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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
Santiago Vilar, Eugenio Uriarte, Lourdes Santana, Carol Friedman, Nicholas Tatonetti .  2014.   State of the Art and Development of a Drug-Drug Interaction Large Scale Predictor Based on 3D Pharmacophoric Similarity.. Curr Drug Metab. 15 (5) :490-501 ▶ Go to Pubmed
Mukesh Bansal, Jichen Yang, Charles Karan, Michael Menden, James Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffrey Allen, Rui Zhong, Beibei Chen, Minsoo Kim, Tao Wang, Laura Heiser, Ronald Realubit, Michela Mattioli, Mariano Alvarez, Yao Shen, NCI-DREAM Community, Daniel Gallahan, Dinah Singer, Julio Saez-Rodriguez, Yang Xie, Gustavo Stolovitzky, Andrea Califano, NCI-DREAM Community .  2014.   A community computational challenge to predict the activity of pairs of compounds.. Nat Biotechnol. ▶ 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
Andrea Califano .  2014.   Predicting protein networks in cancer.. Nat Genet. 46 (12) :1252-3 ▶ Go to Pubmed
Joseph Thome, Naomi Yudanin, Yoshiaki Ohmura, Masaru Kubota, Boris Grinshpun, Taheri Sathaliyawala, Tomoaki Kato, Harvey Lerner, Yufeng Shen, Donna Farber .  2014.   Spatial Map of Human T Cell Compartmentalization and Maintenance over Decades of Life.. Cell. 159 (4) :814-28 ▶ Go to Pubmed
Ziyue Gao, Molly Przeworski, Guy Sella .  2014.   Footprints of ancient balanced polymorphisms in genetic variation data from closely related species.. Evolution. ▶ Go to Pubmed
Jose Angeli, Manuela Schneider, Bettina Proneth, Yulia Tyurina, Vladimir Tyurin, Victoria Hammond, Nadja Herbach, Michaela Aichler, Axel Walch, Elke Eggenhofer, Devaraj Basavarajappa, Olof Rådmark, Sho Kobayashi, Tobias Seibt, Heike Beck, Frauke Neff, Irene Esposito, Rüdiger Wanke, Heidi Förster, Olena Yefremova, Marc Heinrichmeyer, Georg Bornkamm, Edward Geissler, Stephen Thomas, Brent Stockwell, Valerie O'Donnell, Valerian Kagan, Joel Schick, Marcus Conrad .  2014.   Inactivation of the ferroptosis regulator Gpx4 triggers acute renal failure in mice.. Nat Cell Biol. 16 (12) :1180-91 ▶ Go to Pubmed
Christian Munck, Heidi Gumpert, Annika Wallin, Harris Wang, Morten Sommer .  2014.   Prediction of resistance development against drug combinations by collateral responses to component drugs.. Sci Transl Med. 6 (262) :262ra156 ▶ Go to Pubmed
Andreas Linkermann, Rachid Skouta, Nina Himmerkus, Shrikant Mulay, Christin Dewitz, Federica De Zen, Agnes Prokai, Gabriele Zuchtriegel, Fritz Krombach, Patrick-Simon Welz, Ricardo Weinlich, Tom Berghe, Peter Vandenabeele, Manolis Pasparakis, Markus Bleich, Joel Weinberg, Christoph Reichel, Jan Bräsen, Ulrich Kunzendorf, Hans-Joachim Anders, Brent Stockwell, Douglas Green, Stefan Krautwald .  2014.   Synchronized renal tubular cell death involves ferroptosis.. Proc Natl Acad Sci U S A. ▶ 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
Hua-Sheng Chiu, David Llobet-Navas, Xuerui Yang, Wei-Jen Chung, Alberto Ambesi-Impiombato, Archana Iyer, Hyunjae Kim, Elena Seviour, Zijun Luo, Vasudha Sehgal, Tyler Moss, Yiling Lu, Prahlad Ram, Jose Silva, Gordon Mills, Andrea Califano, Pavel Sumazin .  2014.   Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.. Genome Res. ▶ Go to Pubmed
Germán Plata, Christopher Henry, Dennis Vitkup .  2015.   Long-term phenotypic evolution of bacteria.. Nature. 517 (7534) :369-72 ▶ Go to Pubmed
Michael Mingueneau, Smita Krishnaswamy, Matthew Spitzer, Sean Bendall, Erica Stone, Stephen Hedrick, Dana Pe'er, Diane Mathis, Garry Nolan, Christophe Benoist .  2014.   Single-cell mass cytometry of TCR signaling: Amplification of small initial differences results in low ERK activation in NOD mice.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
César Mendes, Soumya Rajendren V, Imre Bartos, Szabolcs Márka, Richard Mann .  2014.   Kinematic Responses to Changes in Walking Orientation and Gravitational Load in Drosophila melanogaster.. PLoS One. 9 (10) :e109204 ▶ Go to Pubmed
David-Emlyn Parfitt, Michael Shen .  2014.   From blastocyst to gastrula: gene regulatory networks of embryonic stem cells and early mouse embryogenesis.. Philos Trans R Soc Lond B Biol Sci. 369 (1657) ▶ Go to Pubmed
Kyung-Ae Yang, Mihaela Barbu, Marlin Halim, Payal Pallavi, Benjamin Kim, Dmitry Kolpashchikov, Stevan Pecic, Steven Taylor, Tilla Worgall, Milan Stojanovic .  2014.   Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors.. Nat Chem. 6 (11) :1003-8 ▶ Go to Pubmed
Smita Krishnaswamy, Matthew Spitzer, Michael Mingueneau, Sean Bendall, Oren Litvin, Erica Stone, Dana Pe'er, Garry Nolan .  2014.   Conditional density-based analysis of T cell signaling in single-cell data.. Science. ▶ Go to Pubmed
Ritu Kushwaha, Nirmala Jagadish, Manjunath Kustagi, Mark Tomishima, Geetu Mendiratta, Mukesh Bansal, Hyunjae Kim, Pavel Sumazin, Mariano Alvarez, Celine Lefebvre, Patricia Villagrasa-Gonzalez, Agnes Viale, James Korkola, Jane Houldsworth, Darren Feldman, George Bosl, Andrea Califano, R Chaganti .  2014.   Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency.. Stem Cells. ▶ Go to Pubmed
Andreas Linkermann, Brent Stockwell, Stefan Krautwald, Hans-Joachim Anders .  2014.   Regulated cell death and inflammation: an auto-amplification loop causes organ failure.. Nat Rev Immunol. ▶ Go to Pubmed
Ana Machado, Tianyin Zhou, Satyanarayan Rao, Pragya Goel, Chaitanya Rastogi, Allan Lazarovici, Harmen Bussemaker, Remo Rohs .  2014.   Evolving insights on how cytosine methylation affects protein-DNA binding.. Brief Funct Genomics. ▶ Go to Pubmed
Paul Boutros, Adam Margolin, Joshua Stuart, Andrea Califano, Gustavo Stolovitzky .  2014.   Toward better benchmarking: challenge-based methods assessment in cancer genomics.. Genome Biol. 15 (9) :462 ▶ Go to Pubmed
Federico Giorgi, Gonzalo Lopez, Jung Woo, Brygida Bisikirska, Andrea Califano, Mukesh Bansal .  2014.   Inferring protein modulation from gene expression data using conditional mutual information.. PLoS One. 9 (10) :e109569 ▶ Go to Pubmed
Yaara Oren, Mark Smith, Nathan Johns, Millie Zeevi, Dvora Biran, Eliora Ron, Jukka Corander, Harris Wang, Eric Alm, Tal Pupko .  2014.   Transfer of noncoding DNA drives regulatory rewiring in bacteria.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
James Chen, Mariano Alvarez, Flaminia Talos, Harshil Dhruv, Gabrielle Rieckhof, Archana Iyer, Kristin Diefes, Kenneth Aldape, Michael Berens, Michael Shen, Andrea Califano .  2014.   Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks.. Cell. 159 (2) :402-14 ▶ Go to Pubmed
Albert Lee, Hossein Khiabanian, Jeffrey Kugelman, Oliver Elliott, Elyse Nagle, Guo-Yun Yu, Travis Warren, Gustavo Palacios, Raul Rabadan .  2014.   Transcriptome reconstruction and annotation of cynomolgus and African green monkey.. BMC Genomics. 15 (1) :846 ▶ Go to Pubmed
Ranjan Batra, Konstantinos Charizanis, Mini Manchanda, Apoorva Mohan, Moyi Li, Dustin Finn, Marianne Goodwin, Chaolin Zhang, Krzysztof Sobczak, Charles Thornton, Maurice Swanson .  2014.   Loss of MBNL Leads to Disruption of Developmentally Regulated Alternative Polyadenylation in RNA-Mediated Disease.. Mol Cell. ▶ Go to Pubmed
Olivier Julien, Martin Kampmann, Michael Bassik, Julie Zorn, Vincent Venditto, Kazutaka Shimbo, Nicholas Agard, Kenichi Shimada, Arnold Rheingold, Brent Stockwell, Jonathan Weissman, James Wells .  2014.   Unraveling the mechanism of cell death induced by chemical fibrils.. Nat Chem Biol. ▶ Go to Pubmed
Keith Hoffman, Andrea Demakas, Mo Dimbil, Nicholas Tatonetti, Colin Erdman .  2014.   Stimulated Reporting: The Impact of US Food and Drug Administration-Issued Alerts on the Adverse Event Reporting System (FAERS).. Drug Saf. ▶ Go to Pubmed
Jeremie Vendome, Klara Felsovalyi, Hang Song, Zhongyu Yang, Xiangshu Jin, Julia Brasch, Oliver Harrison, Goran Ahlsen, Fabiana Bahna, Anna Kaczynska, Phinikoula Katsamba, Darwin Edmond, Wayne Hubbell, Lawrence Shapiro, Barry Honig .  2014.   Structural and energetic determinants of adhesive binding specificity in type I cadherins.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
S Vilar, P Ryan, D Madigan, P Stang, M Schuemie, C Friedman, N Tatonetti, G Hripcsak .  2014.   Similarity-based modeling applied to signal detection in pharmacovigilance.. CPT Pharmacometrics Syst Pharmacol. 3 :e137 ▶ Go to Pubmed
Tai-Hsien Yang, Wei-Yi Cheng, Tian Zheng, Matthew Maurer, Dimitris Anastassiou .  2014.   Breast Cancer Prognostic Biomarker Using Attractor Metagenes and the FGD3-SUSD3 Metagene.. Cancer Epidemiol Biomarkers Prev. ▶ Go to Pubmed
Chee Chua, Maho Shibata, Ming Lei, Roxanne Toivanen, Lamont Barlow, Sarah Bergren, Ketan Badani, James McKiernan, Mitchell Benson, Hanina Hibshoosh, Michael Shen .  2014.   Single luminal epithelial progenitors can generate prostate organoids in culture.. Nat Cell Biol. ▶ Go to Pubmed
Nikolaos Panousis, Maria Gutierrez-Arcelus, Emmanouil Dermitzakis, Tuuli Lappalainen .  2014.   Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies.. Genome Biol. 15 (9) :467 ▶ Go to Pubmed
Anat Kreimer, Itsik Pe'er .  2014.   Co-regulated Transcripts Associated to Cooperating eSNPs Define Bi-fan Motifs in Human Gene Networks.. PLoS Genet. 10 (9) :e1004587 ▶ Go to Pubmed
Joseph Glessner, Alexander Bick, Kaoru Ito, Jason Homsy, Laura Rodriguez-Murillo, Menachem Fromer, Erica Mazaika, Badri Vardarajan, Michael Italia, Jeremy Leipzig, Steven DePalma, Ryan Golhar, Stephan Sanders, Boris Yamrom, Michael Ronemus, Ivan Iossifov, A Willsey, Matthew State, Jonathan Kaltman, Peter White, Yufeng Shen, Dorothy Warburton, Martina Brueckner, Christine Seidman, Elizabeth Goldmuntz, Bruce Gelb, Richard Lifton, Jonathan Seidman, Hakon Hakonarson, Wendy Chung .  2014.   Increased Frequency of De Novo Copy Number Variations in Congenital Heart Disease by Integrative Analysis of SNP Array and Exome Sequence Data.. Circ Res. ▶ Go to Pubmed
Shai Carmi, Ken Hui, Ethan Kochav, Xinmin Liu, James Xue, Fillan Grady, Saurav Guha, Kinnari Upadhyay, Dan Ben-Avraham, Semanti Mukherjee, Monica Bowen, Tinu Thomas, Joseph Vijai, Marc Cruts, Guy Froyen, Diether Lambrechts, Stéphane Plaisance, Christine Van Broeckhoven, Philip Van Damme, Herwig Van Marck, Nir Barzilai, Ariel Darvasi, Kenneth Offit, Susan Bressman, Laurie Ozelius, Inga Peter, Judy Cho, Harry Ostrer, Gil Atzmon, Lorraine Clark, Todd Lencz, Itsik Pe'er .  2014.   Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins.. Nat Commun. 5 :4835 ▶ Go to Pubmed
Daniel Herranz, Alberto Ambesi-Impiombato, Teresa Palomero, Stephanie Schnell, Laura Belver, Agnieszka Wendorff, Luyao Xu, Mireia Castillo-Martin, David Llobet-Navas, Carlos Cordon-Cardo, Emmanuelle Clappier, Jean Soulier, Adolfo Ferrando .  2014.   A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia.. Nat Med. 20 (10) :1130-7 ▶ Go to Pubmed
Ye Zhang, Kenian Chen, Steven Sloan, Mariko Bennett, Anja Scholze, Sean O'Keeffe, Hemali Phatnani, Paolo Guarnieri, Christine Caneda, Nadine Ruderisch, Shuyun Deng, Shane Liddelow, Chaolin Zhang, Richard Daneman, Tom Maniatis, Ben Barres, Jia Wu .  2014.   An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex.. J Neurosci. 34 (36) :11929-47 ▶ Go to Pubmed
Francesco Abate, Sakellarios Zairis, Elisa Ficarra, Andrea Acquaviva, Chris Wiggins, Veronique Frattini, Anna Lasorella, Antonio Iavarone, Giorgio Inghirami, Raul Rabadan .  2014.   Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.. BMC Syst Biol. 8 (1) :97 ▶ Go to Pubmed
Zhu Wang, Roxanne Toivanen, Sarah Bergren, Pierre Chambon, Michael Shen .  2014.   Luminal Cells Are Favored as the Cell of Origin for Prostate Cancer.. Cell Rep. ▶ Go to Pubmed
Chan Thu, Weisheng Chen V, Rotem Rubinstein, Maxime Chevee, Holly Wolcott, Klara Felsovalyi, Juan Tapia, Lawrence Shapiro, Barry Honig, Tom Maniatis .  2014.   Single-Cell Identity Generated by Combinatorial Homophilic Interactions between α, β, and γ Protocadherins.. Cell. 158 (5) :1045-59 ▶ Go to Pubmed
Joris van Arensbergen, Bas van Steensel, Harmen Bussemaker .  2014.   In search of the determinants of enhancer-promoter interaction specificity.. Trends Cell Biol. ▶ Go to Pubmed
Marios Agelopoulos, Daniel McKay, Richard Mann .  2014.   cgChIP: A Cell Type- and Gene-Specific Method for Chromatin Analysis.. Methods Mol Biol. 1196 :291-306 ▶ Go to Pubmed
Todd Riley, Matthew Slattery, Namiko Abe, Chaitanya Rastogi, Dahong Liu, Richard Mann, Harmen Bussemaker .  2014.   SELEX-seq: A Method for Characterizing the Complete Repertoire of Binding Site Preferences for Transcription Factor Complexes.. Methods Mol Biol. 1196 :255-78 ▶ Go to Pubmed
Ambrose Carr, Dana Pe'er .  2014.   Broadening horizons: holistic viewpoints from the Biology of Genomes.. Genome Biol. 15 (7) :416 ▶ Go to Pubmed
Liliana Greger, Jing Su, Johan Rung, Pedro Ferreira, Geuvadis consortium, Tuuli Lappalainen, Emmanouil Dermitzakis, Alvis Brazma .  2014.   Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.. PLoS One. 9 (8) :e104567 ▶ Go to Pubmed
Christian Gonzalez, Jennifer Sims, Nicholas Hornstein, Angeliki Mela, Franklin Garcia, Liang Lei, David Gass, Benjamin Amendolara, Jeffrey Bruce, Peter Canoll, Peter Sims .  2014.   Ribosome profiling reveals a cell-type-specific translational landscape in brain tumors.. J Neurosci. 34 (33) :10924-36 ▶ Go to Pubmed
Alicia Martin, Helio Costa, Tuuli Lappalainen, Brenna Henn, Jeffrey Kidd, Muh-Ching Yee, Fabian Grubert, Howard Cann, Michael Snyder, Stephen Montgomery, Carlos Bustamante .  2014.   Transcriptome sequencing from diverse human populations reveals differentiated regulatory architecture.. PLoS Genet. 10 (8) :e1004549 ▶ Go to Pubmed
Stephanie Johnson, Jan-Willem van de Meent, Rob Phillips, Chris Wiggins, Martin Lindén .  2014.   Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.. Nucleic Acids Res. 42 (16) :10265-77 ▶ Go to Pubmed
Evangelos Pefanis, Jiguang Wang, Gerson Rothschild, Junghyun Lim, Jaime Chao, Raul Rabadan, Aris Economides, Uttiya Basu .  2014.   Noncoding RNA transcription targets AID to divergently transcribed loci in B cells.. Nature. ▶ Go to Pubmed
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