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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
Vinay Varadan, David Miller, Dimitris Anastassiou .  2006.   Computational inference of the molecular logic for synaptic connectivity in C. elegans.. Bioinformatics. 22 (14) :e497-506 ▶ Go to Pubmed
Yanay Ofran, Guy Yachdav, Eyal Mozes, Ta-tsen Soong, Rajesh Nair, Burkhard Rost .  2006.   Create and assess protein networks through molecular characteristics of individual proteins.. Bioinformatics. 22 (14) :e402-7 ▶ Go to Pubmed
Barrett Foat, Alexandre Morozov V, Harmen Bussemaker .  2006.   Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.. Bioinformatics. 22 (14) :e141-9 ▶ Go to Pubmed
Carol Friedman, Tara Borlawsky, Lyudmila Shagina, Rosie Xing, Yves Lussier .  2006.   Bio-Ontology and text: bridging the modeling gap.. Bioinformatics. 22 (19) :2421-9 ▶ Go to Pubmed
Gabor Halasz, Marinus van Batenburg, Joelle Perusse, Sujun Hua, Xiang-Jun Lu, Kevin White, Harmen Bussemaker .  2006.   Detecting transcriptionally active regions using genomic tiling arrays.. Genome Biol. 7 (7) :R59 ▶ Go to Pubmed
Harmen Bussemaker .  2006.   Modeling gene expression control using Omes Law.. Mol Syst Biol. 2 :2006.0013 ▶ Go to Pubmed
Adam Margolin, Ilya Nemenman, Katia Basso, Chris Wiggins, Gustavo Stolovitzky, Riccardo Dalla-Favera, Andrea Califano .  2006.   ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.. BMC Bioinformatics. 7 Suppl 1 :S7 ▶ Go to Pubmed
Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chris Wiggins, Yoav Freund, Christina Leslie .  2006.   A classification-based framework for predicting and analyzing gene regulatory response.. BMC Bioinformatics. 7 Suppl 1 :S5 ▶ Go to Pubmed
Dimitris Anastassiou, Hairuo Liu, Vinay Varadan .  2006.   Variable window binding for mutually exclusive alternative splicing.. Genome Biol. 7 (1) :R2 ▶ Go to Pubmed
Daniel Koster, Chris Wiggins, Nynke Dekker .  2006.   Multiple events on single molecules: unbiased estimation in single-molecule biophysics.. Proc Natl Acad Sci U S A. 103 (6) :1750-5 ▶ Go to Pubmed
André Boorsma, Barrett Foat, Daniel Vis, Frans Klis, Harmen Bussemaker .  2005.   T-profiler: scoring the activity of predefined groups of genes using gene expression data.. Nucleic Acids Res. 33 (Web Server issue) :W592-5 ▶ Go to Pubmed
German Cavelier, Dimitris Anastassiou .  2005.   Phenotype analysis using network motifs derived from changes in regulatory network dynamics.. Proteins. 60 (3) :525-46 ▶ Go to Pubmed
Chien Chen, Shoshana Posy, Avinoam Ben-Shaul, Lawrence Shapiro, Barry Honig .  2005.   Specificity of cell-cell adhesion by classical cadherins: Critical role for low-affinity dimerization through beta-strand swapping.. Proc Natl Acad Sci U S A. 102 (24) :8531-6 ▶ Go to Pubmed
Jason Weston, Christina Leslie, Eugene Ie, Dengyong Zhou, Andre Elisseeff, William Noble .  2005.   Semi-supervised protein classification using cluster kernels.. Bioinformatics. 21 (15) :3241-7 ▶ Go to Pubmed
Marco Punta, Burkhard Rost .  2005.   PROFcon: novel prediction of long-range contacts.. Bioinformatics. 21 (13) :2960-8 ▶ Go to Pubmed
M Alarcón, A Yonan, T Gilliam, Rita Cantor, D Geschwind .  2005.   Quantitative genome scan and Ordered-Subsets Analysis of autism endophenotypes support language QTLs.. Mol Psychiatry. 10 (8) :747-57 ▶ Go to Pubmed
Hao Fan, Alan Mark, Jiang Zhu, Barry Honig .  2005.   Comparative study of generalized Born models: protein dynamics.. Proc Natl Acad Sci U S A. 102 (19) :6760-4 ▶ Go to Pubmed
Rajesh Nair, Burkhard Rost .  2005.   Mimicking cellular sorting improves prediction of subcellular localization.. J Mol Biol. 348 (1) :85-100 ▶ Go to Pubmed
Katia Basso, Adam Margolin, Gustavo Stolovitzky, Ulf Klein, Riccardo Dalla-Favera, Andrea Califano .  2005.   Reverse engineering of regulatory networks in human B cells.. Nat Genet. 37 (4) :382-90 ▶ Go to Pubmed
Michael Cantor, Indra Sarkar, Olivier Bodenreider, Yves Lussier .  2005.   Genestrace: phenomic knowledge discovery via structured terminology.. Pac Symp Biocomput. :103-14 ▶ Go to Pubmed
Trevor Siggers, Antonina Silkov, Barry Honig .  2005.   Structural alignment of protein--DNA interfaces: insights into the determinants of binding specificity.. J Mol Biol. 345 (5) :1027-45 ▶ Go to Pubmed
Ying Tao, Carol Friedman, Yves Lussier .  2005.   Visualizing information across multidimensional post-genomic structured and textual databases.. Bioinformatics. 21 (8) :1659-67 ▶ Go to Pubmed
Viktor Stolc, Zareen Gauhar, Christopher Mason, Gabor Halasz, Marinus van Batenburg, Scott Rifkin, Sujun Hua, Tine Herreman, Waraporn Tongprasit, Paolo Barbano, Harmen Bussemaker, Kevin White .  2004.   A gene expression map for the euchromatic genome of Drosophila melanogaster.. Science. 306 (5696) :655-60 ▶ Go to Pubmed
Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina Leslie .  2004.   Predicting genetic regulatory response using classification.. Bioinformatics. 20 Suppl 1 :i232-40 ▶ Go to Pubmed
Rajesh Nair, Burkhard Rost .  2004.   LOCnet and LOCtarget: sub-cellular localization for structural genomics targets.. Nucleic Acids Res. 32 (Web Server issue) :W517-21 ▶ Go to Pubmed
Burkhard Rost, Guy Yachdav, Jinfeng Liu .  2004.   The PredictProtein server.. Nucleic Acids Res. 32 (Web Server issue) :W321-6 ▶ Go to Pubmed
Feng Gao, Barrett Foat, Harmen Bussemaker .  2004.   Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.. BMC Bioinformatics. 5 :31 ▶ Go to Pubmed
Jinfeng Liu, Burkhard Rost .  2004.   CHOP proteins into structural domain-like fragments.. Proteins. 55 (3) :678-88 ▶ Go to Pubmed
Jason Weston, Andre Elisseeff, Dengyong Zhou, Christina Leslie, William Noble .  2004.   Protein ranking: from local to global structure in the protein similarity network.. Proc Natl Acad Sci U S A. 101 (17) :6559-63 ▶ Go to Pubmed
Yves Lussier, Jianrong Li .  2004.   Terminological mapping for high throughput comparative biology of phenotypes.. Pac Symp Biocomput. :202-13 ▶ Go to Pubmed
Xiang Zhang, Katherine Heller, Ilana Hefter, Christina Leslie, Lawrence Chasin .  2003.   Sequence information for the splicing of human pre-mRNA identified by support vector machine classification.. Genome Res. 13 (12) :2637-50 ▶ Go to Pubmed
Christopher Tang, Lei Xie, Ingrid Y Y Koh, Shoshana Posy, Emil Alexov, Barry Honig .  2003.   On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles.. J Mol Biol. 334 (5) :1043-62 ▶ Go to Pubmed
Donald Petrey, Zhexin Xiang, Christopher Tang, Lei Xie, Marina Gimpelev, Therese Mitros, Cinque Soto, Sharon Goldsmith-Fischman, Andrew Kernytsky, Avner Schlessinger, Ingrid Y Y Koh, Emil Alexov, Barry Honig .  2003.   Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling.. Proteins. 53 Suppl 6 :430-5 ▶ Go to Pubmed
Ulf Klein, Yuhai Tu, Gustavo Stolovitzky, Jeffrey Keller, Joseph Haddad, Vladan Miljkovic, Giorgio Cattoretti, Andrea Califano, Riccardo Dalla-Favera .  2003.   Gene expression dynamics during germinal center transit in B cells.. Ann N Y Acad Sci. 987 :166-72 ▶ Go to Pubmed
Agatha Liu, Xinmin Zhang, Gustavo Stolovitzky, Andrea Califano, Stuart Firestein .  2003.   Motif-based construction of a functional map for mammalian olfactory receptors.. Genomics. 81 (5) :443-56 ▶ Go to Pubmed
Harmen Bussemaker, H Li, E Siggia .  2001.   Regulatory element detection using correlation with expression.. Nat Genet. 27 (2) :167-71 ▶ Go to Pubmed
Dimitris Anastassiou .  2000.   Frequency-domain analysis of biomolecular sequences.. Bioinformatics. 16 (12) :1073-81 ▶ Go to Pubmed
Andrea Califano, Gustavo Stolovitzky, Yuhai Tu .  2000.   Analysis of gene expression microarrays for phenotype classification.. Proc Int Conf Intell Syst Mol Biol. 8 :75-85 ▶ Go to Pubmed
Harmen Bussemaker, H Li, E Siggia .  2000.   Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis.. Proc Natl Acad Sci U S A. 97 (18) :10096-100 ▶ Go to Pubmed
I Rigoutsos, A Floratos, C Ouzounis, Y Gao, L Parida .  1999.   Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins.. Proteins. 37 (2) :264-77 ▶ Go to Pubmed