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2013

2013 Publications

Vladimir Trifonov, Laura Pasqualucci, Enrico Tiacci, Brunangelo Falini, Raul Rabadan .  2013.   SAVI: a statistical algorithm for variant frequency identification.. BMC Syst Biol. 7 Suppl 2 :S2 ▶ Go to Pubmed
In Jang, Adam Margolin, Andrea Califano .  2013.   hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests.. Interface Focus. 3 (4) :20130011 ▶ Go to Pubmed
Scott Dixon, Brent Stockwell .  2013.   The Role of Iron and Reactive Oxygen Secies in Cell Death.. Nat Chem Biol. 10 (1) :9-17 ▶ Go to Pubmed
Liang Liu, Hyunmi Kim, Alex Casta, Yuki Kobayashi, Lawrence Shapiro, Angela Christiano .  2013.   Hairless Is a Histone H3K9 Demethylase.. FASEB J. ▶ Go to Pubmed
Marie Harton, Laura Wingler, Virginia Cornish .  2013.   Transcriptional regulation improves the throughput of three-hybrid counter selections in Saccharomyces cerevisiae.. Biotechnol J. 8 (12) :1485-91 ▶ Go to Pubmed
Peter Freddolino, Hani Goodarzi, Saeed Tavazoie .  2013.   Revealing the Genetic Basis of Natural Bacterial Phenotypic Divergence.. J Bacteriol. ▶ Go to Pubmed
Erich Piovan, Jiyang Yu, Valeria Tosello, Daniel Herranz, Alberto Ambesi-Impiombato, Ana Da Silva, Marta Sanchez-Martin, Arianne Perez-Garcia, Isaura Rigo, Mireia Castillo-Martin, Stefano Indraccolo, Justin Cross, Elisa de Stanchina, Elisabeth Paietta, Janis Racevskis, Jacob Rowe, Martin Tallman, Giuseppe Basso, Jules Meijerink, Carlos Cordon-Cardo, Andrea Califano, Adolfo Ferrando .  2013.   Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia.. Cancer Cell. 24 (6) :766-76 ▶ Go to Pubmed
Germán Plata, Dennis Vitkup .  2013.   Genetic Robustness and Functional Evolution of Gene Duplicates.. Nucleic Acids Res. ▶ Go to Pubmed
Todd Lencz, Saurav Guha, Chunyu Liu, Jeffrey Rosenfeld, Semanti Mukherjee, Pamela Derosse, Majnu John, Lijun Cheng, Chunling Zhang, Judith Badner, Masashi Ikeda, Nakao Iwata, Sven Cichon, Marcella Rietschel, Markus Nöthen, A Cheng, Colin Hodgkinson, Qiaoping Yuan, John Kane, Annette Lee, Anne Pisanté, Peter Gregersen, Itsik Pe'er, Anil Malhotra, David Goldman, Ariel Darvasi .  2013.   Genome-wide association study implicates NDST3 in schizophrenia and bipolar disorder.. Nat Commun. 4 :2739 ▶ Go to Pubmed
Sabine Becker-Weimann, Gaofeng Xiong, Saori Furuta, Ju Han, Irene Kuhn, Uri Akavia, Dana Pe'er, Mina Bissell, Ren Xu .  2013.   NFkB disrupts tissue polarity in 3D by preventing integration of microenvironmental signals.. Oncotarget. ▶ Go to Pubmed
Elijah Behr, Marylyn Ritchie, Toshihiro Tanaka, Stefan Kääb, Dana Crawford, Paola Nicoletti, Aris Floratos, Moritz Sinner, Prince Kannankeril, Arthur Wilde, Connie Bezzina, Eric Schulze-Bahr, Sven Zumhagen, Pascale Guicheney, Nanette Bishopric, Vanessa Marshall, Saad Shakir, Chrysoula Dalageorgou, Steve Bevan, Yalda Jamshidi, Rachel Bastiaenen, Robert Myerburg, Jean-Jacques Schott, John Camm, Gerhard Steinbeck, Kris Norris, Russ Altman, Nicholas Tatonetti, Steve Jeffery, Michiaki Kubo, Yusuke Nakamura, Yufeng Shen, Alfred George, Dan Roden .  2013.   Genome wide analysis of drug-induced torsades de pointes: lack of common variants with large effect sizes.. PLoS One. 8 (11) :e78511 ▶ Go to Pubmed
Ross Lippert, Cristian Predescu, Douglas Ierardi, Kenneth Mackenzie, Michael Eastwood, Ron Dror, David Shaw .  2013.   Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure.. J Chem Phys. 139 (16) :164106 ▶ Go to Pubmed
Cory Abate-Shen, PP Pandolfi .  2013.   Effective utilization and appropriate selection of genetically engineered mouse models for translational integration of mouse and human trials.. Cold Spring Harb Protoc. 2013 (11) ▶ Go to Pubmed
Joseph Chan, Gunnar Carlsson, Raul Rabadan .  2013.   Topology of viral evolution.. Proc Natl Acad Sci U S A. 110 (46) :18566-71 ▶ Go to Pubmed
sbv team, Sam Ansari, Jean Binder, Stephanie Boue, Anselmo Di Fabio, William Hayes, Julia Hoeng, Anita Iskandar, Robin Kleiman, Raquel Norel, Bruce O'Neel, Manuel Peitsch, Carine Poussin, Dexter Pratt, Kahn Rhrissorrakrai, Walter Schlage, Gustavo Stolovitzky, Marja Talikka .  2013.   On crowd-verification of biological networks.. Bioinform Biol Insights. 7 :307-25 ▶ Go to Pubmed
Marc Lajoie, Alexis Rovner, Daniel Goodman, Hans-Rudolf Aerni, Adrian Haimovich, Gleb Kuznetsov, Jaron Mercer, Harris Wang, Peter Carr, Joshua Mosberg, Nadin Rohland, Peter Schultz, Joseph Jacobson, Jesse Rinehart, George Church, Farren Isaacs .  2013.   Genomically recoded organisms expand biological functions.. Science (New York, N.Y.). 342 (6156) :357-60 ▶ Go to Pubmed
Giulia Fabbri, Hossein Khiabanian, Antony Holmes, Jiguang Wang, Monica Messina, Charles Mullighan, Laura Pasqualucci, Raul Rabadan, Riccardo Dalla-Favera .  2013.   Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome.. J Exp Med. 210 (11) :2273-88 ▶ Go to Pubmed
Ron Dror, Hillary Green, Celine Valant, David Borhani, James Valcourt, Albert Pan, Daniel Arlow, Meritxell Canals, Robert Lane, Raphaël Rahmani, Jonathan Baell, Patrick Sexton, Arthur Christopoulos, David Shaw .  2013.   Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs.. Nature. 503 (7475) :295-9 ▶ Go to Pubmed
Charles Leduc, Elizabeth Crouch, Ashley Wilson, Jay Lefkowitch, Mirjam Wamelink, Cornelis Jakobs, Gajja Salomons, Xiaoyun Sun, Yufeng Shen, Wendy Chung .  2013.   Novel association of early onset hepatocellular carcinoma with transaldolase deficiency.. JIMD Rep. ▶ Go to Pubmed
Xiaochen Sun, Santiago Vilar, Nicholas Tatonetti .  2013.   High-throughput methods for combinatorial drug discovery.. Sci Transl Med. 5 (205) :205rv1 ▶ Go to Pubmed
David Blair, Christopher Lyttle, Jonathan Mortensen, Charles Bearden, Anders Jensen, Hossein Khiabanian, Rachel Melamed, Raul Rabadan, Elmer Bernstam V, Søren Brunak, Lars Jensen, Dan Nicolae, Nigam Shah, Robert Grossman, Nancy Cox, Kevin White, Andrey Rzhetsky .  2013.   A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk.. Cell. 155 (1) :70-80 ▶ Go to Pubmed
Cancer Network, John Weinstein, Eric Collisson, Gordon Mills, Kenna Shaw, Brad Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua Stuart .  2013.   The Cancer Genome Atlas Pan-Cancer Analysis Project.. Nat Genet. 45 (10) :1113-20 ▶ Go to Pubmed
Julien Gagneur, Oliver Stegle, Chenchen Zhu, Petra Jakob, Manu Tekkedil, Raeka Aiyar, Ann-Kathrin Schuon, Dana Pe'er, Lars Steinmetz .  2013.   Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.. PLoS Genet. 9 (9) :e1003803 ▶ Go to Pubmed
Ying Li, Nicole Altorelli, Fabiana Bahna, Barry Honig, Lawrence Shapiro, Arthur Palmer .  2013.   Mechanism of E-cadherin dimerization probed by NMR relaxation dispersion.. Proc Natl Acad Sci U S A. 110 (41) :16462-7 ▶ Go to Pubmed
Sonia Hernandez, Debarshi Banerjee, Alejandro Garcia, Thaned Kangsamaksin, Wei-Yi Cheng, Dimitris Anastassiou, Yasuhiro Funahashi, Angela Kadenhe-Chiweshe, Carrie Shawber, Jan Kitajewski, Jessica Kandel, Darrell Yamashiro .  2013.   Notch and VEGF pathways play distinct but complementary roles in tumor angiogenesis.. Vasc Cell. 5 (1) :17 ▶ Go to Pubmed
Charles Sawyers, Cory Abate-Shen, Kenneth Anderson, Anna Barker, Jose Baselga, Nathan Berger, Margaret Foti, Ahmedin Jemal, Theodore Lawrence, Christopher Li, Elaine Mardis, Peter Neumann, Drew Pardoll, George Prendergast, John Reed, George Weiner, AACR Committee .  2013.   AACR Cancer Progress Report 2013.. Clin Cancer Res. 19 (20 Suppl) :S1-S98 ▶ Go to Pubmed
Gal Romano, Yaniv Harari, Tal Yehuda, Ariel Podhorzer, Linda Rubinstein, Ron Shamir, Assaf Gottlieb, Yael Silberberg, Dana Pe'er, Eytan Ruppin, Roded Sharan, Martin Kupiec .  2013.   Environmental stresses disrupt telomere length homeostasis.. PLoS Genet. 9 (9) :e1003721 ▶ Go to Pubmed
F Mancini, Chris Wiggins, M Marsili, A Walczak .  2013.   Time-dependent information transmission in a model regulatory circuit.. Phys Rev E Stat Nonlin Soft Matter Phys. 88 (2) :022708 ▶ Go to Pubmed
Lamont Barlow, Michael Shen .  2013.   SnapShot: Prostate cancer.. Cancer Cell. 24 (3) :400.e1 ▶ Go to Pubmed
Shazia Irshad, Mukesh Bansal, Mireia Castillo-Martin, Tian Zheng, Alvaro Aytes, Sven Wenske, Clémentine Le Magnen, Paolo Guarnieri, Pavel Sumazin, Mitchell Benson, Michael Shen, Andrea Califano, Cory Abate-Shen .  2013.   A molecular signature predictive of indolent prostate cancer.. Sci Transl Med. 5 (202) :202ra122 ▶ Go to Pubmed
Brian Anton, Yi-Chien Chang, Peter Brown, Han-Pil Choi, Lina Faller, Jyotsna Guleria, Zhenjun Hu, Niels Klitgord, Ami Levy-Moonshine, Almaz Maksad, Varun Mazumdar, Mark McGettrick, Lais Osmani, Revonda Pokrzywa, John Rachlin, Rajeswari Swaminathan, Benjamin Allen, Genevieve Housman, Caitlin Monahan, Krista Rochussen, Kevin Tao, Ashok Bhagwat, Steven Brenner, Linda Columbus, Valérie de Crécy-Lagard, Donald Ferguson, Alexey Fomenkov, Giovanni Gadda, Richard Morgan, Andrei Osterman, Dmitry Rodionov, Irina Rodionova, Kenneth Rudd, Dieter Söll, James Spain, Shuang-Yong Xu, Alex Bateman, Robert Blumenthal, Martin Bollinger, Woo-Suk Chang, Manuel Ferrer, Iddo Friedberg, Michael Galperin, Julien Gobeill, Daniel Haft, John Hunt, Peter Karp, William Klimke, Carsten Krebs, Dana Macelis, Ramana Madupu, Maria Martin, Jeffrey Miller, Claire O'Donovan, Bernhard Palsson, Patrick Ruch, Aaron Setterdahl, Granger Sutton, John Tate, Alexander Yakunin, Dmitri Tchigvintsev, Germán Plata, Jie Hu, Russell Greiner, David Horn, Kimmen Sjölander, Steven Salzberg, Dennis Vitkup, Stanley Letovsky, Daniel Segrè, Charles Delisi, Richard Roberts, Martin Steffen, Simon Kasif .  2013.   The COMBREX project: design, methodology, and initial results.. PLoS Biol. 11 (8) :e1001638 ▶ Go to Pubmed
Guido Jajamovich, Alexandros Iliadis, Dimitris Anastassiou, Xiaodong Wang .  2013.   Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA.. BMC Bioinformatics. 14 (1) :270 ▶ Go to Pubmed
A Jacunski, Nicholas Tatonetti .  2013.   Connecting the dots: applications of network medicine in pharmacology and disease.. Clin Pharmacol Ther. 94 (6) :659-69 ▶ Go to Pubmed
Amrita Basu, Nicole Bodycombe, Jaime Cheah, Edmund Price V, Ke Liu, Giannina Schaefer, Richard Ebright, Michelle Stewart, Daisuke Ito, Stephanie Wang, Abigail Bracha, Ted Liefeld, Mathias Wawer, Joshua Gilbert, Andrew Wilson, Nicolas Stransky, Gregory Kryukov V, Vlado Dancik, Jordi Barretina, Levi Garraway, Suk-Yee Hon, Benito Munoz, Joshua Bittker, Brent Stockwell, Dineo Khabele, Andrew Stern, Paul Clemons, Alykhan Shamji, Stuart Schreiber .  2013.   An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules.. Cell. 154 (5) :1151-61 ▶ Go to Pubmed
Saeed Tavazoie .  2013.   Synaptic state matching: a dynamical architecture for predictive internal representation and feature detection.. PLoS One. 8 (8) :e72865 ▶ Go to Pubmed
Carol Ying, David Dominguez-Sola, Melissa Fabi, Ivo Lorenz, Shafinaz Hussein, Mukesh Bansal, Andrea Califano, Laura Pasqualucci, Katia Basso, Riccardo Dalla-Favera .  2013.   MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma.. Nat Immunol. ▶ Go to Pubmed
Adi Tarca, Mario Lauria, Michael Unger, Erhan Bilal, Stephanie Boue, Kushal Dey, Julia Hoeng, Heinz Koeppl, Florian Martin, Pablo Meyer, Preetam Nandy, Raquel Norel, Manuel Peitsch, Jeremy Rice, Roberto Romero, Gustavo Stolovitzky, Marja Talikka, Yang Xiang, Christoph Zechner, IMPROVER Collaborators .  2013.   Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge.. Bioinformatics. 29 (22) :2892-9 ▶ Go to Pubmed
Jianbo Sun, Celia Keim, Jiguang Wang, David Kazadi, Paula Oliver, Raul Rabadan, Uttiya Basu .  2013.   E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells.. Genes Dev. 27 (16) :1821-33 ▶ Go to Pubmed
Pablo Meyer, Geoffrey Siwo, Danny Zeevi, Eilon Sharon, Raquel Norel, DREAM6 Consortium, Eran Segal, Gustavo Stolovitzky .  2013.   Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach.. Genome Res. 23 (11) :1928-37 ▶ Go to Pubmed
Yaron Antebi, Shlomit Reich-Zeliger, Yuval Hart, Avi Mayo, Inbal Eizenberg, Jacob Rimer, Prabhakar Putheti, Dana Pe'er, Nir Friedman .  2013.   Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates.. PLoS Biol. 11 (7) :e1001616 ▶ Go to Pubmed
Alvaro Aytes, Antonina Mitrofanova, Carolyn Kinkade, Celine Lefebvre, Ming Lei, Vanessa Phelan, Carl Lekaye, Jason Koutcher, Robert Cardiff, Andrea Califano, Michael Shen, Cory Abate-Shen .  2013.   ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Veronique Frattini, Vladimir Trifonov, Joseph Chan, Angelica Castano, Marie Lia, Francesco Abate, Stephen Keir, Alan Ji, Pietro Zoppoli, Francesco Niola, Carla Danussi, Igor Dolgalev, Paola Porrati, Serena Pellegatta, Adriana Heguy, Gaurav Gupta, David Pisapia, Peter Canoll, Jeffrey Bruce, Roger McLendon, Hai Yan, Ken Aldape, Gaetano Finocchiaro, Tom Mikkelsen, Gilbert Privé, Darell Bigner, Anna Lasorella, Raul Rabadan, Antonio Iavarone .  2013.   The integrated landscape of driver genomic alterations in glioblastoma.. Nat Genet. ▶ Go to Pubmed
Ronald Tepper, Jasmine Ashraf, Rachel Kaletsky, Gunnar Kleemann, Coleen Murphy, Harmen Bussemaker .  2013.   PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity.. Cell. 154 (3) :676-90 ▶ Go to Pubmed
Arianne Perez-Garcia, Alberto Ambesi-Impiombato, Michael Hadler, Isaura Rigo, Charles Leduc, Kara Kelly, Chaim Jalas, Elisabeth Paietta, Janis Racevskis, Jacob Rowe, Martin Tallman, Maddalena Paganin, Giuseppe Basso, Wei Tong, Wendy Chung, Adolfo Ferrando .  2013.   Genetic loss of SH2B3 in acute lymphoblastic leukemia.. Blood. ▶ Go to Pubmed
Maria Rudchenko, Steven Taylor, Payal Pallavi, Alesia Dechkovskaia, Safana Khan, Vincent Butler, Sergei Rudchenko, Milan Stojanovic .  2013.   Autonomous molecular cascades for evaluation of cell surfaces.. Nat Nanotechnol. 8 (8) :580-6 ▶ Go to Pubmed
Stefano Piana, Kresten Lindorff-Larsen, David Shaw .  2013.   Atomistic description of the folding of a dimeric protein.. J Phys Chem B. ▶ Go to Pubmed
Anton Arkhipov, Yibing Shan, Eric Kim, Ron Dror, David Shaw .  2013.   Her2 activation mechanism reflects evolutionary preservation of asymmetric ectodomain dimers in the human EGFR family.. Elife. 2 :e00708 ▶ Go to Pubmed
Nicholas Tatonetti, Joshua Denny, Russ Altman .  2013.   Response to 'Use of an algorithm for identifying hidden drug-drug interactions in adverse event reports' by Gooden et al.. J Am Med Inform Assoc. 20 (3) :591 ▶ Go to Pubmed
Alison Hottes, Peter Freddolino, Anupama Khare, Zachary Donnell, Julia Liu, Saeed Tavazoie .  2013.   Bacterial adaptation through loss of function.. PLoS Genet. 9 (7) :e1003617 ▶ Go to Pubmed
Isaac Chiu, Emiko Morimoto, Hani Goodarzi, Jennifer Liao, Sean O'Keeffe, Hemali Phatnani, Michael Muratet, Michael Carroll, Shawn Levy, Saeed Tavazoie, Richard Myers, Tom Maniatis .  2013.   A neurodegeneration-specific gene-expression signature of acutely isolated microglia from an amyotrophic lateral sclerosis mouse model.. Cell Rep. 4 (2) :385-401 ▶ Go to Pubmed
Anat Kreimer, Itsik Pe'er .  2013.   Variants in exons and in transcription factors affect gene expression in trans.. Genome Biol. 14 (7) :R71 ▶ Go to Pubmed
Michael Eastwood, Tarun Chitra, John Jumper, Kim Palmo, Albert Pan, David Shaw .  2013.   Rotational relaxation in ortho-terphenyl: using atomistic simulations to bridge theory and experiment.. J Phys Chem B. ▶ Go to Pubmed
Chaoran Jing, Virginia Cornish .  2013.   Design, synthesis, and application of the trimethoprim-based chemical tag for live-cell imaging.. Curr Protoc Chem Biol. 5 (2) :131-55 ▶ Go to Pubmed
Roxana Daneshjou, Nicholas Tatonetti, Konrad Karczewski, Hersh Sagreiya, Stephane Bourgeois, Katarzyna Drozda, James Burmester, Tatsuhiko Tsunoda, Yusuke Nakamura, Michiaki Kubo, Matthew Tector, Nita Limdi, Larisa Cavallari, Minoli Perera, Julie Johnson, Teri Klein, Russ Altman .  2013.   Pathway analysis of genome-wide data improves warfarin dose prediction.. BMC Genomics. 14 Suppl 3 :S11 ▶ Go to Pubmed
Takashi Kobayashi, Jingqiang Wang, Hikmat Al-Ahmadie, Cory Abate-Shen .  2013.   ARF regulates the stability of p16 protein via REGγ-dependent proteasome degradation.. Mol Cancer Res. ▶ Go to Pubmed
Marianna de Julio, Maho Shibata, Nishita Desai, Melissa Reynon, Vivienne Halili, Ya-Ping Hu, Sandy Price, Cory Abate-Shen, Michael Shen .  2013.   Canonical Wnt signaling regulates Nkx3.1 expression and luminal epithelial differentiation during prostate organogenesis.. Dev Dyn. ▶ Go to Pubmed
Pier Palamara, Itsik Pe'er .  2013.   Inference of historical migration rates via haplotype sharing.. Bioinformatics. 29 (13) :i180-i188 ▶ Go to Pubmed
Carla Danussi, Uri Akavia, Francesco Niola, Andreja Jovic, Anna Lasorella, Dana Pe'er, Antonio Iavarone .  2013.   RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation.. Cancer Res. ▶ Go to Pubmed
Zhixing Chen, Virginia Cornish, Wei Min .  2013.   Chemical tags: inspiration for advanced imaging techniques.. Curr Opin Chem Biol. ▶ Go to Pubmed
Chaoran Jing, Virginia Cornish .  2013.   A fluorogenic TMP-tag for high signal-to-background intracellular live cell imaging.. ACS Chem Biol. ▶ Go to Pubmed
Jihuan Chen, Vez Repunte-Canonigo, Tomoya Kawamura, Celine Lefebvre, William Shin, Leonard Howell, Scott Hemby, Brandon Harvey, Andrea Califano, Marisela Morales, George Koob, Pietro Sanna .  2013.   Hypothalamic proteoglycan syndecan-3 is a novel cocaine addiction resilience factor.. Nat Commun. 4 :1955 ▶ Go to Pubmed
Valeria Tosello, Adolfo Ferrando .  2013.   The NOTCH signaling pathway: role in the pathogenesis of T-cell acute lymphoblastic leukemia and implication for therapy.. Ther Adv Hematol. 4 (3) :199-210 ▶ Go to Pubmed
Tae Kim, Ka Chung, Aashish Manglik, Alexandar Hansen, Ron Dror, Thomas Mildorf, David Shaw, Brian Kobilka, Scott Prosser .  2013.   The role of ligands on the equilibria between functional states of a G protein-coupled receptor.. J Am Chem Soc. 135 (25) :9465-74 ▶ Go to Pubmed
Erika Haydu, Adolfo Ferrando .  2013.   Early T-cell precursor acute lymphoblastic leukaemia.. Curr Opin Hematol. 20 (4) :369-73 ▶ Go to Pubmed
Pieter Van Vlierberghe, Alberto Ambesi-Impiombato, Kim De Keersmaecker, Michael Hadler, Elisabeth Paietta, Martin Tallman, Jacob Rowe, Carles Forne, Montserrat Rue, Adolfo Ferrando .  2013.   Prognostic relevance of integrated genetic profiling in adult T-cell acute lymphoblastic leukemia.. Blood. 122 (1) :74-82 ▶ Go to Pubmed
Chaolin Zhang, Kuang-Yung Lee, Maurice Swanson, Robert Darnell .  2013.   Prediction of clustered RNA-binding protein motif sites in the mammalian genome.. Nucleic Acids Res. ▶ Go to Pubmed
El-Ad Amir, Kara Davis, Michelle Tadmor, Erin Simonds, Jacob Levine, Sean Bendall, Daniel Shenfeld, Smita Krishnaswamy, Garry Nolan, Dana Pe'er .  2013.   viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.. Nat Biotechnol. ▶ Go to Pubmed
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
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