8 (5) :422-3 ▶ Go to Pubmed
Adam Margolin, Kai Wang, Wei Lim, Manjunath Kustagi, Ilya Nemenman, Andrea Califano .  2006.   Reverse engineering cellular networks.. Nat Protoc. 1 (2) :662-71 ▶ Go to Pubmed
Alona Sosinsky, Barry Honig, Richard Mann, Andrea Califano .  2007.   Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting.. Proc Natl Acad Sci U S A. 104 (15) :6305-10 ▶ Go to Pubmed
Autism Consortium, Peter Szatmari, Andrew Paterson, Lonnie Zwaigenbaum, Wendy Roberts, Jessica Brian, Xiao-Qing Liu, John Vincent, Jennifer Skaug, Ann Thompson, Lili Senman, Lars Feuk, Cheng Qian, Susan Bryson, Marshall Jones, Christian Marshall, Stephen Scherer, Veronica Vieland, Christopher Bartlett, La Mangin, Rhinda Goedken, Alberto Segre, Margaret Pericak-Vance, Michael Cuccaro, John Gilbert, Harry Wright, Ruth Abramson, Catalina Betancur, Thomas Bourgeron, Christopher Gillberg, Marion Leboyer, Joseph Buxbaum, Kenneth Davis, Eric Hollander, Jeremy Silverman, Joachim Hallmayer, Linda Lotspeich, James Sutcliffe, Jonathan Haines, Susan Folstein, Joseph Piven, Thomas Wassink, Val Sheffield, Daniel Geschwind, Maja Bucan, Ted Brown, Rita Cantor, John Constantino, Conrad Gilliam, Martha Herbert, Clara Lajonchere, David Ledbetter, Christa Lese-Martin, Janet Miller, Stan Nelson, Carol Samango-Sprouse, Sarah Spence, Matthew State, Rudolph Tanzi, Hilary Coon, Geraldine Dawson, Bernie Devlin, Annette Estes, Pamela Flodman, Lambertus Klei, William McMahon, Nancy Minshew, Jeff Munson, Elena Korvatska, Patricia Rodier, Gerard Schellenberg, Moyra Smith, Anne Spence, Chris Stodgell, Ping Tepper, Ellen Wijsman, Chang-En Yu, Bernadette Rogé, Carine Mantoulan, Kerstin Wittemeyer, Annemarie Poustka, Bärbel Felder, Sabine Klauck, Claudia Schuster, Fritz Poustka, Sven Bölte, Sabine Feineis-Matthews, Evelyn Herbrecht, Gabi Schmötzer, John Tsiantis, Katerina Papanikolaou, Elena Maestrini, Elena Bacchelli, Francesca Blasi, Simona Carone, Claudio Toma, Herman Van Engeland, Maretha de Jonge, Chantal Kemner, Frederieke Koop, Frederike Koop, Marjolein Langemeijer, Marjolijn Langemeijer, Channa Hijmans, Channa Hijmans, Wouter Staal, Gillian Baird, Patrick Bolton, Michael Rutter, Emma Weisblatt, Jonathan Green, Catherine Aldred, Julie-Anne Wilkinson, Andrew Pickles, Ann Le Couteur, Tom Berney, Helen McConachie, Anthony Bailey, Kostas Francis, Gemma Honeyman, Aislinn Hutchinson, Jeremy Parr, Simon Wallace, Anthony Monaco, Gabrielle Barnby, Kazuhiro Kobayashi, Janine Lamb, Ines Sousa, Nuala Sykes, Edwin Cook, Stephen Guter, Bennett Leventhal, Jeff Salt, Catherine Lord, Christina Corsello, Vanessa Hus, Daniel Weeks, Fred Volkmar, Maïté Tauber, Eric Fombonne, Andy Shih, Kacie Meyer .  2007.   Mapping autism risk loci using genetic linkage and chromosomal rearrangements.. Nat Genet. 39 (3) :319-28 ▶ Go to Pubmed
Harmen Bussemaker, Barrett Foat, Lucas Ward .  2007.   Predictive modeling of genome-wide mRNA expression: from modules to molecules.. Annu Rev Biophys Biomol Struct. 36 :329-47 ▶ Go to Pubmed
Dimitris Anastassiou .  2007.   Computational analysis of the synergy among multiple interacting genes.. Mol Syst Biol. 3 :83 ▶ Go to Pubmed
Frauke Greil, Elzo de Wit, Harmen Bussemaker, Bas van Steensel .  2007.   HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila.. EMBO J. 26 (3) :741-51 ▶ Go to Pubmed
Yves Lussier, Yang Liu .  2007.   Computational approaches to phenotyping: high-throughput phenomics.. Proc Am Thorac Soc. 4 (1) :18-25 ▶ Go to Pubmed
Hemant Varma, Cindy Voisine, Todd DeMarco, Elena Cattaneo, Donald Lo, Anne Hart, Brent Stockwell .  2007.   Selective inhibitors of death in mutant huntingtin cells.. Nat Chem Biol. 3 (2) :99-100 ▶ Go to Pubmed
Teresa Palomero, Wei Lim, Duncan Odom, Maria Sulis, Pedro Real, Adam Margolin, Kelly Barnes, Jennifer O'Neil, Donna Neuberg, Andrew Weng, Jon Aster, Francois Sigaux, Jean Soulier, Thomas Look, Richard Young, Andrea Califano, Adolfo Ferrando .  2006.   NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth.. Proc Natl Acad Sci U S A. 103 (48) :18261-6 ▶ Go to Pubmed
Yang Liu, Jianrong Li, Lee Sam, Chern-Sing Goh, Mark Gerstein, Yves Lussier .  2006.   An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.. PLoS Comput Biol. 2 (11) :e159 ▶ Go to Pubmed
Yves Lussier, Tara Borlawsky, Daniel Rappaport, Yang Liu, Carol Friedman .  2006.   PhenoGO: assigning phenotypic context to gene ontology annotations with natural language processing.. Pac Symp Biocomput. :64-75 ▶ Go to Pubmed
Raul Rodriguez-Esteban, Ivan Iossifov, Andrey Rzhetsky .  2006.   Imitating manual curation of text-mined facts in biomedicine.. PLoS Comput Biol. 2 (9) :e118 ▶ Go to Pubmed
Hans-Günther Döbereiner, Benjamin Dubin-Thaler, Jake Hofman, Harry Xenias, Tasha Sims, Grégory Giannone, Michael Dustin, Chris Wiggins, Michael Sheetz .  2006.   Lateral membrane waves constitute a universal dynamic pattern of motile cells.. Phys Rev Lett. 97 (3) :038102 ▶ Go to Pubmed
Celine Moorman, Ling Sun V, Junbai Wang, Elzo de Wit, Wendy Talhout, Lucas Ward, Frauke Greil, Xiang-Jun Lu, Kevin White, Harmen Bussemaker, Bas van Steensel .  2006.   Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.. Proc Natl Acad Sci U S A. 103 (32) :12027-32 ▶ Go to Pubmed