Search Publications

Filter Publications

By Year
Saurav Guha, Jeffrey Rosenfeld, Anil Malhotra, Annette Lee, Peter Gregersen, John Kane, Itsik Pe'er, Ariel Darvasi, Todd Lencz .  2012.   Implications for health and disease in the genetic signature of the Ashkenazi Jewish population.. Genome Biol. 13 (1) :R2 ▶ Go to Pubmed
Paola Nicoletti, Vassiliki Cartsos, Penelope Palaska, Yufeng Shen, Aris Floratos, Athanasios Zavras .  2012.   Genomewide pharmacogenetics of bisphosphonate-induced osteonecrosis of the jaw: the role of RBMS3.. The oncologist. 17 (2) :279-87 ▶ Go to Pubmed
Paola Nicoletti, Vassiliki Cartsos, Penelope Palaska, Yufeng Shen, Aris Floratos, Athanasios Zavras .  2012.   Genomewide pharmacogenetics of bisphosphonate-induced osteonecrosis of the jaw: the role of RBMS3.. Oncologist. 17 (2) :279-87 ▶ Go to Pubmed
Caroline Ferreira, James Chen, Jianrong Li, Kazuhiro Shimomura, Xinan Yang, Yves Lussier, Lawrence Pinto, Julian Solway .  2012.   Genetic interactions between chromosomes 11 and 18 contribute to airway hyperresponsiveness in mice.. PLoS One. 7 (1) :e29579 ▶ Go to Pubmed
Celine Lefebvre, Gabrielle Rieckhof, Andrea Califano .  2012.   Reverse-engineering human regulatory networks.. Wiley Interdiscip Rev Syst Biol Med. 4 (4) :311-25 ▶ Go to Pubmed
Panagiotis Ntziachristos, Aristotelis Tsirigos, Pieter Van Vlierberghe, Jelena Nedjic, Thomas Trimarchi, Maria Flaherty, Dolors Ferres-Marco, Vanina da Ros, Zuojian Tang, Jasmin Siegle, Patrik Asp, Michael Hadler, Isaura Rigo, Kim De Keersmaecker, Jay Patel, Tien Huynh, Filippo Utro, Sandrine Poglio, Jeremy Samon, Elisabeth Paietta, Janis Racevskis, Jacob Rowe, Raul Rabadan, Ross Levine, Stuart Brown, Francoise Pflumio, Maria Dominguez, Adolfo Ferrando, Iannis Aifantis .  2012.   Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia.. Nat Med. 18 (2) :298-301 ▶ Go to Pubmed
Alexander Eletsky, Donald Petrey, Qiangfeng Zhang, Hsiau-Wei Lee, Thomas Acton, Rong Xiao, John Everett, James Prestegard, Barry Honig, Gaetano Montelione, Thomas Szyperski .  2012.   Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771.. J Struct Funct Genomics. 13 (1) :1-7 ▶ Go to Pubmed
Dimitris Anastassiou, Viktoria Rumjantseva, Wei-Yi Cheng, Jianzhong Huang, Peter Canoll, Darrell Yamashiro, Jessica Kandel .  2011.   Human cancer cells express Slug-based epithelial-mesenchymal transition gene expression signature obtained in vivo.. BMC Cancer. 11 :529 ▶ Go to Pubmed
Kyle Chard, Michael Russell, Yves Lussier, Eneida Mendonça, Jonathan Silverstein .  2011.   A cloud-based approach to medical NLP.. AMIA Annu Symp Proc. 2011 :207-16 ▶ Go to Pubmed
David Borhani, David Shaw .  2012.   The future of molecular dynamics simulations in drug discovery.. J Comput Aided Mol Des. 26 (1) :15-26 ▶ Go to Pubmed
Yves Lussier, Rosie Xing, Joseph Salama, Nikolai Khodarev, Yong Huang, Qingbei Zhang, Sajid Khan, Xinan Yang, Michael Hasselle, Thomas Darga, Renuka Malik, Hanli Fan, Samantha Perakis, Matthew Filippo, Kimberly Corbin, Younghee Lee, Mitchell Posner, Steven Chmura, Samuel Hellman, Ralph Weichselbaum .  2011.   MicroRNA expression characterizes oligometastasis(es).. PLoS One. 6 (12) :e28650 ▶ Go to Pubmed
Anil Raj, Michael Dewar, Gustavo Palacios, Raul Rabadan, Christopher Wiggins .  2011.   Identifying hosts of families of viruses: a machine learning approach.. PLoS One. 6 (12) :e27631 ▶ Go to Pubmed
Xiangshu Jin, Melissa Walker, Klara Felsovalyi, Jeremie Vendome, Fabiana Bahna, Seetha Mannepalli, Filip Cosmanescu, Goran Ahlsen, Barry Honig, Lawrence Shapiro .  2012.   Crystal structures of Drosophila N-cadherin ectodomain regions reveal a widely used class of Ca²+-free interdomain linkers.. Proc Natl Acad Sci U S A. 109 (3) :E127-34 ▶ Go to Pubmed
Matthew Slattery, Todd Riley, Peng Liu, Namiko Abe, Pilar Gomez-Alcala, Iris Dror, Tianyin Zhou, Remo Rohs, Barry Honig, Harmen Bussemaker, Richard Mann .  2011.   Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.. Cell. 147 (6) :1270-82 ▶ Go to Pubmed
Alexander Gusev, M Shah, Eimear Kenny, A Ramachandran, Jennifer Lowe, Jacqueline Salit, C Lee, E Levandowsky, T Weaver, Q Doan, H Peckham, S McLaughlin, M Lyons, N Sheth V, Markus Stoffel, F De La Vega, Jeffrey Friedman, Jan Breslow, Itsik Pe'er .  2012.   Low-pass genome-wide sequencing and variant inference using identity-by-descent in an isolated human population.. Genetics. 190 (2) :679-89 ▶ Go to Pubmed
Ninad Dewal, Yang Hu, Matthew Freedman, Thomas Laframboise, Itsik Pe'er .  2012.   Calling amplified haplotypes in next generation tumor sequence data.. Genome Res. 22 (2) :362-74 ▶ Go to Pubmed
Peter Freddolino, Sasan Amini, Saeed Tavazoie .  2012.   Newly identified genetic variations in common Escherichia coli MG1655 stock cultures.. J Bacteriol. 194 (2) :303-6 ▶ Go to Pubmed
Aris Floratos, Barry Honig, Dana Pe'er, Andrea Califano .  2012.   Using systems and structure biology tools to dissect cellular phenotypes.. J Am Med Inform Assoc. 19 (2) :171-5 ▶ Go to Pubmed
Binquan Luan, Gustavo Stolovitzky, Glenn Martyna .  2012.   Slowing and controlling the translocation of DNA in a solid-state nanopore.. Nanoscale. 4 (4) :1068-77 ▶ Go to Pubmed
Davide Rossi, Silvia Rasi, Giulia Fabbri, Valeria Spina, Marco Fangazio, Francesco Forconi, Roberto Marasca, Luca Laurenti, Alessio Bruscaggin, Michaela Cerri, Sara Monti, Stefania Cresta, Rosella Famà, Lorenzo De Paoli, Pietro Bulian, Valter Gattei, Anna Guarini, Silvia Deaglio, Daniela Capello, Raul Rabadan, Laura Pasqualucci, Riccardo Dalla-Favera, Robin Foá, Gianluca Gaidano .  2012.   Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia.. Blood. 119 (2) :521-9 ▶ Go to Pubmed
Binquan Luan, Glenn Martyna, Gustavo Stolovitzky .  2011.   Characterizing and controlling the motion of ssDNA in a solid-state nanopore.. Biophys J. 101 (9) :2214-22 ▶ Go to Pubmed
Davide Rossi, Alessio Bruscaggin, Valeria Spina, Silvia Rasi, Hossein Khiabanian, Monica Messina, Marco Fangazio, Tiziana Vaisitti, Sara Monti, Sabina Chiaretti, Anna Guarini, Ilaria Del Giudice, Michaela Cerri, Stefania Cresta, Clara Deambrogi, Ernesto Gargiulo, Valter Gattei, Francesco Forconi, Francesco Bertoni, Silvia Deaglio, Raul Rabadan, Laura Pasqualucci, Robin Foá, Riccardo Dalla-Favera, Gianluca Gaidano .  2011.   Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness.. Blood. 118 (26) :6904-8 ▶ Go to Pubmed
Sasan Amini, Alison Hottes, Lincoln Smith, Saeed Tavazoie .  2011.   Fitness landscape of antibiotic tolerance in Pseudomonas aeruginosa biofilms.. PLoS Pathog. 7 (10) :e1002298 ▶ Go to Pubmed
Pavel Sumazin, Xuerui Yang, Hua-Sheng Chiu, Wei-Jen Chung, Archana Iyer, David Llobet-Navas, Presha Rajbhandari, Mukesh Bansal, Paolo Guarnieri, Jose Silva, Andrea Califano .  2011.   An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma.. Cell. 147 (2) :370-81 ▶ Go to Pubmed
Andrew Kuziemko, Barry Honig, Donald Petrey .  2011.   Using structure to explore the sequence alignment space of remote homologs.. PLoS Comput Biol. 7 (10) :e1002175 ▶ Go to Pubmed
Kivanç Birsoy, Ryan Berry, Tim Wang, Ozge Ceyhan, Saeed Tavazoie, Jeffrey Friedman, Matthew Rodeheffer .  2011.   Analysis of gene networks in white adipose tissue development reveals a role for ETS2 in adipogenesis.. Development. 138 (21) :4709-19 ▶ Go to Pubmed
Yufeng Shen, Yiwei Gu, Itsik Pe'er .  2011.   A hidden Markov model for copy number variant prediction from whole genome resequencing data.. BMC Bioinformatics. 12 Suppl 6 :S4 ▶ Go to Pubmed
Katia Basso, Lara Mussolin, Antonella Lettieri, Manisha Brahmachary, Wei Lim, Andrea Califano, Giuseppe Basso, Andrea Biondi, Giovanni Cazzaniga, Angelo Rosolen .  2011.   T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses.. Genes Chromosomes Cancer. 50 (12) :1063-75 ▶ Go to Pubmed
Sabrina Iñigo, Mariano Alvarez, Bárbara Strasser, Andrea Califano, Pablo Cerdán .  2012.   PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis.. Plant J. 69 (4) :601-12 ▶ Go to Pubmed
Alexander Gusev, Pier Palamara, Gregory Aponte, Zhong Zhuang, Ariel Darvasi, Peter Gregersen, Itsik Pe'er .  2012.   The architecture of long-range haplotypes shared within and across populations.. Mol Biol Evol. 29 (2) :473-86 ▶ Go to Pubmed
Andrea Califano .  2011.   Striking a balance between feasible and realistic biological models.. Sci Transl Med. 3 (103) :103ps39 ▶ Go to Pubmed
Eric Bishop, Remo Rohs, Stephen Parker, Sean West, Peng Liu, Richard Mann, Barry Honig, Thomas Tullius .  2011.   A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA.. ACS Chem Biol. 6 (12) :1314-20 ▶ Go to Pubmed
Santiago Vilar, Rave Harpaz, Herbert Chase, Stefano Costanzi, Raul Rabadan, Carol Friedman .  2011.   Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis.. J Am Med Inform Assoc. 18 Suppl 1 :i73-80 ▶ Go to Pubmed
Mukesh Bansal, Andrea Califano .  2012.   Genome-wide dissection of posttranscriptional and posttranslational interactions.. Methods Mol Biol. 786 :131-49 ▶ Go to Pubmed
Pablo Meyer, Leonidas Alexopoulos, Thomas Bonk, Andrea Califano, Carolyn Cho, Alberto de la Fuente, David de Graaf, Alexander Hartemink, Julia Hoeng, Nikolai Ivanov V, Heinz Koeppl, Rune Linding, Daniel Marbach, Raquel Norel, Manuel Peitsch, Jeremy Rice, Ajay Royyuru, Frank Schacherer, Jörg Sprengel, Katrin Stolle, Dennis Vitkup, Gustavo Stolovitzky .  2011.   Verification of systems biology research in the age of collaborative competition.. Nat Biotechnol. 29 (9) :811-5 ▶ Go to Pubmed
Robert Prill, Julio Saez-Rodriguez, Leonidas Alexopoulos, Peter Sorger, Gustavo Stolovitzky .  2011.   Crowdsourcing network inference: the DREAM predictive signaling network challenge.. Sci Signal. 4 (189) :mr7 ▶ Go to Pubmed
Adam Wolpaw, Kenichi Shimada, Rachid Skouta, Matthew Welsch, Uri Akavia, Dana Pe'er, Fatima Shaik, Chloe Bulinski, Brent Stockwell .  2011.   Modulatory profiling identifies mechanisms of small molecule-induced cell death.. Proc Natl Acad Sci U S A. 108 (39) :E771-80 ▶ Go to Pubmed
Laura Wingler, Virginia Cornish .  2011.   Reiterative Recombination for the in vivo assembly of libraries of multigene pathways.. Proc Natl Acad Sci U S A. 108 (37) :15135-40 ▶ Go to Pubmed
Marianna de Julio, Mariano Alvarez, Antonella Galli, Jianhua Chu, Sandy Price, Andrea Califano, Michael Shen .  2011.   Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling.. Development. 138 (18) :3885-95 ▶ Go to Pubmed
Sasan Amini, Saeed Tavazoie .  2011.   Antibiotics and the post-genome revolution.. Curr Opin Microbiol. 14 (5) :513-8 ▶ Go to Pubmed
Alison Hottes, Saeed Tavazoie .  2011.   Microarray-based genetic footprinting strategy to identify strain improvement genes after competitive selection of transposon libraries.. Methods Mol Biol. 765 :83-97 ▶ Go to Pubmed
Laura Pasqualucci, Vladimir Trifonov, Giulia Fabbri, Jing Ma, Davide Rossi, Annalisa Chiarenza, Victoria Wells, Adina Grunn, Monica Messina, Oliver Elliot, Joseph Chan, Govind Bhagat, Amy Chadburn, Gianluca Gaidano, Charles Mullighan, Raul Rabadan, Riccardo Dalla-Favera .  2011.   Analysis of the coding genome of diffuse large B-cell lymphoma.. Nat Genet. 43 (9) :830-7 ▶ Go to Pubmed
Yinghao Wu, Jeremie Vendome, Lawrence Shapiro, Avinoam Ben-Shaul, Barry Honig .  2011.   Transforming binding affinities from three dimensions to two with application to cadherin clustering.. Nature. 475 (7357) :510-3 ▶ Go to Pubmed
C Velez, Pier Palamara, J Guevara-Aguirre, L Hao, T Karafet, M Guevara-Aguirre, Alexander Pearlman, Carole Oddoux, M Hammer, Edward Burns, Itsik Pe'er, G Atzmon, Harry Ostrer .  2012.   The impact of Converso Jews on the genomes of modern Latin Americans.. Hum Genet. 131 (2) :251-63 ▶ Go to Pubmed
Antony Holmes, Alexander Hawson, Feng Liu, Carol Friedman, Hossein Khiabanian, Raul Rabadan .  2011.   Discovering disease associations by integrating electronic clinical data and medical literature.. PLoS One. 6 (6) :e21132 ▶ Go to Pubmed
Laura Patwa, Ting-Jia Fan, Sandrine Tchaptchet, Yang Liu, Yves Lussier, Balfour Sartor, Jonathan Hansen .  2011.   Chronic intestinal inflammation induces stress-response genes in commensal Escherichia coli.. Gastroenterology. 141 (5) :1842-51.e1-10 ▶ Go to Pubmed
Biji Mathew, Jeffrey Jacobson, Evgeny Berdyshev, Yong Huang, Xiaoguang Sun, Yutong Zhao, Lynnette Gerhold, Jessica Siegler, Carrie Evenoski, Ting Wang, Tong Zhou, Rafe Zaidi, Liliana Moreno-Vinasco, Robert Bittman, Chin Chen, Patrick LaRiviere, Saad Sammani, Yves Lussier, Steven Dudek, Viswanathan Natarajan, Ralph Weichselbaum, Joe Garcia .  2011.   Role of sphingolipids in murine radiation-induced lung injury: protection by sphingosine 1-phosphate analogs.. FASEB J. 25 (10) :3388-400 ▶ Go to Pubmed
Markus Fischer, Qiangfeng Zhang, Fabian Dey, Brian Chen, Barry Honig, Donald Petrey .  2011.   MarkUs: a server to navigate sequence-structure-function space.. Nucleic Acids Res. 39 (Web Server issue) :W357-61 ▶ Go to Pubmed
James Chen, Jianrong Li, Walter Stadler, Yves Lussier .  2011.   Protein-network modeling of prostate cancer gene signatures reveals essential pathways in disease recurrence.. J Am Med Inform Assoc. 18 (4) :392-402 ▶ Go to Pubmed
Giulia Fabbri, Silvia Rasi, Davide Rossi, Vladimir Trifonov, Hossein Khiabanian, Jing Ma, Adina Grunn, Marco Fangazio, Daniela Capello, Sara Monti, Stefania Cresta, Ernesto Gargiulo, Francesco Forconi, Anna Guarini, Luca Arcaini, Marco Paulli, Luca Laurenti, Luigi Larocca, Roberto Marasca, Valter Gattei, David Oscier, Francesco Bertoni, Charles Mullighan, Robin Foá, Laura Pasqualucci, Raul Rabadan, Riccardo Dalla-Favera, Gianluca Gaidano .  2011.   Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation.. J Exp Med. 208 (7) :1389-401 ▶ Go to Pubmed
Enrico Tiacci, Vladimir Trifonov, Gianluca Schiavoni, Antony Holmes, Wolfgang Kern, Maria Martelli, Alessandra Pucciarini, Barbara Bigerna, Roberta Pacini, Victoria Wells, Paolo Sportoletti, Valentina Pettirossi, Roberta Mannucci, Oliver Elliott, Arcangelo Liso, Achille Ambrosetti, Alessandro Pulsoni, Francesco Forconi, Livio Trentin, Gianpietro Semenzato, Giorgio Inghirami, Monia Capponi, Francesco Di Raimondo, Caterina Patti, Luca Arcaini, Pellegrino Musto, Stefano Pileri, Claudia Haferlach, Susanne Schnittger, Giovanni Pizzolo, Robin Foá, Laurent Farinelli, Torsten Haferlach, Laura Pasqualucci, Raul Rabadan, Brunangelo Falini .  2011.   BRAF mutations in hairy-cell leukemia.. N Engl J Med. 364 (24) :2305-15 ▶ Go to Pubmed
Sarah Gilman, Ivan Iossifov, Dan Levy, Michael Ronemus, Michael Wigler, Dennis Vitkup .  2011.   Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses.. Neuron. 70 (5) :898-907 ▶ Go to Pubmed
Jiang Zhu, Yong Yu, Maximilian Ulbrich, Ming-hui Li, Ehud Isacoff, Barry Honig, Jian Yang .  2011.   Structural model of the TRPP2/PKD1 C-terminal coiled-coil complex produced by a combined computational and experimental approach.. Proc Natl Acad Sci U S A. 108 (25) :10133-8 ▶ Go to Pubmed
Yufeng Shen, Ruijie Song, Itsik Pe'er .  2011.   Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association.. Bioinformatics. 27 (14) :1995-7 ▶ Go to Pubmed
Alexander Gusev, Eimear Kenny, Jennifer Lowe, Jacqueline Salit, Richa Saxena, Sekar Kathiresan, David Altshuler, Jeffrey Friedman, Jan Breslow, Itsik Pe'er .  2011.   DASH: a method for identical-by-descent haplotype mapping uncovers association with recent variation.. Am J Hum Genet. 88 (6) :706-17 ▶ Go to Pubmed
Qiangfeng Zhang, Lei Deng, Markus Fisher, Jihong Guan, Barry Honig, Donald Petrey .  2011.   PredUs: a web server for predicting protein interfaces using structural neighbors.. Nucleic Acids Res. 39 (Web Server issue) :W283-7 ▶ Go to Pubmed
Stefan Harrer, Philip Waggoner, Binquan Luan, Ali Afzali-Ardakani, Dario Goldfarb, Hongbo Peng, Glenn Martyna, Stephen Rossnagel, Gustavo Stolovitzky .  2011.   Electrochemical protection of thin film electrodes in solid state nanopores.. Nanotechnology. 22 (27) :275304 ▶ Go to Pubmed
Cynthia Rudin, David Waltz, Roger Anderson, Albert Boulanger, Ansaf Salleb-Aouissi, Maggie Chow, Haimonti Dutta, Philip Gross, Bert Huang, Steve Ierome, Delfina Isaac, Arthur Kressner, Rebecca Passonneau, Axinia Radeva, Leon Wu .  2012.   Machine learning for the New York City power grid.. IEEE Trans Pattern Anal Mach Intell. 34 (2) :328-45 ▶ Go to Pubmed
Jeremie Vendome, Shoshana Posy, Xiangshu Jin, Fabiana Bahna, Goran Ahlsen, Lawrence Shapiro, Barry Honig .  2011.   Molecular design principles underlying β-strand swapping in the adhesive dimerization of cadherins.. Nat Struct Mol Biol. 18 (6) :693-700 ▶ Go to Pubmed
Xiaoyuan Xie, Joshua Ho, Christian Murphy, Gail Kaiser, Baowen Xu, Tsong Chen .  2011.   Testing and Validating Machine Learning Classifiers by Metamorphic Testing.. J Syst Softw. 84 (4) :544-558 ▶ Go to Pubmed
Huning Dai, Christian Murphy, Gail Kaiser .  2010.   Configuration Fuzzing for Software Vulnerability Detection.. Proc Int Conf Availab Reliab Secur. :525-530 ▶ Go to Pubmed
Hoon Kim, John Watkinson, Dimitris Anastassiou .  2011.   Biomarker discovery using statistically significant gene sets.. J Comput Biol. 18 (10) :1329-38 ▶ Go to Pubmed
Xinan Yang, Jianrong Li, Younghee Lee, Yves Lussier .  2011.   GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns.. Bioinformatics. 27 (10) :1444-6 ▶ Go to Pubmed
Dana Pe'er, Nir Hacohen .  2011.   Principles and strategies for developing network models in cancer.. Cell. 144 (6) :864-73 ▶ Go to Pubmed
Aaron Hoskins, Larry Friedman, Sarah Gallagher, Daniel Crawford, Eric Anderson, Richard Wombacher, Nicholas Ramirez, Virginia Cornish, Jeff Gelles, Melissa Moore .  2011.   Ordered and dynamic assembly of single spliceosomes.. Science. 331 (6022) :1289-95 ▶ Go to Pubmed
Laura Pasqualucci, David Dominguez-Sola, Annalisa Chiarenza, Giulia Fabbri, Adina Grunn, Vladimir Trifonov, Lawryn Kasper, Stephanie Lerach, Hongyan Tang, Jing Ma, Davide Rossi, Amy Chadburn, Vundavalli Murty V, Charles Mullighan, Gianluca Gaidano, Raul Rabadan, Paul Brindle, Riccardo Dalla-Favera .  2011.   Inactivating mutations of acetyltransferase genes in B-cell lymphoma.. Nature. 471 (7337) :189-95 ▶ 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
Oliver Harrison, Xiangshu Jin, Soonjin Hong, Fabiana Bahna, Goran Ahlsen, Julia Brasch, Yinghao Wu, Jeremie Vendome, Klara Felsovalyi, Cheri Hampton, Regina Troyanovsky, Avinoam Ben-Shaul, Joachim Frank, Sergey Troyanovsky, Lawrence Shapiro, Barry Honig .  2011.   The extracellular architecture of adherens junctions revealed by crystal structures of type I cadherins.. Structure. 19 (2) :244-56 ▶ Go to Pubmed
Kenneth Ross .  2011.   Evidence for somatic gene conversion and deletion in bipolar disorder, Crohn's disease, coronary artery disease, hypertension, rheumatoid arthritis, type-1 diabetes, and type-2 diabetes.. BMC Med. 9 :12 ▶ Go to Pubmed
Julia Brasch, Oliver Harrison, Goran Ahlsen, Stewart Carnally, Robert Henderson, Barry Honig, Lawrence Shapiro .  2011.   Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin.. J Mol Biol. 408 (1) :57-73 ▶ Go to Pubmed
Caryn Shechtman, Annette Henneberry, Tracie Seimon, Arthur Tinkelenberg, Lisa Wilcox, Eunjee Lee, Mina Fazlollahi, Andrew Munkacsi, Harmen Bussemaker, Ira Tabas, Stephen Sturley .  2011.   Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response.. J Biol Chem. 286 (14) :11951-9 ▶ Go to Pubmed
Lixia Yao, Anna Divoli, Ilya Mayzus, James Evans, Andrey Rzhetsky .  2011.   Benchmarking ontologies: bigger or better?. PLoS Comput Biol. 7 (1) :e1001055 ▶ 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
Yufeng Shen, Paola Nicoletti, Aris Floratos, Munir Pirmohamed, Mariam Molokhia, P Geppetti, S Benemei, B Giomi, D Schena, A Vultaggio, R Stern, M Daly, Sally John, M Nelson, Itsik Pe'er, International Consortium .  2012.   Genome-wide association study of serious blistering skin rash caused by drugs.. Pharmacogenomics J. 12 (2) :96-104 ▶ 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
Rave Harpaz, H Perez, Herbert Chase, Raul Rabadan, G Hripcsak, Carol Friedman .  2011.   Biclustering of adverse drug events in the FDA's spontaneous reporting system.. Clin Pharmacol Ther. 89 (2) :243-50 ▶ Go to Pubmed
Andrew Mugler, Boris Grinshpun, Riley Franks, Chris Wiggins .  2011.   Statistical method for revealing form-function relations in biological networks.. Proc Natl Acad Sci U S A. 108 (2) :446-51 ▶ Go to Pubmed
William Behnke-Parks, Jeremie Vendome, Barry Honig, Zoltan Maliga, Carolyn Moores, Steven Rosenfeld .  2011.   Loop L5 acts as a conformational latch in the mitotic kinesin Eg5.. J Biol Chem. 286 (7) :5242-53 ▶ 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
Eimear Kenny, Minseung Kim, Alexander Gusev, Jennifer Lowe, Jacqueline Salit, Gustav Smith, Sirisha Kovvali, Hyun Kang, Christopher Newton-Cheh, Mark Daly, Markus Stoffel, David Altshuler, Jeffrey Friedman, Eleazar Eskin, Jan Breslow, Itsik Pe'er .  2011.   Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population.. Hum Mol Genet. 20 (4) :827-39 ▶ Go to Pubmed
Richard Roberts, Yi-Chien Chang, Zhenjun Hu, John Rachlin, Brian Anton, Revonda Pokrzywa, Han-Pil Choi, Lina Faller, Jyotsna Guleria, Genevieve Housman, Niels Klitgord, Varun Mazumdar, Mark McGettrick, Lais Osmani, Rajeswari Swaminathan, Kevin Tao, Stanley Letovsky, Dennis Vitkup, Daniel Segrè, Steven Salzberg, Charles Delisi, Martin Steffen, Simon Kasif .  2011.   COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.. Nucleic Acids Res. 39 (Database issue) :D11-4 ▶ 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
Yee Cheung, John Watkinson, Dimitris Anastassiou .  2011.   Conditional meta-analysis stratifying on detailed HLA genotypes identifies a novel type 1 diabetes locus around TCF19 in the MHC.. Hum Genet. 129 (2) :161-76 ▶ 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
A Mugler, E Ziv, I Nemenman, C Wiggins .  2009.   Quantifying evolvability in small biological networks.. IET Syst Biol. 3 (5) :379-87 ▶ 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