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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
Martin Cadeiras, Manuel von Bayern, Anshu Sinha, Khurram Shahzad, Farhana Latif, Wei Lim, Hernan Grenett, Esteban Tabak, Tod Klingler, Andrea Califano, Mario Deng .  2011.   Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation.. J Cell Mol Med. 15 (4) :949-56 ▶ Go to Pubmed
Spiro Pantazatos, Jianrong Li, Paul Pavlidis, Yves Lussier .  2009.   Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes.. Cancer Inform. 8 :75-94 ▶ 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
Mariano Alvarez, Pavel Sumazin, Presha Rajbhandari, Andrea Califano .  2009.   Correlating measurements across samples improves accuracy of large-scale expression profile experiments.. Genome Biol. 10 (12) :R143 ▶ 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
Hossein Khiabanian, Vladimir Trifonov, Raul Rabadan .  2009.   Reassortment patterns in Swine influenza viruses.. PLoS Curr. 1 :RRN1008 ▶ 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
Philip Effraim, Jiangning Wang, Michael Englander, Josh Avins, Thomas Leyh, Ruben Gonzalez, Virginia Cornish .  2009.   Natural amino acids do not require their native tRNAs for efficient selection by the ribosome.. Nat Chem Biol. 5 (12) :947-53 ▶ Go to Pubmed
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