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Ash Alizadeh, Victoria Aranda, Alberto Bardelli, Cedric Blanpain, Christoph Bock, Christine Borowski, Carlos Caldas, Andrea Califano, Michael Doherty, Markus Elsner, Manel Esteller, Rebecca Fitzgerald, Jan Korbel, Peter Lichter, Christopher Mason, Nicholas Navin, Dana Pe'er, Kornelia Polyak, Charles Roberts, Lillian Siu, Alexandra Snyder, Hannah Stower, Charles Swanton, Roel Verhaak, Jean Zenklusen, Johannes Zuber, Jessica Zucman-Rossi .  2015.   Toward understanding and exploiting tumor heterogeneity.. Nat Med. 21 (8) :846-53 ▶ Go to Pubmed
Huijuan Feng, Xuegong Zhang, Chaolin Zhang .  2015.   mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data.. Nat Commun. 6 :7816 ▶ Go to Pubmed
Ruth Rodriguez-Barrueco, Jiyang Yu, Laura Saucedo-Cuevas, Mireia Olivan, David Llobet-Navas, Preeti Putcha, Verónica Castro, Eva Murga-Penas, Ana Collazo-Lorduy, Mireia Castillo-Martin, Mariano Alvarez, Carlos Cordon-Cardo, Kevin Kalinsky, Matthew Maurer, Andrea Califano, Jose Silva .  2015.   Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers.. Genes Dev. 29 (15) :1631-48 ▶ Go to Pubmed
Joshua Tasoff, Michael Mee, Harris Wang .  2015.   An Economic Framework of Microbial Trade.. PLoS One. 10 (7) :e0132907 ▶ Go to Pubmed
Xuewen Liu, Yuxia Jia, Mark Stoopler, Yufeng Shen, Haiying Cheng, Jinli Chen, Mahesh Mansukhani, Sanjay Koul, Balazs Halmos, Alain Borczuk .  2015.   Next-Generation Sequencing of Pulmonary Sarcomatoid Carcinoma Reveals High Frequency of Actionable MET Gene Mutations.. J Clin Oncol. ▶ Go to Pubmed
Lars Brichta, William Shin, Vernice Jackson-Lewis, Javier Blesa, Ee-Lynn Yap, Zachary Walker, Jack Zhang, Jean-Pierre Roussarie, Mariano Alvarez, Andrea Califano, Serge Przedborski, Paul Greengard .  2015.   Identification of neurodegenerative factors using translatome-regulatory network analysis.. Nat Neurosci. ▶ Go to Pubmed
Xose Puente, Silvia Beà, Rafael Valdés-Mas, Neus Villamor, Jesús Gutiérrez-Abril, José Martín-Subero, Marta Munar, Carlota Rubio-Pérez, Pedro Jares, Marta Aymerich, Tycho Baumann, Renée Beekman, Laura Belver, Anna Carrio, Giancarlo Castellano, Guillem Clot, Enrique Colado, Dolors Colomer, Dolors Costa, Julio Delgado, Anna Enjuanes, Xavier Estivill, Adolfo Ferrando, Josep Gelpí, Blanca González, Santiago González, Marcos González, Marta Gut, Jesús Hernández-Rivas, Mónica López-Guerra, David Martín-García, Alba Navarro, Pilar Nicolás, Modesto Orozco, Ángel Payer, Magda Pinyol, David Pisano, Diana Puente, Ana Queirós, Víctor Quesada, Carlos Romeo-Casabona, Cristina Royo, Romina Royo, María Rozman, Nuria Russiñol, Itziar Salaverría, Kostas Stamatopoulos, Hendrik Stunnenberg, David Tamborero, María Terol, Alfonso Valencia, Nuria López-Bigas, David Torrents, Ivo Gut, Armando López-Guillermo, Carlos López-Otín, Elias Campo .  2015.   Non-coding recurrent mutations in chronic lymphocytic leukaemia.. Nature. ▶ Go to Pubmed
Wynn Meyer, Aarti Venkat, Amir Kermany, Bryce van de Geijn, Sidi Zhang, Molly Przeworski .  2015.   Evolutionary history inferred from the de novo assembly of a non-model organism, the blue-eyed black lemur.. Mol Ecol. ▶ Go to Pubmed
César Mendes, Imre Bartos, Zsuzsanna Márka, Turgay Akay, Szabolcs Márka, Richard Mann .  2015.   Quantification of gait parameters in freely walking rodents.. BMC Biol. 13 :50 ▶ Go to Pubmed
Jung Woo, Yishai Shimoni, Wan Yang, Prem Subramaniam, Archana Iyer, Paola Nicoletti, María Martínez, Gonzalo Lopez, Michela Mattioli, Ronald Realubit, Charles Karan, Brent Stockwell, Mukesh Bansal, Andrea Califano .  2015.   Elucidating Compound Mechanism of Action by Network Perturbation Analysis.. Cell. 162 (2) :441-51 ▶ Go to Pubmed
M Hayano, WS Yang, CK Corn, NC Pagano, BR Stockwell .  2015.   Loss of cysteinyl-tRNA synthetase (CARS) induces the transsulfuration pathway and inhibits ferroptosis induced by cystine deprivation.. Cell Death Differ. ▶ Go to Pubmed
Xiang-Jun Lu, Harmen Bussemaker, Wilma Olson .  2015.   DSSR: an integrated software tool for dissecting the spatial structure of RNA.. Nucleic Acids Res. ▶ Go to Pubmed
Howook Hwang, Donald Petrey, Barry Honig .  2015.   A hybrid method for protein-protein interface prediction.. Protein Sci. ▶ Go to Pubmed
Jonathan Goodwin, Vishal Kothari, Justin Drake, Shuang Zhao, Emanuela Dylgjeri, Jeffry Dean, Matthew Schiewer, Christopher McNair, Jennifer Jones, Alvaro Aytes, Michael Magee, Adam Snook, Ziqi Zhu, Robert Den, Ruth Birbe, Leonard Gomella, Nicholas Graham, Ajay Vashisht, James Wohlschlegel, Thomas Graeber, Jeffrey Karnes, Mandeep Takhar, Elai Davicioni, Scott Tomlins, Cory Abate-Shen, Nima Sharifi, Owen Witte, Felix Feng, Karen Knudsen .  2015.   DNA-PKcs-Mediated Transcriptional Regulation Drives Prostate Cancer Progression and Metastasis.. Cancer Cell. 28 (1) :97-113 ▶ Go to Pubmed
Daniel Freedberg, Nora Toussaint, Sway Chen, Adam Ratner, Susan Whittier, Timothy Wang, Harris Wang, Julian Abrams .  2015.   Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial.. Gastroenterology. ▶ Go to Pubmed
Berta Vidal, Anthony Santella, Esther Serrano-Saiz, Zhirong Bao, Chiou-Fen Chuang, Oliver Hobert .  2015.   C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types.. Development. 142 (14) :2464-77 ▶ Go to Pubmed
Burcin Ikiz, Mariano Alvarez, Diane Ré, Virginia Le Verche, Kristin Politi, Francesco Lotti, Sudarshan Phani, Radhika Pradhan, Changhao Yu, Gist Croft, Arnaud Jacquier, Christopher Henderson, Andrea Califano, Serge Przedborski .  2015.   The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis.. Cell Rep. ▶ Go to Pubmed
R Rabadan .  2015.   WE-D-BRB-03: Geometrization of Tumor Evolution.. Med Phys. 42 (6) :3666 ▶ Go to Pubmed
Matthew Nelson, Hannah Tipney, Jeffery Painter, Judong Shen, Paola Nicoletti, Yufeng Shen, Aris Floratos, Pak Sham, Mulin Li, Junwen Wang, Lon Cardon, John Whittaker, Philippe Sanseau .  2015.   The support of human genetic evidence for approved drug indications.. Nature genetics. 47 (8) :856-60 ▶ Go to Pubmed
Paola Nicoletti, Mukesh Bansal, Celine Lefebvre, Paolo Guarnieri, Yufeng Shen, Itsik Pe'er, Andrea Califano, Aris Floratos .  2015.   ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and toxic epidermal necrolysis across multiple drugs.. PloS one. 10 (6) :e0131038 ▶ Go to Pubmed
Paola Nicoletti, Mukesh Bansal, Celine Lefebvre, Paolo Guarnieri, Yufeng Shen, Itsik Pe'er, Andrea Califano, Aris Floratos .  2015.   ABC Transporters and the Proteasome Complex Are Implicated in Susceptibility to Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis across Multiple Drugs.. PLoS One. 10 (6) :e0131038 ▶ Go to Pubmed
Satyanarayan Rao, Ana Machado, Tianyin Zhou, Chaitanya Rastogi, Harmen Bussemaker, Remo Rohs .  2015.   22 Evolving insights on how cytosine methylation affects protein-DNA binding.. J Biomol Struct Dyn. 33 Suppl 1 :12 ▶ Go to Pubmed
Tianyin Zhou, Ning Shen, Lin Yang, Namiko Abe, John Horton, Richard Mann, Harmen Bussemaker, Raluca Gordân, Remo Rohs .  2015.   14 Quantitative modeling of transcription factor binding specificities using DNA shape.. J Biomol Struct Dyn. 33 Suppl 1 :8-9 ▶ Go to Pubmed
Young Kwon, Marie Pancera, Priyamvada Acharya, Ivelin Georgiev, Emma Crooks, Jason Gorman, Gordon Joyce, Miklos Guttman, Xiaochu Ma, Sandeep Narpala, Cinque Soto, Daniel Terry, Yongping Yang, Tongqing Zhou, Goran Ahlsen, Robert Bailer, Michael Chambers, Gwo-Yu Chuang, Nicole Doria-Rose, Aliaksandr Druz, Mark Hallen, Adam Harned, Tatsiana Kirys, Mark Louder, Sijy O'Dell, Gilad Ofek, Keiko Osawa, Madhu Prabhakaran, Mallika Sastry, Guillaume Stewart-Jones, Jonathan Stuckey, Paul Thomas V, Tishina Tittley, Constance Williams, Baoshan Zhang, Hong Zhao, Zhou Zhou, Bruce Donald, Lawrence Lee, Susan Zolla-Pazner, Ulrich Baxa, Arne Schön, Ernesto Freire, Lawrence Shapiro, Kelly Lee, James Arthos, James Munro, Scott Blanchard, Walther Mothes, James Binley, Adrian McDermott, John Mascola, Peter Kwong .  2015.   Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env.. Nat Struct Mol Biol. ▶ Go to Pubmed
Patricia Gordon, Oliver Hobert .  2015.   A Competition Mechanism for a Homeotic Neuron Identity Transformation in C. elegans.. Dev Cell. ▶ Go to Pubmed
Jacob Levine, Erin Simonds, Sean Bendall, Kara Davis, El-Ad Amir, Michelle Tadmor, Oren Litvin, Harris Fienberg, Astraea Jager, Eli Zunder, Rachel Finck, Amanda Gedman, Ina Radtke, James Downing, Dana Pe'er, Garry Nolan .  2015.   Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.. Cell. ▶ Go to Pubmed
Kelly Howell, John White, Oliver Hobert .  2015.   Spatiotemporal control of a novel synaptic organizer molecule.. Nature. ▶ Go to Pubmed
Sabrina Murgan, Willi Kari, Ute Rothbächer, Magali Iché-Torres, Pauline Mélénec, Oliver Hobert, Vincent Bertrand .  2015.   Atypical Transcriptional Activation by TCF via a Zic Transcription Factor in C. elegans Neuronal Precursors.. Dev Cell. 33 (6) :737-45 ▶ Go to Pubmed
Santiago Vilar, Tal Lorberbaum, George Hripcsak, Nicholas Tatonetti .  2015.   Improving Detection of Arrhythmia Drug-Drug Interactions in Pharmacovigilance Data through the Implementation of Similarity-Based Modeling.. PLoS One. 10 (6) :e0129974 ▶ Go to Pubmed
Lauren Pitt, Anastasia Tikhonova, Hai Hu, Thomas Trimarchi, Bryan King, Yixiao Gong, Marta Sanchez-Martin, Aris Tsirigos, Dan Littman, Adolfo Ferrando, Sean Morrison, David Fooksman, Iannis Aifantis, Susan Schwab .  2015.   CXCL12-Producing Vascular Endothelial Niches Control Acute T Cell Leukemia Maintenance.. Cancer Cell. 27 (6) :755-68 ▶ Go to Pubmed
Hyung-Ok Lee, Xiao He, Jayati Mookerjee-Basu, Dai Zhongping, Xiang Hua, Emmanuelle Nicolas, Maria Sulis, Adolfo Ferrando, Joseph Testa, Dietmar Kappes .  2015.   Disregulated expression of the transcription factor ThPOK during T-cell development leads to high incidence of T-cell lymphomas.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Elizabeth Ostrowski, Yufeng Shen, Xiangjun Tian, Richard Sucgang, Huaiyang Jiang, Jiaxin Qu, Mariko Katoh-Kurasawa, Debra Brock, Christopher Dinh, Fremiet Lara-Garduno, Sandra Lee, Christie Kovar, Huyen Dinh, Viktoriya Korchina, LaRonda Jackson, Shobha Patil, Yi Han, Lesley Chaboub, Gad Shaulsky, Donna Muzny, Kim Worley, Richard Gibbs, Stephen Richards, Adam Kuspa, Joan Strassmann, David Queller .  2015.   Genomic Signatures of Cooperation and Conflict in the Social Amoeba.. Curr Biol. 25 (12) :1661-5 ▶ Go to Pubmed
Sayantan Bose, Zhenmao Wan, Ambrose Carr, Abbas Rizvi, Gregory Vieira, Dana Pe'er, Peter Sims .  2015.   Scalable microfluidics for single cell RNA printing and sequencing.. Genome Biol. 16 (1) :120 ▶ Go to Pubmed
Mary Boland, Zachary Shahn, David Madigan, George Hripcsak, Nicholas Tatonetti .  2015.   Birth Month Affects Lifetime Disease Risk: A Phenome-Wide Method.. J Am Med Inform Assoc. ▶ Go to Pubmed
Mukesh Bansal, Geetu Mendiratta, Santosh Anand, Ritu Kushwaha, Ryan Kim, Manju Kustagi, Archana Iyer, Raju Chaganti, Andrea Califano, Pavel Sumazin .  2015.   Direct ChIP-Seq significance analysis improves target prediction.. BMC Genomics. 16 Suppl 5 :S4 ▶ Go to Pubmed
Lan Yu, Ashley Sawle, Julia Wynn, Gudrun Aspelund, Charles Stolar, Marc Arkovitz, Douglas Potoka, Kenneth Azarow, George Mychaliska, Yufeng Shen, Wendy Chung .  2015.   Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia.. Hum Mol Genet. ▶ Go to Pubmed
Carlos Nascimento, Leandro Barbosa, Claudson Brito, Roberta Fernandes, Renata Mann, Ana Pinto, Haniel Oliveira, Mike Dodson V, Simone Guimarães, Marcio Duarte .  2015.   Identification of Suitable Reference Genes for Real Time Quantitative Polymerase Chain Reaction Assays on Pectoralis major Muscle in Chicken (Gallus gallus ).. PLoS One. 10 (5) :e0127935 ▶ Go to Pubmed
Joseph DiGiuseppe, Michelle Tadmor, Dana Pe'er .  2015.   Detection of Minimal Residual Disease in B Lymphoblastic Leukemia Using viSNE.. Cytometry B Clin Cytom. ▶ Go to Pubmed
Scott Dixon, Georg Winter, Leila Musavi, Eric Lee, Berend Snijder, Manuele Rebsamen, Giulio Superti-Furga, Brent Stockwell .  2015.   Human haploid cell genetics reveals roles for lipid metabolism genes in non-apoptotic cell death.. ACS Chem Biol. ▶ Go to Pubmed
Jonathan Enriquez, Lalanti Venkatasubramanian, Myungin Baek, Meredith Peterson, Ulkar Aghayeva, Richard Mann .  2015.   Specification of individual adult motor neuron morphologies by combinatorial transcription factor codes.. Neuron. ▶ Go to Pubmed
Evangelos Pefanis, Jiguang Wang, Gerson Rothschild, Junghyun Lim, David Kazadi, Jianbo Sun, Alexander Federation, Jaime Chao, Oliver Elliott, Zhi-Ping Liu, Aris Economides, James Bradner, Raul Rabadan, Uttiya Basu .  2015.   RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity.. Cell. 161 (4) :774-89 ▶ Go to Pubmed
Manuel Rivas, Matti Pirinen, Donald Conrad, Monkol Lek, Emily Tsang, Konrad Karczewski, Julian Maller, Kimberly Kukurba, David DeLuca, Menachem Fromer, Pedro Ferreira, Kevin Smith, Rui Zhang, Fengmei Zhao, Eric Banks, Ryan Poplin, Douglas Ruderfer, Shaun Purcell, Taru Tukiainen, Eric Minikel V, Peter Stenson, David Cooper, Katharine Huang, Timothy Sullivan, Jared Nedzel, GTEx Consortium, Geuvadis consortium, Carlos Bustamante, Jin Li, Mark Daly, Roderic Guigo, Peter Donnelly, Kristin Ardlie, Michael Sammeth, Emmanouil Dermitzakis, Mark McCarthy, Stephen Montgomery, Tuuli Lappalainen, Daniel MacArthur .  2015.   Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.. Science. 348 (6235) :666-9 ▶ Go to Pubmed
Marta Melé, Pedro Ferreira, Ferran Reverter, David DeLuca, Jean Monlong, Michael Sammeth, Taylor Young, Jakob Goldmann, Dmitri Pervouchine, Timothy Sullivan, Rory Johnson, Ayellet Segrè V, Sarah Djebali, Anastasia Niarchou, GTEx Consortium, Fred Wright, Tuuli Lappalainen, Miquel Calvo, Gad Getz, Emmanouil Dermitzakis, Kristin Ardlie, Roderic Guigo .  2015.   Human genomics. The human transcriptome across tissues and individuals.. Science. 348 (6235) :660-5 ▶ Go to Pubmed
GTEx Consortium .  2015.   Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.. Science. 348 (6235) :648-60 ▶ Go to Pubmed
GTEx Consortium .  2015.   Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.. Science. 348 (6235) :648-60 ▶ Go to Pubmed
Yael Baran, Meena Subramaniam, Anne Biton, Taru Tukiainen, Emily Tsang, Manuel Rivas, Matti Pirinen, Maria Gutierrez-Arcelus, Kevin Smith, Kim Kukurba, Rui Zhang, Celeste Eng, Dara Torgerson, Cydney Urbanek, GTEx Consortium, Jin Li, Jose Rodriguez-Santana, Esteban Burchard, Max Seibold, Daniel MacArthur, Stephen Montgomery, Noah Zaitlen, Tuuli Lappalainen .  2015.   The landscape of genomic imprinting across diverse adult human tissues.. Genome Res. ▶ Go to Pubmed
Joey Trampush, Todd Lencz, Emma Knowles, Gail Davies, Saurav Guha, Itsik Pe'er, David Liewald, John Starr, Srdjan Djurovic, Ingrid Melle, Kjetil Sundet, Andrea Christoforou, Ivar Reinvang, Semanti Mukherjee, Pamela Derosse, Astri Lundervold, Vidar Steen, Majnu John, Thomas Espeseth, Katri Räikkönen, Elisabeth Widen, Aarno Palotie, Johan Eriksson, Ina Giegling, Bettina Konte, Masashi Ikeda, Panos Roussos, Stella Giakoumaki, Katherine Burdick, Antony Payton, William Ollier, Mike Horan, Matthew Scult, Dwight Dickinson, Richard Straub, Gary Donohoe, Derek Morris, Aiden Corvin, Michael Gill, Ahmad Hariri, Daniel Weinberger, Neil Pendleton, Nakao Iwata, Ariel Darvasi, Panos Bitsios, Dan Rujescu, Jari Lahti, Stephanie Le Hellard, Matthew Keller, Ole Andreassen, Ian Deary, David Glahn, Anil Malhotra .  2015.   Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment.. Am J Med Genet B Neuropsychiatr Genet. ▶ Go to Pubmed
Rachel Melamed, Jiguang Wang, Antonio Iavarone, Raul Rabadan .  2015.   An information theoretic method to identify combinations of genomic alterations that promote glioblastoma.. J Mol Cell Biol. ▶ Go to Pubmed
Scott Chen, Donald Petrey, José Garzón, Barry Honig .  2015.   Predicting peptide-mediated interactions on a genome-wide scale.. PLoS Comput Biol. 11 (5) :e1004248 ▶ Go to Pubmed
Rachel Melamed, Kevin Emmett, Chioma Madubata, Andrey Rzhetsky, Raul Rabadan .  2015.   Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes.. Nat Commun. 6 :7033 ▶ Go to Pubmed
Michael Englander, Joshua Avins, Rachel Fleisher, Bo Liu, Philip Effraim, Jiangning Wang, Klaus Schulten, Thomas Leyh, Ruben Gonzalez, Virginia Cornish .  2015.   The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center.. Proc Natl Acad Sci U S A. 112 (19) :6038-43 ▶ Go to Pubmed
Serkan Ayvaz, John Horn, Oktie Hassanzadeh, Qian Zhu, Johann Stan, Nicholas Tatonetti, Santiago Vilar, Mathias Brochhausen, Matthias Samwald, Majid Rastegar-Mojarad, Michel Dumontier, Richard Boyce .  2015.   Toward a complete dataset of drug-drug interaction information from publicly available sources.. J Biomed Inform. ▶ Go to Pubmed
Paschalis Kratsios, Bérangère Pinan-Lucarré, Sze Kerk, Alexis Weinreb, Jean-Louis Bessereau, Oliver Hobert .  2015.   Transcriptional Coordination of Synaptogenesis and Neurotransmitter Signaling.. Curr Biol. ▶ Go to Pubmed
Kevin Emmett, Jacob Rosenstein, Jan-Willem van de Meent, Ken Shepard, Chris Wiggins .  2015.   Statistical inference for nanopore sequencing with a biased random walk model.. Biophys J. 108 (8) :1852-5 ▶ Go to Pubmed
Vez Repunte-Canonigo, William Shin, Leandro Vendruscolo, Celine Lefebvre, Lena van der Stap, Tomoya Kawamura, Joel Schlosburg, Mariano Alvarez, George Koob, Andrea Califano, Pietro Sanna .  2015.   Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks.. Genome Biol. 16 (1) :68 ▶ Go to Pubmed
Helen Causton, Kevin Feeney, Christine Ziegler, John O'Neill .  2015.   Metabolic Cycles in Yeast Share Features Conserved among Circadian Rhythms.. Curr Biol. 25 (8) :1056-62 ▶ Go to Pubmed
Xueling Wu, Zhenhai Zhang, Chaim Schramm, Gordon Joyce, Young Kwon, Tongqing Zhou, Zizhang Sheng, Baoshan Zhang, Sijy O'Dell, Krisha McKee, Ivelin Georgiev, Gwo-Yu Chuang, Nancy Longo, Rebecca Lynch, Kevin Saunders, Cinque Soto, Sanjay Srivatsan, Yongping Yang, Robert Bailer, Mark Louder, NISC Program, James Mullikin, Mark Connors, Peter Kwong, John Mascola, Lawrence Shapiro .  2015.   Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.. Cell. ▶ Go to Pubmed
Mary Boland, Nicholas Tatonetti, George Hripcsak .  2015.   Development and validation of a classification approach for extracting severity automatically from electronic health records.. J Biomed Semantics. 6 :14 ▶ Go to Pubmed
Anna Kaplan, Michael Gaschler, Denise Dunn, Ryan Colligan, Lewis Brown, Arthur Palmer, Donald Lo, Brent Stockwell .  2015.   Small molecule-induced oxidation of protein disulfide isomerase is neuroprotective.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Andrea Califano, Manolis Kellis, Gustavo Stolovitzky .  2015.   Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue.. J Comput Biol. 22 (4) :251-2 ▶ Go to Pubmed
Namiko Abe, Iris Dror, Lin Yang, Matthew Slattery, Tianyin Zhou, Harmen Bussemaker, Remo Rohs, Richard Mann .  2015.   Deconvolving the Recognition of DNA Shape from Sequence.. Cell. ▶ Go to Pubmed
Michael Shen .  2015.   Cancer: The complex seeds of metastasis.. Nature. ▶ Go to Pubmed
Matti Pirinen, Tuuli Lappalainen, Noah Zaitlen, GTEx Consortium, Emmanouil Dermitzakis, Peter Donnelly, Mark McCarthy, Manuel Rivas .  2015.   Assessing allele-specific expression across multiple tissues from RNA-seq read data.. Bioinformatics. ▶ Go to Pubmed
Amy Williams, Giulio Genovese, Thomas Dyer, Nicolas Altemose, Katherine Truax, Goo Jun, Nick Patterson, Simon Myers, Joanne Curran, Ravi Duggirala, John Blangero, David Reich, Molly Przeworski .  2015.   Non-crossover gene conversions show strong GC bias and unexpected clustering in humans.. Elife. 4 ▶ Go to Pubmed
Stephanie Schnell, Alberto Ambesi-Impiombato, Marta Sanchez-Martin, Laura Belver, Luyao Xu, Yue Qin, Ryoichiro Kageyama, Adolfo Ferrando .  2015.   Therapeutic targeting of HES1 transcriptional programs in T-ALL.. Blood. ▶ Go to Pubmed
Soline Aubry, William Shin, John Crary, Roger Lefort, Yasir Qureshi, Celine Lefebvre, Andrea Califano, Michael Shelanski .  2015.   Assembly and Interrogation of Alzheimer's Disease Genetic Networks Reveal Novel Regulators of Progression.. PLoS One. 10 (3) :e0120352 ▶ Go to Pubmed
Tianyin Zhou, Ning Shen, Lin Yang, Namiko Abe, John Horton, Richard Mann, Harmen Bussemaker, Raluca Gordân, Remo Rohs .  2015.   Quantitative modeling of transcription factor binding specificities using DNA shape.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Stephanie Yaung, Luxue Deng, Ning Li, Jonathan Braff, George Church, Lynn Bry, Harris Wang, Georg Gerber .  2015.   Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics.. Mol Syst Biol. 11 (3) :788 ▶ Go to Pubmed
Laura Belver, Adolfo Ferrando .  2015.   Aberrant Cytokine Production by Nonmalignant Cells in the Pathogenesis of Myeloproliferative Tumors and Response to JAK Inhibitor Therapies.. Cancer Discov. 5 (3) :234-6 ▶ Go to Pubmed
Megan Hogan, David-Emlyn Parfitt, Cinthya Zepeda-Mendoza, Michael Shen, David Spector .  2015.   Transient pairing of homologous oct4 alleles accompanies the onset of embryonic stem cell differentiation.. Cell Stem Cell. 16 (3) :275-88 ▶ Go to Pubmed
Santiago Vilar, Nicholas Tatonetti, George Hripcsak .  2015.   3D Pharmacophoric Similarity improves Multi Adverse Drug Event Identification in Pharmacovigilance.. Sci Rep. 5 :8809 ▶ Go to Pubmed
Kevin Emmett, Albert Lee, Hossein Khiabanian, Raul Rabadan .  2015.   High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants.. PLoS Curr. 7 ▶ Go to Pubmed
Qinghong Yan, Sebastien Weyn-Vanhentenryck, Jie Wu, Steven Sloan, Ye Zhang, Kenian Chen, Jia Wu, Ben Barres, Chaolin Zhang .  2015.   Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Michael Lisby, Rodney Rothstein .  2015.   Cell biology of mitotic recombination.. Cold Spring Harb Perspect Biol. 7 (3) :a016535 ▶ Go to Pubmed
Ziyue Gao, Darrel Waggoner, Matthew Stephens, Carole Ober, Molly Przeworski .  2015.   An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans.. Genetics. ▶ Go to Pubmed
Oren Litvin, Sarit Schwartz, Zhenmao Wan, Tanya Schild, Mark Rocco, Nul Oh, Bo-Juen Chen, Noel Goddard, Christine Pratilas, Dana Pe'er .  2015.   Interferon α/β Enhances the Cytotoxic Response of MEK Inhibition in Melanoma.. Mol Cell. ▶ Go to Pubmed
Donald Petrey, Scott Chen, Lei Deng, José Garzón, Howook Hwang, Gorka Lasso, Hunjoong Lee, Antonina Silkov, Barry Honig .  2015.   Template-based prediction of protein function.. Curr Opin Struct Biol. 32C :33-38 ▶ Go to Pubmed
T Lorberbaum, M Nasir, Mj Keiser, S Vilar, G Hripcsak, Np Tatonetti .  2015.   Systems pharmacology augments drug safety surveillance.. Clin Pharmacol Ther. 97 (2) :151-8 ▶ Go to Pubmed
Samuel Vidal, Veronica Rodriguez-Bravo, Aidan Quinn, Ruth Rodriguez-Barrueco, Amaia Lujambio, Estrelania Williams, Xiaochen Sun, Janis de la Iglesia-Vicente, Albert Lee, Ben Readhead, Xintong Chen, Matthew Galsky, Berta Esteve, Daniel Petrylak, Joel Dudley, Raul Rabadan, Jose Silva, Yujin Hoshida, Scott Lowe, Carlos Cordon-Cardo, Josep Domingo-Domenech .  2015.   A Targetable GATA2-IGF2 Axis Confers Aggressiveness in Lethal Prostate Cancer.. Cancer Cell. 27 (2) :223-39 ▶ Go to Pubmed
Matthew Bouchard, Venkatakaushik Voleti, César Mendes, Clay Lacefield, Wesley Grueber, Richard Mann, Randy Bruno, Elizabeth Hillman .  2015.   Swept confocally-aligned planar excitation (SCAPE) microscopy for high speed volumetric imaging of behaving organisms.. Nat Photonics. 9 (2) :113-119 ▶ Go to Pubmed
Yao Lu, Qiong Xue, Markus Eisele, Endah Sulistijo, Kara Brower, Lin Han, El-Ad Amir, Dana Pe'er, Kathryn Miller-Jensen, Rong Fan .  2015.   Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands.. Proc Natl Acad Sci U S A. 112 (7) :E607-15 ▶ Go to Pubmed
Maria Gutierrez-Arcelus, Halit Ongen, Tuuli Lappalainen, Stephen Montgomery, Alfonso Buil, Alisa Yurovsky, Julien Bryois, Ismael Padioleau, Luciana Romano, Alexandra Planchon, Emilie Falconnet, Deborah Bielser, Maryline Gagnebin, Thomas Giger, Christelle Borel, Audrey Letourneau, Periklis Makrythanasis, Michel Guipponi, Corinne Gehrig, Stylianos Antonarakis, Emmanouil Dermitzakis .  2015.   Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing.. PLoS Genet. 11 (1) :e1004958 ▶ Go to Pubmed
Heather Morris, Susan DeWolf, Harlan Robins, Ben Sprangers, Samuel LoCascio, Brittany Shonts, Tatsuo Kawai, Waichi Wong, Suxiao Yang, Julien Zuber, Yufeng Shen, Megan Sykes .  2015.   Tracking donor-reactive T cells: Evidence for clonal deletion in tolerant kidney transplant patients.. Sci Transl Med. 7 (272) :272ra10 ▶ Go to Pubmed
Harmen Bussemaker .  2015.   Recent progress in understanding transcription factor binding specificity.. Brief Funct Genomics. 14 (1) :1-2 ▶ Go to Pubmed
Eli Zunder, Rachel Finck, Gregory Behbehani, El-Ad Amir, Smita Krishnaswamy, Veronica Gonzalez, Cynthia Lorang, Zach Bjornson, Matthew Spitzer, Bernd Bodenmiller, Wendy Fantl, Dana Pe'er, Garry Nolan .  2015.   Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.. Nat Protoc. 10 (2) :316-33 ▶ Go to Pubmed
Michael Shelanski, William Shin, Soline Aubry, Peter Sims, Mariano Alvarez, Andrea Califano .  2015.   A systems approach to drug discovery in Alzheimer's disease.. Neurotherapeutics. 12 (1) :126-31 ▶ Go to Pubmed
Max Greenfeld, Jan-Willem van de Meent, Dmitri Pavlichin, Hideo Mabuchi, Chris Wiggins, Ruben Gonzalez, Daniel Herschlag .  2015.   Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data.. BMC Bioinformatics. 16 (1) :3 ▶ Go to Pubmed
Daniel Herranz, Adolfo Ferrando .  2015.   An oncogenic enhancer enemy (N-Me) in T-ALL.. Cell Cycle. 14 (2) :167-8 ▶ Go to Pubmed
Hossein Khiabanian, Zachary Carpenter, Jeffrey Kugelman, Joseph Chan, Vladimir Trifonov, Elyse Nagle, Travis Warren, Patrick Iversen, Sina Bavari, Gustavo Palacios, Raul Rabadan .  2014.   Viral diversity and clonal evolution from unphased genomic data.. BMC Genomics. 15 (Suppl 6) :S17 ▶ Go to Pubmed
Justin Crocker, Namiko Abe, Lucrezia Rinaldi, Alistair McGregor, Nicolás Frankel, Shu Wang, Ahmad Alsawadi, Philippe Valenti, Serge Plaza, François Payre, Richard Mann, David Stern .  2015.   Low affinity binding site clusters confer hox specificity and regulatory robustness.. Cell. 160 (1-2) :191-203 ▶ Go to Pubmed
F Abate, M Todaro, J-A van der Krogt, M Boi, I Landra, R Machiorlatti, F Tabbò, K Messana, C Abele, A Barreca, D Novero, M Gaudiano, S Aliberti, F Di Giacomo, T Tousseyn, E Lasorsa, R Crescenzo, L Bessone, E Ficarra, A Acquaviva, A Rinaldi, M Ponzoni, D Longo, S Aime, M Cheng, B Ruggeri, P Piccaluga, S Pileri, E Tiacci, B Falini, B Pera-Gresely, L Cerchietti, J Iqbal, W Chan, L Shultz, I Kwee, R Piva, I Wlodarska, R Rabadan, F Bertoni, G Inghirami, the Group .  2014.   A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation.. Leukemia. ▶ Go to Pubmed
Takashi Kobayashi, Tomasz Owczarek, James McKiernan, Cory Abate-Shen .  2015.   Modelling bladder cancer in mice: opportunities and challenges.. Nat Rev Cancer. 15 (1) :42-54 ▶ Go to Pubmed
Jonathan Chang, Sarah Gilman, Andrew Chiang, Stephan Sanders, Dennis Vitkup .  2014.   Genotype to phenotype relationships in autism spectrum disorders.. Nat Neurosci. ▶ Go to Pubmed
Oriol Guitart-Pla, Manjunath Kustagi, Frank Rügheimer, Andrea Califano, Benno Schwikowski .  2014.   The Cyni framework for network inference in Cytoscape.. Bioinformatics. ▶ Go to Pubmed
Jiguang Wang, Hossein Khiabanian, Davide Rossi, Giulia Fabbri, Valter Gattei, Francesco Forconi, Luca Laurenti, Roberto Marasca, Giovanni Del Poeta, Robin Foá, Laura Pasqualucci, Gianluca Gaidano, Raul Rabadan .  2014.   Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia.. Elife. 3 ▶ Go to Pubmed
Raajit Rampal, Altuna Alkalin, Jozef Madzo, Aparna Vasanthakumar, Elodie Pronier, Jay Patel, Yushan Li, Jihae Ahn, Omar Abdel-Wahab, Alan Shih, Chao Lu, Patrick Ward, Jennifer Tsai, Todd Hricik, Valeria Tosello, Jacob Tallman, Xinyang Zhao, Danette Daniels, Qing Dai, Luisa Ciminio, Iannis Aifantis, Chuan He, Francois Fuks, Martin Tallman, Adolfo Ferrando, Stephen Nimer, Elisabeth Paietta, Craig Thompson, Jonathan Licht, Christopher Mason, Lucy Godley, Ari Melnick, Maria Figueroa, Ross Levine .  2014.   DNA Hydroxymethylation Profiling Reveals that WT1 Mutations Result in Loss of TET2 Function in Acute Myeloid Leukemia.. Cell Rep. ▶ Go to Pubmed
Konstantin Popadin, Maria Gutierrez-Arcelus, Tuuli Lappalainen, Alfonso Buil, Julia Steinberg, Sergey Nikolaev, Samuel Lukowski, Georgii Bazykin, Vladimir Seplyarskiy, Panagiotis Ioannidis, Evgeny Zdobnov, Emmanouil Dermitzakis, Stylianos Antonarakis .  2014.   Gene age predicts the strength of purifying selection acting on gene expression variation in humans.. Am J Hum Genet. 95 (6) :660-74 ▶ Go to Pubmed
Viveka Mayya, Willie Neiswanger, Ricardo Medina, Chris Wiggins, Michael Dustin .  2015.   Integrative analysis of T cell motility from multi-channel microscopy data using TIAM.. J Immunol Methods. 416 :84-93 ▶ Go to Pubmed
Alfonso Buil, Andrew Brown, Tuuli Lappalainen, Ana Viñuela, Matthew Davies, Hou-Feng Zheng, Brent Richards, Daniel Glass, Kerrin Small, Richard Durbin, Timothy Spector, Emmanouil Dermitzakis .  2014.   Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins.. Nat Genet. ▶ Go to Pubmed
Felix Sanchez-Garcia, Patricia Villagrasa, Junji Matsui, Dylan Kotliar, Verónica Castro, Uri-David Akavia, Bo-Juen Chen, Laura Saucedo-Cuevas, Ruth Barrueco, David Llobet-Navas, Jose Silva, Dana Pe'er .  2014.   Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers.. Cell. ▶ Go to Pubmed