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Michael Shen .  2013.   Chromoplexy: a new category of complex rearrangements in the cancer genome.. Cancer Cell. 23 (5) :567-9 ▶ Go to Pubmed
Evan Bardot, Victor Valdes, Jisheng Zhang, Carolina Perdigoto, Silvia Nicolis, Stephen Hearn, Jose Silva, Elena Ezhkova .  2013.   Polycomb subunits Ezh1 and Ezh2 regulate the Merkel cell differentiation program in skin stem cells.. EMBO J. ▶ Go to Pubmed
Fabrizio Tabbò, Maurilio Ponzoni, Raul Rabadan, Francesco Bertoni, Giorgio Inghirami, the Group .  2013.   Beyond NPM-anaplastic lymphoma kinase driven lymphomagenesis: alternative drivers in anaplastic large cell lymphoma.. Curr Opin Hematol. ▶ Go to Pubmed
Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Jang, Benjamin Logsdon, Gaurav Pandey, Benjamin Sauerwine, Yishai Shimoni, Hans Vollan, Brigham Mecham, Oscar Rueda, Jorg Tost, Christina Curtis, Mariano Alvarez, Vessela Kristensen, Samuel Aparicio, Anne-Lise Børresen-Dale, Carlos Caldas, Andrea Califano, Stephen Friend, Trey Ideker, Eric Schadt, Gustavo Stolovitzky, Adam Margolin .  2013.   Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling.. PLoS Comput Biol. 9 (5) :e1003047 ▶ Go to Pubmed
Samir Zaidi, Murim Choi, Hiroko Wakimoto, Lijiang Ma, Jianming Jiang, John Overton, Angela Romano-Adesman, Robert Bjornson, Roger Breitbart, Kerry Brown, Nicholas Carriero, Yee Cheung, John Deanfield, Steve Depalma, Khalid Fakhro, Joseph Glessner, Hakon Hakonarson, Michael Italia, Jonathan Kaltman, Juan Kaski, Richard Kim, Jennie Kline, Teresa Lee, Jeremy Leipzig, Alexander Lopez, Shrikant Mane, Laura Mitchell, Jane Newburger, Michael Parfenov, Itsik Pe'er, George Porter, Amy Roberts, Ravi Sachidanandam, Stephan Sanders, Howard Seiden, Mathew State, Sailakshmi Subramanian, Irina Tikhonova, Wei Wang, Dorothy Warburton, Peter White, Ismee Williams, Hongyu Zhao, Jonathan Seidman, Martina Brueckner, Wendy Chung, Bruce Gelb, Elizabeth Goldmuntz, Christine Seidman, Richard Lifton .  2013.   De novo mutations in histone-modifying genes in congenital heart disease.. Nature. ▶ Go to Pubmed
Andrea Califano, Manolis Kellis, Gustavo Stolovitzky .  2013.   Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue.. J Comput Biol. 20 (5) :373-4 ▶ Go to Pubmed
Megan Keniry, Maira Pires, Sarah Mense, Celine Lefebvre, Boyi Gan, Karen Justiano, Ying-Ka Lau, Ben Hopkins, Cindy Hodakoski, Susan Koujak, Joseph Toole, Franklyn Fenton, Ashley Calahan, Andrea Califano, Ronald Depinho, Matt Maurer, Ramon Parsons .  2013.   Survival factor NFIL3 restricts FOXO-induced gene expression in cancer.. Genes Dev. 27 (8) :916-27 ▶ Go to Pubmed
Richard Gill, Yee Cheung, Yufeng Shen, Patricia Lanzano, Nazrat Mirza, Svetlana Ten, Noel Maclaren, Roja Motaghedi, Joan Han, Jack Yanovski, Rudolph Leibel, Wendy Chung .  2013.   Whole-exome sequencing identifies novel LEPR mutations in individuals with severe early onset obesity.. Obesity (Silver Spring). ▶ Go to Pubmed
Wei Zhang, K Hui, Alexander Gusev, N Warner, Sok Ng, J Ferguson, Murim Choi, A Burberry, Clara Abraham, Lloyd Mayer, Robert Desnick, C Cardinale, Hakon Hakonarson, Matti Waterman, Y Chowers, Amir Karban, Steven Brant, Mark Silverberg, P Gregersen, Seymour Katz, Richard Lifton, H Zhao, G Nuñez, Itsik Pe'er, Inga Peter, Judy Cho .  2013.   Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3.. Genes Immun. ▶ Go to Pubmed
Steven Taylor, Jingxian Wang, Natasa Kostic, Milan Stojanovic .  2013.   Monovalent streptavidin that senses oligonucleotides.. Angew Chem Int Ed Engl. 52 (21) :5509-12 ▶ Go to Pubmed
Jie Hu, Jason Locasale, Jason Bielas, Jacintha O'Sullivan, Kieran Sheahan, Lewis Cantley, Matthew Heiden, Dennis Vitkup .  2013.   Heterogeneity of tumor-induced gene expression changes in the human metabolic network.. Nat Biotechnol. ▶ Go to Pubmed
Gina Destefano, Katherine Fantauzzo, Lynn Petukhova, Mazen Kurban, Marija Tadin-Strapps, Brynn Levy, Dorothy Warburton, Elizabeth Cirulli, Yujun Han, Xiaoyun Sun, Yufeng Shen, Maryam Shirazi, Vaidehi Jobanputra, Rodrigo Cepeda-Valdes, Julio Salas-Alanis, Angela Christiano .  2013.   Position effect on FGF13 associated with X-linked congenital generalized hypertrichosis.. Proc Natl Acad Sci U S A. 110 (19) :7790-5 ▶ Go to Pubmed
Wei-Yi Cheng, Tai-Hsien Yang, Dimitris Anastassiou .  2013.   Development of a prognostic model for breast cancer survival in an open challenge environment.. Sci Transl Med. 5 (181) :181ra50 ▶ Go to Pubmed
Morten Jensen, Vishwanath Jogini, Michael Eastwood, David Shaw .  2013.   Atomic-level simulation of current-voltage relationships in single-file ion channels.. J Gen Physiol. 141 (5) :619-32 ▶ Go to Pubmed
Giulio Ferino, Enzo Cadoni, Maria Matos, Elias Quezada, Eugenio Uriarte, Lourdes Santana, Santiago Vilar, Nicholas Tatonetti, Matilde Yáñez, Dolores Viña, Carmen Picciau, Silvia Serra, Giovanna Delogu .  2013.   MAO Inhibitory Activity of 2-Arylbenzofurans versus 3-Arylcoumarins: Synthesis, in vitro Study, and Docking Calculations.. ChemMedChem. 8 (6) :956-66 ▶ Go to Pubmed
Hemant Varma, Nidhi Gangadhar, Reka Letso, Adam Wolpaw, Rohitha Sriramaratnam, Brent Stockwell .  2013.   Identification of a small molecule that induces ATG5-and-cathepsin-l-dependent cell death and modulates polyglutamine toxicity.. Exp Cell Res. ▶ Go to Pubmed
Yibing Shan, Anton Arkhipov, Eric Kim, Albert Pan, David Shaw .  2013.   Transitions to catalytically inactive conformations in EGFR kinase.. Proc Natl Acad Sci U S A. 110 (18) :7270-5 ▶ Go to Pubmed
Allan Lazarovici, Tianyin Zhou, Anthony Shafer, Ana Machado, Todd Riley, Richard Sandstrom, Peter Sabo, Yan Lu, Remo Rohs, John Stamatoyannopoulos, Harmen Bussemaker .  2013.   Probing DNA shape and methylation state on a genomic scale with DNase I.. Proc Natl Acad Sci U S A. 110 (16) :6376-81 ▶ Go to Pubmed
Jie Wu, Olga Anczuków, Adrian Krainer, Michael Zhang, Chaolin Zhang .  2013.   OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds.. Nucleic Acids Res. 41 (10) :5149-5163 ▶ Go to Pubmed
Joan Delto, Takashi Kobayashi, Mitchell Benson, James McKiernan, Cory Abate-Shen .  2013.   Preclinical analyses of intravesical chemotherapy for prevention of bladder cancer progression.. Oncotarget. 4 (2) :269-76 ▶ Go to Pubmed
Feng Jin, Shazia Irshad, Wei Yu, Madesh Belakavadi, Marina Chekmareva, Michael Ittmann, Cory Abate-Shen, Joseph Fondell .  2013.   ERK and AKT signaling pathways promote MED1 overexpression in prostate cancer cells in association with elevated proliferation and tumorigenicity.. Mol Cancer Res. ▶ Go to Pubmed
Vladimir Trifonov, Laura Pasqualucci, Riccardo Dalla-Favera, Raul Rabadan .  2013.   MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples.. BMC Syst Biol. 7 (1) :25 ▶ Go to Pubmed
Yinghao Wu, Barry Honig, Avinoam Ben-Shaul .  2013.   Theory and simulations of adhesion receptor dimerization on membrane surfaces.. Biophys J. 104 (6) :1221-9 ▶ Go to Pubmed
Santiago Vilar, Eugenio Uriarte, Lourdes Santana, Nicholas Tatonetti, Carol Friedman .  2013.   Detection of drug-drug interactions by modeling interaction profile fingerprints.. PLoS One. 8 (3) :e58321 ▶ Go to Pubmed
Rachel Finck, Erin Simonds, Astraea Jager, Smita Krishnaswamy, Karen Sachs, Wendy Fantl, Dana Pe'er, Garry Nolan, Sean Bendall .  2013.   Normalization of mass cytometry data with bead standards.. Cytometry A. ▶ Go to Pubmed
Adam Sonabend, Jonathan Yun, Liang Lei, Richard Leung, Craig Soderquist, Celina Crisman, Brian Gill, Arthur Carminucci, Julia Sisti, Mike Castelli, Peter Sims, Jeffrey Bruce, Peter Canoll .  2013.   Murine cell line model of proneural glioma for evaluation of anti-tumor therapies.. J Neurooncol. 112 (3) :375-82 ▶ Go to Pubmed
Stefano Piana, Kresten Lindorff-Larsen, David Shaw .  2013.   Atomic-level description of ubiquitin folding.. Proc Natl Acad Sci U S A. 110 (15) :5915-20 ▶ Go to Pubmed
Reka Letso, Andras Bauer, Mitchell Lunn, Wan Yang, Brent Stockwell .  2013.   Small Molecule Screen Reveals Regulation of Survival Motor Neuron Protein Abundance by Ras Proteins.. ACS Chem Biol. ▶ Go to Pubmed
Maria Matos, Santiago Vilar, Rosa Gonzalez-Franco, Eugenio Uriarte, Lourdes Santana, Carol Friedman, Nicholas Tatonetti, Dolores Viña, José Fontenla .  2013.   Novel (coumarin-3-yl)carbamates as selective MAO-B inhibitors: Synthesis, in vitro and in vivo assays, theoretical evaluation of ADME properties and docking study.. Eur J Med Chem. 63C :151-161 ▶ Go to Pubmed
Wei-Yi Cheng, Tai-Hsien Yang, Dimitris Anastassiou .  2013.   Biomolecular events in cancer revealed by attractor metagenes.. PLoS Comput Biol. 9 (2) :e1002920 ▶ Go to Pubmed
Ryen White, Nicholas Tatonetti, Nigam Shah, Russ Altman, Eric Horvitz .  2013.   Web-scale pharmacovigilance: listening to signals from the crowd.. J Am Med Inform Assoc. 20 (3) :404-8 ▶ Go to Pubmed
Albert Pan, David Borhani, Ron Dror, David Shaw .  2013.   Molecular determinants of drug-receptor binding kinetics.. Drug Discov Today. ▶ Go to Pubmed
Zhu Wang, Antonina Mitrofanova, Sarah Bergren, Cory Abate-Shen, Robert Cardiff, Andrea Califano, Michael Shen .  2013.   Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity.. Nat Cell Biol. 15 (3) :274-83 ▶ Go to Pubmed
Angad Singh, Samreen Zafer, Itsik Pe'er .  2013.   Metaseq: privacy preserving meta-analysis of sequencing-based association studies.. Pac Symp Biocomput. :356-67 ▶ Go to Pubmed
Nili Ostrov, Laura Wingler, Virginia Cornish .  2013.   Gene assembly and combinatorial libraries in S. cerevisiae via reiterative recombination.. Methods Mol Biol. 978 :187-203 ▶ Go to Pubmed
Dante Romanini, Pamela Peralta-Yahya, Vanessa Mondol, Virginia Cornish .  2012.   A Heritable Recombination System for Synthetic Darwinian Evolution in Yeast.. ACS Synth Biol. 1 (12) :602-609 ▶ Go to Pubmed
Angela Jia, Mireia Castillo-Martin, Josep Domingo-Domenech, Dennis Bonal, Marta Sánchez-Carbayo, Jose Silva, Carlos Cordon-Cardo .  2013.   A Common MicroRNA Signature Consisting of miR-133a, miR-139-3p, and miR-142-3p Clusters Bladder Carcinoma in Situ with Normal Umbrella Cells.. Am J Pathol. 182 (4) :1171-9 ▶ Go to Pubmed
Hoda Eydgahi, William Chen, Jeremy Muhlich, Dennis Vitkup, John Tsitsiklis, Peter Sorger .  2013.   Properties of cell death models calibrated and compared using Bayesian approaches.. Mol Syst Biol. 9 :644 ▶ Go to Pubmed
Gannie Tzoneva, Arianne Perez-Garcia, Zachary Carpenter, Hossein Khiabanian, Valeria Tosello, Maddalena Allegretta, Elisabeth Paietta, Janis Racevskis, Jacob Rowe, Martin Tallman, Maddalena Paganin, Giuseppe Basso, Jana Hof, Renate Kirschner-Schwabe, Teresa Palomero, Raul Rabadan, Adolfo Ferrando .  2013.   Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL.. Nat Med. 19 (3) :368-71 ▶ Go to Pubmed
Qiyuan Li, Ji-Heui Seo, Barbara Stranger, Aaron McKenna, Itsik Pe'er, Thomas Laframboise, Myles Brown, Svitlana Tyekucheva, Matthew Freedman .  2013.   Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.. Cell. 152 (3) :633-41 ▶ Go to Pubmed
Anton Arkhipov, Yibing Shan, Rahul Das, Nicholas Endres, Michael Eastwood, David Wemmer, John Kuriyan, David Shaw .  2013.   Architecture and membrane interactions of the EGF receptor.. Cell. 152 (3) :557-69 ▶ Go to Pubmed
Nicholas Endres, Rahul Das, Adam Smith, Anton Arkhipov, Erika Kovacs, Yongjian Huang, Jeffrey Pelton, Yibing Shan, David Shaw, David Wemmer, Jay Groves, John Kuriyan .  2013.   Conformational coupling across the plasma membrane in activation of the EGF receptor.. Cell. 152 (3) :543-56 ▶ Go to Pubmed
Rie Nygaard, Yaozhong Zou, Ron Dror, Thomas Mildorf, Daniel Arlow, Aashish Manglik, Albert Pan, Corey Liu, Juan Fung, Michael Bokoch, Foon Thian, Tong Kobilka, David Shaw, Luciano Mueller, Scott Prosser, Brian Kobilka .  2013.   The dynamic process of β(2)-adrenergic receptor activation.. Cell. 152 (3) :532-42 ▶ Go to Pubmed
Joseph Chan, Raul Rabadan .  2013.   Quantifying pathogen surveillance using temporal genomic data.. MBio. 4 (1) :e00524-12 ▶ Go to Pubmed
Taesun Eom, Chaolin Zhang, Huidong Wang, Kenneth Lay, John Fak, Jeffrey Noebels, Robert Darnell .  2013.   NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure.. Elife. 2 :e00178 ▶ Go to Pubmed
Jiyang Yu, Preeti Putcha, Andrea Califano, Jose Silva .  2013.   Pooled shRNA screenings: computational analysis.. Methods Mol Biol. 980 :371-84 ▶ Go to Pubmed
Ruth Rodriguez-Barrueco, Netonia Marshall, Jose Silva .  2013.   Pooled shRNA screenings: experimental approach.. Methods Mol Biol. 980 :353-70 ▶ Go to Pubmed
Matthew Weirauch, Atina Cote, Raquel Norel, Matti Annala, Yue Zhao, Todd Riley, Julio Saez-Rodriguez, Thomas Cokelaer, Anastasia Vedenko, Shaheynoor Talukder, DREAM5 Consortium, Harmen Bussemaker, Quaid Morris, Martha Bulyk, Gustavo Stolovitzky, Timothy Hughes .  2013.   Evaluation of methods for modeling transcription factor sequence specificity.. Nat Biotechnol. 31 (2) :126-34 ▶ Go to Pubmed
Fabian Dey, Qiangfeng Zhang, Donald Petrey, Barry Honig .  2013.   Toward a "Structural BLAST": Using structural relationships to infer function.. Protein Sci. 22 (4) :359-66 ▶ Go to Pubmed
Xinan Yang, Haiquan Li, Kelly Regan, Jianrong Li, Yong Huang, Yves Lussier .  2012.   Towards mechanism classifiers: expression-anchored Gene Ontology signature predicts clinical outcome in lung adenocarcinoma patients.. AMIA Annu Symp Proc. 2012 :1040-9 ▶ Go to Pubmed
Jorge Contreras, Aris Floratos, Arthur Holden .  2013.   The International Serious Adverse Events Consortium's data sharing model.. Nat Biotechnol. 31 (1) :17-9 ▶ Go to Pubmed
Roy Maute, Christof Schneider, Pavel Sumazin, Antony Holmes, Andrea Califano, Katia Basso, Riccardo Dalla-Favera .  2013.   tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma.. Proc Natl Acad Sci U S A. 110 (4) :1404-9 ▶ Go to Pubmed
Shai Carmi, Pier Palamara, Vladimir Vacic, Todd Lencz, Ariel Darvasi, Itsik Pe'er .  2013.   The variance of identity-by-descent sharing in the Wright-Fisher model.. Genetics. 193 (3) :911-28 ▶ Go to Pubmed
Davide Rossi, Silvia Rasi, Valeria Spina, Alessio Bruscaggin, Sara Monti, Carmela Ciardullo, Clara Deambrogi, Hossein Khiabanian, Roberto Serra, Francesco Bertoni, Francesco Forconi, Luca Laurenti, Roberto Marasca, Michele Dal-Bo, Francesca Rossi, Pietro Bulian, Josep Nomdedeu, Giovanni Del Poeta, Valter Gattei, Laura Pasqualucci, Raul Rabadan, Robin Foá, Riccardo Dalla-Favera, Gianluca Gaidano .  2013.   Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia.. Blood. 121 (8) :1403-12 ▶ Go to Pubmed
Cheng Zhang, Yoga Srinivasan, Daniel Arlow, Juan Fung, Daniel Palmer, Yaowu Zheng, Hillary Green, Anjali Pandey, Ron Dror, David Shaw, William Weis, Shaun Coughlin, Brian Kobilka .  2012.   High-resolution crystal structure of human protease-activated receptor 1.. Nature. 492 (7429) :387-92 ▶ Go to Pubmed
Qiangfeng Zhang, Donald Petrey, José Garzón, Lei Deng, Barry Honig .  2013.   PrePPI: a structure-informed database of protein-protein interactions.. Nucleic Acids Res. 41 (Database issue) :D828-33 ▶ Go to Pubmed
Brygida Bisikirska, S Adam, Mariano Alvarez, Presha Rajbhandari, R Cox, Celine Lefebvre, Kai Wang, Gabrielle Rieckhof, D Felsher, Andrea Califano .  2012.   STK38 is a critical upstream regulator of MYC's oncogenic activity in human B-cell lymphoma.. Oncogene. ▶ Go to Pubmed
Aaron Schmidt, Huafeng Xu, Amir Khan, Timothy O'Donnell, Surender Khurana, Lisa King, Jody Manischewitz, Hana Golding, Pirada Suphaphiphat, Andrea Carfi, Ethan Settembre, Philip Dormitzer, Thomas Kepler, Ruijun Zhang, Anthony Moody, Barton Haynes, Hua-Xin Liao, David Shaw, Stephen Harrison .  2013.   Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody.. Proc Natl Acad Sci U S A. 110 (1) :264-9 ▶ Go to Pubmed
Sarah Gilman, Jonathan Chang, Bin Xu, Tejdeep Bawa, Joseph Gogos, Maria Karayiorgou, Dennis Vitkup .  2012.   Diverse types of genetic variation converge on functional gene networks involved in schizophrenia.. Nat Neurosci. 15 (12) :1723-8 ▶ Go to Pubmed
Lan Yu, Julia Wynn, Yee Cheung, Yufeng Shen, George Mychaliska, Timothy Crombleholme, Kenneth Azarow, Foong-Yen Lim, Dai Chung, Douglas Potoka, Brad Warner, Brian Bucher, Charles Stolar, Gudrun Aspelund, Marc Arkovitz, Wendy Chung .  2013.   Variants in GATA4 are a rare cause of familial and sporadic congenital diaphragmatic hernia.. Hum Genet. 132 (3) :285-92 ▶ Go to Pubmed
Alexandros Iliadis, Dimitris Anastassiou, Xiaodong Wang .  2012.   Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data.. BMC Genet. 13 :94 ▶ Go to Pubmed
Pier Palamara, Todd Lencz, Ariel Darvasi, Itsik Pe'er .  2012.   Length distributions of identity by descent reveal fine-scale demographic history.. Am J Hum Genet. 91 (5) :809-22 ▶ Go to Pubmed
Stephan Singer, Ruiying Zhao, Anthony Barsotti, Anette Ouwehand, Mina Fazlollahi, Elias Coutavas, Kai Breuhahn, Olaf Neumann, Thomas Longerich, Tobias Pusterla, Maureen Powers, Keith Giles, Peter Leedman, Jochen Hess, David Grunwald, Harmen Bussemaker, Robert Singer, Peter Schirmacher, Carol Prives .  2012.   Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes.. Mol Cell. 48 (5) :799-810 ▶ Go to Pubmed
Zhong Zhuang, Alexander Gusev, Judy Cho, Itsik Pe'er .  2012.   Detecting identity by descent and homozygosity mapping in whole-exome sequencing data.. PLoS One. 7 (10) :e47618 ▶ Go to Pubmed
Maho Shibata, Michael Shen .  2013.   The roots of cancer: stem cells and the basis for tumor heterogeneity.. Bioessays. 35 (3) :253-60 ▶ Go to Pubmed
Qiangfeng Zhang, Donald Petrey, Lei Deng, Li Qiang, Yu Shi, Chan Thu, Brygida Bisikirska, Celine Lefebvre, Domenico Accili, Tony Hunter, Tom Maniatis, Andrea Califano, Barry Honig .  2012.   Structure-based prediction of protein-protein interactions on a genome-wide scale.. Nature. 490 (7421) :556-60 ▶ Go to Pubmed
Thomas Urban, Yufeng Shen, Andrew Stolz, Naga Chalasani, Robert Fontana, James Rochon, Dongliang Ge, Kevin Shianna V, Ann Daly, Isabel Lucena, Matthew Nelson, Mariam Molokhia, Guruprasad Aithal, Aris Floratos, Itsik Pe'er, Jose Serrano, Herbert Bonkovsky, Timothy Davern, William Lee, Victor Navarro, Jayant Talwalkar, David Goldstein, Paul Watkins, Drug-Induced Network, DILIGEN, EUDRAGENE, Spanish Registry, International Consortium .  2012.   Limited contribution of common genetic variants to risk for liver injury due to a variety of drugs.. Pharmacogenet Genomics. 22 (11) :784-95 ▶ Go to Pubmed
Germán Plata, Tobias Fuhrer, Tzu-Lin Hsiao, Uwe Sauer, Dennis Vitkup .  2012.   Global probabilistic annotation of metabolic networks enables enzyme discovery.. Nat Chem Biol. 8 (10) :848-54 ▶ Go to Pubmed
Y Yang, J Wu, A Demir, Mireia Castillo-Martin, Rachel Melamed, G Zhang, M Fukunaga-Kanabis, R Perez-Lorenzo, B Zheng, D Silvers, G Brunner, S Wang, Raul Rabadan, Carlos Cordon-Cardo, J Celebi .  2012.   GAB2 induces tumor angiogenesis in NRAS-driven melanoma.. Oncogene. ▶ Go to Pubmed
Oliver Harrison, Jeremie Vendome, Julia Brasch, Xiangshu Jin, Soonjin Hong, Phinikoula Katsamba, Goran Ahlsen, Regina Troyanovsky, Sergey Troyanovsky, Barry Honig, Lawrence Shapiro .  2012.   Nectin ectodomain structures reveal a canonical adhesive interface.. Nat Struct Mol Biol. 19 (9) :906-15 ▶ Go to Pubmed
Davide Rossi, Vladimir Trifonov, Marco Fangazio, Alessio Bruscaggin, Silvia Rasi, Valeria Spina, Sara Monti, Tiziana Vaisitti, Francesca Arruga, Rosella Famà, Carmela Ciardullo, Mariangela Greco, Stefania Cresta, Daniela Piranda, Antony Holmes, Giulia Fabbri, Monica Messina, Andrea Rinaldi, Jiguang Wang, Claudio Agostinelli, Pier Piccaluga, Marco Lucioni, Fabrizio Tabbò, Roberto Serra, Silvia Franceschetti, Clara Deambrogi, Giulia Daniele, Valter Gattei, Roberto Marasca, Fabio Facchetti, Luca Arcaini, Giorgio Inghirami, Francesco Bertoni, Stefano Pileri, Silvia Deaglio, Robin Foá, Riccardo Dalla-Favera, Laura Pasqualucci, Raul Rabadan, Gianluca Gaidano .  2012.   The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development.. J Exp Med. 209 (9) :1537-51 ▶ Go to Pubmed
Christopher Campbell, Pier Palamara, Maya Dubrovsky, Laura Botigué, Marc Fellous, Gil Atzmon, Carole Oddoux, Alexander Pearlman, Li Hao, Brenna Henn, Edward Burns, Carlos Bustamante, David Comas, Eitan Friedman, Itsik Pe'er, Harry Ostrer .  2012.   North African Jewish and non-Jewish populations form distinctive, orthogonal clusters.. Proc Natl Acad Sci U S A. 109 (34) :13865-70 ▶ Go to Pubmed
S Anthony, J St Leger, K Pugliares, H Ip, Joseph Chan, Zachary Carpenter, I Navarrete-Macias, M Sanchez-Leon, J Saliki, J Pedersen, W Karesh, P Daszak, Raul Rabadan, T Rowles, W Lipkin .  2012.   Emergence of fatal avian influenza in New England harbor seals.. MBio. 3 (4) :e00166-12 ▶ Go to Pubmed
Devendra Singh, Joseph Chan, Pietro Zoppoli, Francesco Niola, Ryan Sullivan, Angelica Castano, Eric Liu, Jonathan Reichel, Paola Porrati, Serena Pellegatta, Kunlong Qiu, Zhibo Gao, Michele Ceccarelli, Riccardo Riccardi, Daniel Brat, Abhijit Guha, Ken Aldape, John Golfinos, David Zagzag, Tom Mikkelsen, Gaetano Finocchiaro, Anna Lasorella, Raul Rabadan, Antonio Iavarone .  2012.   Transforming fusions of FGFR and TACC genes in human glioblastoma.. Science. 337 (6099) :1231-5 ▶ Go to Pubmed
Jingqiang Wang, Takashi Kobayashi, Nicolas Floc'h, Carolyn Kinkade, Alvaro Aytes, David Dankort, Celine Lefebvre, Antonina Mitrofanova, Robert Cardiff, Martin McMahon, Andrea Califano, Michael Shen, Cory Abate-Shen .  2012.   B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer.. Cancer Res. 72 (18) :4765-76 ▶ Go to Pubmed
Andrea Califano, Atul Butte, Stephen Friend, Trey Ideker, Eric Schadt .  2012.   Leveraging models of cell regulation and GWAS data in integrative network-based association studies.. Nat Genet. 44 (8) :841-7 ▶ Go to Pubmed
Samuel Silverstein, Raul Rabadan .  2012.   How many neutrophils are enough (redux, redux)?. J Clin Invest. 122 (8) :2776-9 ▶ Go to Pubmed
Peter Freddolino, Saeed Tavazoie .  2012.   The dawn of virtual cell biology.. Cell. 150 (2) :248-50 ▶ Go to Pubmed
Nicolas Floc'h, Carolyn Kinkade, Takashi Kobayashi, Alvaro Aytes, Celine Lefebvre, Antonina Mitrofanova, Robert Cardiff, Andrea Califano, Michael Shen, Cory Abate-Shen .  2012.   Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model.. Cancer Res. 72 (17) :4483-93 ▶ Go to Pubmed
Hany Girgis, Kendra Harris, Saeed Tavazoie .  2012.   Large mutational target size for rapid emergence of bacterial persistence.. Proc Natl Acad Sci U S A. 109 (31) :12740-5 ▶ Go to Pubmed
Daniel Marbach, James Costello, Robert Küffner, Nicole Vega, Robert Prill, Diogo Camacho, Kyle Allison, DREAM5 Consortium, Manolis Kellis, James Collins, Gustavo Stolovitzky .  2012.   Wisdom of crowds for robust gene network inference.. Nat Methods. 9 (8) :796-804 ▶ Go to Pubmed
Snehit Prabhu, Itsik Pe'er .  2012.   Ultrafast genome-wide scan for SNP-SNP interactions in common complex disease.. Genome Res. 22 (11) :2230-40 ▶ Go to Pubmed
Scott McIsaac, Allegra Petti, Harmen Bussemaker, David Botstein .  2012.   Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.. Mol Biol Cell. 23 (15) :2993-3007 ▶ Go to Pubmed
Allegra Petti, Scott McIsaac, Olivia Ho-Shing, Harmen Bussemaker, David Botstein .  2012.   Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.. Mol Biol Cell. 23 (15) :3008-24 ▶ Go to Pubmed
Peter Freddolino, Hani Goodarzi, Saeed Tavazoie .  2012.   Fitness landscape transformation through a single amino acid change in the rho terminator.. PLoS Genet. 8 (5) :e1002744 ▶ Go to Pubmed
Santiago Vilar, Rave Harpaz, Eugenio Uriarte, Lourdes Santana, Raul Rabadan, Carol Friedman .  2012.   Drug-drug interaction through molecular structure similarity analysis.. J Am Med Inform Assoc. 19 (6) :1066-74 ▶ Go to Pubmed
Alexandros Iliadis, Dimitris Anastassiou, Xiaodong Wang .  2012.   A unified framework for haplotype inference in nuclear families.. Ann Hum Genet. 76 (4) :312-25 ▶ Go to Pubmed
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
Yibing Shan, Michael Eastwood, Xuewu Zhang, Eric Kim, Anton Arkhipov, Ron Dror, John Jumper, John Kuriyan, David Shaw .  2012.   Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization.. Cell. 149 (4) :860-70 ▶ Go to Pubmed
Ron Dror, Robert Dirks, J Grossman, Huafeng Xu, David Shaw .  2012.   Biomolecular simulation: a computational microscope for molecular biology.. Annu Rev Biophys. 41 :429-52 ▶ Go to Pubmed
Bill Andreopoulos, Dimitris Anastassiou .  2012.   Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature.. Cancer Inform. 11 :61-75 ▶ Go to Pubmed
Peter Freddolino, Saeed Tavazoie .  2012.   Beyond homeostasis: a predictive-dynamic framework for understanding cellular behavior.. Annu Rev Cell Dev Biol. 28 :363-84 ▶ Go to Pubmed
Julia Brasch, Oliver Harrison, Barry Honig, Lawrence Shapiro .  2012.   Thinking outside the cell: how cadherins drive adhesion.. Trends Cell Biol. 22 (6) :299-310 ▶ Go to Pubmed
Dianne Dapito, Ali Mencin, Geum-Youn Gwak, Jean-Philippe Pradere, Myoung-Kuk Jang, Ingmar Mederacke, Jorge Caviglia, Hossein Khiabanian, Adebowale Adeyemi, Ramon Bataller, Jay Lefkowitch, Maureen Bower, Richard Friedman, Balfour Sartor, Raul Rabadan, Robert Schwabe .  2012.   Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4.. Cancer Cell. 21 (4) :504-16 ▶ Go to Pubmed
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