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2015

2015 Publications

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
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
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
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
Hayley Davis, Shazia Irshad, Mukesh Bansal, Hannah Rafferty, Tatjana Boitsova, Chiara Bardella, Emma Jaeger, Annabelle Lewis, Luke Freeman-Mills, Francesc Giner, Pedro Rodenas-Cuadrado, Sreelakshmi Mallappa, Susan Clark, Huw Thomas, Rosemary Jeffery, Richard Poulsom, Manuel Rodriguez-Justo, Marco Novelli, Runjan Chetty, Andrew Silver, Owen Sansom, Florian Greten, Lai Wang, James East, Ian Tomlinson, Simon Leedham .  2015.   Aberrant epithelial GREM1 expression initiates colonic tumorigenesis from cells outside the stem cell niche.. Nat Med. 21 (1) :62-70 ▶ Go to Pubmed
Badri Vardarajan, Yalun Zhang, Joseph Lee, Rong Cheng, Christopher Bohm, Mahdi Ghani, Christiane Reitz, Dolly Reyes-Dumeyer, Yufeng Shen, Ekaterina Rogaeva, Peter St George-Hyslop, Richard Mayeux .  2015.   Coding mutations in SORL1 and Alzheimer disease.. Ann Neurol. 77 (2) :215-27 ▶ Go to Pubmed
Germán Plata, Christopher Henry, Dennis Vitkup .  2015.   Long-term phenotypic evolution of bacteria.. Nature. 517 (7534) :369-72 ▶ Go to Pubmed