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2013

2013 Publications

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
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
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
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
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
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
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