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2011

2011 Publications

Ariel Herman, Miki Hayano, Masha Poyurovsky V, Kenichi Shimada, Rachid Skouta, Carol Prives, Brent Stockwell .  2011.   Discovery of Mdm2-MdmX E3 ligase inhibitors using a cell-based ubiquitination assay.. Cancer Discov. 1 (4) :312-25 ▶ Go to Pubmed
Vladimir Trifonov, Laura Pasqualucci, Riccardo Dalla-Favera, Raul Rabadan .  2011.   Fractal-like distributions over the rational numbers in high-throughput biological and clinical data.. Sci Rep. 1 :191 ▶ 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
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
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
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
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
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
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
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
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
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
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
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
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
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