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Stephanie Pavlovich, Sean Lovett, Galina Koroleva, Jonathan Guito, Catherine Arnold, Elyse Nagle, Kirsten Kulcsar, Albert Lee, Francoise Thibaud-Nissen, Adam Hume, Elke Mühlberger, Luke Uebelhoer, Jonathan Towner, Raul Rabadan, Mariano Sanchez-Lockhart, Thomas Kepler, Gustavo Palacios .  2018.   The Egyptian Rousette Genome Reveals Unexpected Features of Bat Antiviral Immunity.. Cell. 173 (5) :1098-1110.e18 ▶ Go to Pubmed
Hua-Sheng Chiu, María Martínez, Elena Komissarova V, David Llobet-Navas, Mukesh Bansal, Evan Paull, Jose Silva, Xuerui Yang, Pavel Sumazin, Andrea Califano .  2018.   The number of titrated microRNA species dictates ceRNA regulation.. Nucleic Acids Res. 46 (9) :4354-4369 ▶ Go to Pubmed
Neda Masoudi, Saeed Tavazoie, Lori Glenwinkel, Leesun Ryu, Kyuhyung Kim, Oliver Hobert .  2018.   Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity.. PLoS Biol. 16 (4) :e2004979 ▶ Go to Pubmed
Hongxu Ding, Eugene Douglass, Adam Sonabend, Angeliki Mela, Sayantan Bose, Christian Gonzalez, Peter Canoll, Peter Sims, Mariano Alvarez, Andrea Califano .  2018.   Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.. Nat Commun. 9 (1) :1471 ▶ Go to Pubmed
Juan Arriaga, Cory Abate-Shen .  2018.   Genetically Engineered Mouse Models of Prostate Cancer in the Postgenomic Era.. Cold Spring Harb Perspect Med. ▶ Go to Pubmed
Weijun Luo, Chaolin Zhang, Yong-Hui Jiang, Cory Brouwer .  2018.   Systematic reconstruction of autism biology from massive genetic mutation profiles.. Sci Adv. 4 (4) :e1701799 ▶ Go to Pubmed
Enrico Tiacci, Erik Ladewig, Gianluca Schiavoni, Alex Penson, Elisabetta Fortini, Valentina Pettirossi, Yuchun Wang, Ariele Rosseto, Alessandra Venanzi, Sofija Vlasevska, Roberta Pacini, Simonetta Piattoni, Alessia Tabarrini, Alessandra Pucciarini, Barbara Bigerna, Alessia Santi, Alessandro Gianni, Simonetta Viviani, Antonello Cabras, Stefano Ascani, Barbara Crescenzi, Cristina Mecucci, Laura Pasqualucci, Raul Rabadan, Brunangelo Falini .  2018.   Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma.. Blood. 131 (22) :2454-2465 ▶ Go to Pubmed
Patrick Cimino, Youngmi Kim, Hua-Jun Wu, Jes Alexander, Hans-Georg Wirsching, Frank Szulzewsky, Ken Pitter, Tatsuya Ozawa, Jiguang Wang, Julio Vazquez, Sonali Arora, Raul Rabadan, Ross Levine, Franziska Michor, Eric Holland .  2018.   Increased expression provides a selective advantage for gain of whole chromosome 7 in IDH wild-type glioblastoma.. Genes Dev. 32 (7-8) :512-523 ▶ Go to Pubmed
Marcella Cesana, Michael Guo, Davide Cacchiarelli, Lara Wahlster, Jessica Barragan, Sergei Doulatov, Linda Vo, Beatrice Salvatori, Cole Trapnell, Kendell Clement, Patrick Cahan, Kaloyan Tsanov, Patricia Sousa, Barbara Tazon-Vega, Adriano Bolondi, Federico Giorgi, Andrea Califano, John Rinn, Alexander Meissner, Joel Hirschhorn, George Daley .  2018.   A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.. Cell Stem Cell. 22 (4) :575-588.e7 ▶ Go to Pubmed
Suk Lee, Wenhuo Hu, Justin Matulay, Mark Silva V, Tomasz Owczarek, Kwanghee Kim, Chee Chua, Lamont Barlow, Cyriac Kandoth, Alanna Williams, Sarah Bergren, Eugene Pietzak, Christopher Anderson, Mitchell Benson, Jonathan Coleman, Barry Taylor, Cory Abate-Shen, James McKiernan, Hikmat Al-Ahmadie, David Solit, Michael Shen .  2018.   Tumor Evolution and Drug Response in Patient-Derived Organoid Models of Bladder Cancer.. Cell. 173 (2) :515-528.e17 ▶ Go to Pubmed
Peter Freddolino, Jamie Yang, Amir Momen-Roknabadi, Saeed Tavazoie .  2018.   Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry.. Elife. 7 ▶ Go to Pubmed
Hanna Levitin, Jinzhou Yuan, Peter Sims .  2018.   Single-Cell Transcriptomic Analysis of Tumor Heterogeneity.. Trends Cancer. 4 (4) :264-268 ▶ Go to Pubmed
Hongxu Ding, Wanxin Wang, Andrea Califano .  2018.   iterClust: a statistical framework for iterative clustering analysis.. Bioinformatics. ▶ Go to Pubmed
Jasper Braun, Lukas Nabergall, Rafik Neme, Laura Landweber, Masahico Saito, Nataša Jonoska .  2018.   Russian Doll Genes and Complex Chromosome Rearrangements in.. G3 (Bethesda). ▶ Go to Pubmed
Roumen Voutev, Richard Mann .  2018.   Robust ΦC31-Mediated Genome Engineering inUsing Minimal attP/attB Phage Sites.. G3 (Bethesda). ▶ Go to Pubmed
Presha Rajbhandari, Gonzalo Lopez, Claudia Capdevila, Beatrice Salvatori, Jiyang Yu, Ruth Rodriguez-Barrueco, Daniel Martinez, Mark Yarmarkovich, Nina Weichert-Leahey, Brian Abraham, Mariano Alvarez, Archana Iyer, Jo Harenza, Derek Oldridge, Katleen De Preter, Jan Koster, Shahab Asgharzadeh, Robert Seeger, Jun Wei, Javed Khan, Jo Vandesompele, Pieter Mestdagh, Rogier Versteeg, Thomas Look, Richard Young, Antonio Iavarone, Anna Lasorella, Jose Silva, John Maris, Andrea Califano .  2018.   Cross-cohort analysis identifies a TEAD4 ↔ MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma.. Cancer Discov. ▶ Go to Pubmed
Tomas Rube, Chaitanya Rastogi, Judith Kribelbauer, Harmen Bussemaker .  2018.   A unified approach for quantifying and interpreting DNA shape readout by transcription factors.. Mol Syst Biol. 14 (2) :e7902 ▶ Go to Pubmed
Robyn Gartrell, Douglas Marks, Thomas Hart, Gen Li, Danielle Davari, Alan Wu, Zoë Blake, Yan Lu, Kayleigh Askin, Anthea Monod, Camden Esancy, Edward Stack, Dan Jia, Paul Armenta, Yichun Fu, Daisuke Izaki, Bret Taback, Raul Rabadan, Howard Kaufman, Charles Drake, Basil Horst, Yvonne Saenger .  2018.   Quantitative Analysis of Immune Infiltrates in Primary Melanoma.. Cancer Immunol Res. ▶ Go to Pubmed
Joseph Juliano, Orlando Gil, Andrea Hawkins-Daarud, Sonal Noticewala, Russell Rockne, Jill Gallaher, Susan Massey, Peter Sims, Alexander Anderson, Kristin Swanson, Peter Canoll .  2018.   Comparative dynamics of microglial and glioma cell motility at the infiltrative margin of brain tumours.. J R Soc Interface. 15 (139) ▶ Go to Pubmed
Luis Arnes, Zhaoqi Liu, Jiguang Wang, Hans Maurer, Irina Sagalovskiy, Marta Sanchez-Martin, Nikhil Bommakanti, Diana Garofalo, Dina Balderes, Lori Sussel, Kenneth Olive, Raul Rabadan .  2018.   Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma.. Gut. ▶ Go to Pubmed
Xichen Bao, Xiangpeng Guo, Menghui Yin, Muqddas Tariq, Yiwei Lai, Shahzina Kanwal, Jiajian Zhou, Na Li, Yuan Lv, Carlos Pulido-Quetglas, Xiwei Wang, Lu Ji, Muhammad Khan, Xihua Zhu, Zhiwei Luo, Changwei Shao, Do-Hwan Lim, Xiao Liu, Nan Li, Wei Wang, Minghui He, Yu-Lin Liu, Carl Ward, Tong Wang, Gong Zhang, Dongye Wang, Jianhua Yang, Yiwen Chen, Chaolin Zhang, Ralf Jauch, Yun-Gui Yang, Yangming Wang, Baoming Qin, Minna-Liisa Anko, Andrew Hutchins, Hao Sun, Huating Wang, Xiang-Dong Fu, Biliang Zhang, Miguel Esteban .  2018.   Capturing the interactome of newly transcribed RNA.. Nat Methods. 15 (3) :213-220 ▶ Go to Pubmed
Kathryn Manheimer, Felix Richter, Lisa Edelmann, Sunita D'Souza, Lisong Shi, Yufeng Shen, Jason Homsy, Marko Boskovski, Angela Tai, Joshua Gorham, Christopher Yasso, Elizabeth Goldmuntz, Martina Brueckner, Richard Lifton, Wendy Chung, Christine Seidman, J Seidman, Bruce Gelb .  2018.   Robust identification of mosaic variants in congenital heart disease.. Hum Genet. 137 (2) :183-193 ▶ Go to Pubmed
Satyanarayan Rao, Tsu-Pei Chiu, Judith Kribelbauer, Richard Mann, Harmen Bussemaker, Remo Rohs .  2018.   Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding.. Epigenetics Chromatin. 11 (1) :6 ▶ Go to Pubmed
Martin Jacko, Sebastien Weyn-Vanhentenryck, John Smerdon, Rui Yan, Huijuan Feng, Damian Williams, Joy Pai, Ke Xu, Hynek Wichterle, Chaolin Zhang .  2018.   Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly.. Neuron. ▶ Go to Pubmed
S Raponi, I Del Giudice, M Marinelli, J Wang, L Cafforio, C Ilari, A Piciocchi, M Messina, S Bonina, S Tavolaro, M Bordyuh, P Mariglia, N Peragine, F Mauro, S Chiaretti, S Molica, M Gentile, A Visentin, L Trentin, G Rigolin, A Cuneo, F Diop, D Rossi, G Gaidano, A Guarini, R Rabadan, R Foà .  2018.   Genetic Landscape of Ultra-Stable Chronic Lymphocytic Leukemia Patients.. Ann Oncol. ▶ Go to Pubmed
Magdolna Djurec, Osvaldo Graña, Albert Lee, Kevin Troulé, Elisa Espinet, Lavinia Cabras, Carolina Navas, María Blasco, Laura Martín-Díaz, Miranda Burdiel, Jing Li, Zhaoqi Liu, Mireia Vallespinós, Francisco Sanchez-Bueno, Martin Sprick, Andreas Trumpp, Bruno Sainz, Fátima Al-Shahrour, Raul Rabadan, Carmen Guerra, Mariano Barbacid .  2018.   Saa3 is a key mediator of the protumorigenic properties of cancer-associated fibroblasts in pancreatic tumors.. Proc Natl Acad Sci U S A. 115 (6) :E1147-E1156 ▶ Go to Pubmed
Gannie Tzoneva, Chelsea Dieck, Koichi Oshima, Alberto Ambesi-Impiombato, Marta Sanchez-Martin, Chioma Madubata, Hossein Khiabanian, Jiangyan Yu, Esme Waanders, Ilaria Iacobucci, Maria Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Julie Gastier-Foster, Mignon Loh, Renate Kirschner-Schwabe, Charles Mullighan, Raul Rabadan, Adolfo Ferrando .  2018.   Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia.. Nature. 553 (7689) :511-514 ▶ Go to Pubmed
Chee Chua, Nusrat Epsi, Eva Leung, Shouhong Xuan, Ming Lei, Bo Li, Sarah Bergren, Hanina Hibshoosh, Antonina Mitrofanova, Michael Shen .  2018.   Differential requirements of androgen receptor in luminal progenitors during prostate regeneration and tumor initiation.. Elife. 7 ▶ Go to Pubmed
Ken Hui, Heriberto Fernandez-Hernandez, Jianzhong Hu, Adam Schaffner, Nathan Pankratz, Nai-Yun Hsu, Ling-Shiang Chuang, Shai Carmi, Nicole Villaverde, Xianting Li, Manual Rivas, Adam Levine, Xiuliang Bao, Philippe Labrias, Talin Haritunians, Darren Ruane, Kyle Gettler, Ernie Chen, Dalin Li, Elena Schiff, Nikolas Pontikos, Nir Barzilai, Steven Brant, Susan Bressman, Adam Cheifetz, Lorraine Clark, Mark Daly, Robert Desnick, Richard Duerr, Seymour Katz, Todd Lencz, Richard Myers, Harry Ostrer, Laurie Ozelius, Haydeh Payami, Yakov Peter, John Rioux, Anthony Segal, William Scott, Mark Silverberg, Jeffery Vance, Iban Ubarretxena-Belandia, Tatiana Foroud, Gil Atzmon, Itsik Pe'er, Yiannis Ioannou, Dermot McGovern, Zhenyu Yue, Eric Schadt, Judy Cho, Inga Peter .  2018.   Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease.. Sci Transl Med. 10 (423) ▶ Go to Pubmed
Viveka Mayya, Edward Judokusumo, Enas Shah, Christopher Peel, Willie Neiswanger, David Depoil, David Blair, Chris Wiggins, Lance Kam, Michael Dustin .  2018.   Durable Interactions of T Cells with T Cell Receptor Stimuli in the Absence of a Stable Immunological Synapse.. Cell Rep. 22 (2) :340-349 ▶ Go to Pubmed
Nicholas Tatonetti .  2018.   The Next Generation of Drug Safety Science: Coupling Detection, Corroboration, and Validation to Discover Novel Drug Effects and Drug-Drug Interactions.. Clin Pharmacol Ther. 103 (2) :177-179 ▶ Go to Pubmed
Flor Evangelista, Aleeza Roth, Phillip Prisayanh, Brenda Temple, Ning Li, Ye Qian, Donna Culton, Zhi Liu, Oliver Harrison, Julia Brasch, Barry Honig, Lawrence Shapiro, Luis Diaz .  2018.   Pathogenic IgG4 autoantibodies from endemic pemphigus foliaceus recognize a desmoglein-1 conformational epitope.. J Autoimmun. ▶ Go to Pubmed
H Grillo, B Wilcox .  1989.   Choosing cardiothoracic surgical residents.. Ann Thorac Surg. 47 (3) :333 ▶ Go to Pubmed
Krzysztof Kiryluk, Andrew Bomback, Yim-Ling Cheng, Katherine Xu, Pablo Camara, Raul Rabadan, Peter Sims, Jonathan Barasch .  2018.   Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics.. Semin Nephrol. 38 (1) :40-51 ▶ Go to Pubmed
Chioma Madubata, Alireza Roshan-Ghias, Timothy Chu, Samuel Resnick, Junfei Zhao, Luis Arnes, Jiguang Wang, Raul Rabadan .  2017.   Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas.. NPJ Genom Med. 2 :29 ▶ Go to Pubmed
Zheng Xu, Chih-Chao Chang, Muyang Li, Qing-Yin Zhang, Elena-Rodica Vasilescu, Vivette D'Agati, Aristidis Floratos, George Vlad, Nicole Suciu-Foca .  2018.   ILT3.Fc-CD166 Interaction Induces Inactivation of p70 S6 Kinase and Inhibits Tumor Cell Growth.. J Immunol. 200 (3) :1207-1219 ▶ Go to Pubmed
Zheng Xu, Chih-Chao Chang, Muyang Li, Qing-Yin Zhang, Elena-Rodica Vasilescu, Vivette D'Agati, Aristidis Floratos, George Vlad, Nicole Suciu-Foca .  2018.   ILT3.Fc-CD166 Interaction Induces Inactivation of p70 S6 Kinase and Inhibits Tumor Cell Growth.. Journal of immunology (Baltimore, Md. : 1950). 200 (3) :1207-1219 ▶ Go to Pubmed
Jens Hansen, David Meretzky, Simeneh Woldesenbet, Gustavo Stolovitzky, Ravi Iyengar .  2017.   A flexible ontology for inference of emergent whole cell function from relationships between subcellular processes.. Sci Rep. 7 (1) :17689 ▶ Go to Pubmed
Hye Kim, Young Son, Wei Mao, Kam Leong, Hyuk Yoo .  2018.   Atom Transfer Radical Polymerization of Multishelled Cationic Corona for the Systemic Delivery of siRNA.. Nano Lett. 18 (1) :314-325 ▶ Go to Pubmed
Howook Hwang, Fabian Dey, Donald Petrey, Barry Honig .  2017.   Structure-based prediction of ligand-protein interactions on a genome-wide scale.. Proc Natl Acad Sci U S A. 114 (52) :13685-13690 ▶ Go to Pubmed
David Requena, Jose Álvarez, Hugo Gabilondo, Ryan Loker, Richard Mann, Carlos Estella .  2017.   Origins and Specification of the Drosophila Wing.. Curr Biol. 27 (24) :3826-3836.e5 ▶ Go to Pubmed
Bülent Aksoy, Vlado Dancik, Kenneth Smith, Jessica Mazerik, Zhou Ji, Benjamin Gross, Olga Nikolova, Nadia Jaber, Andrea Califano, Stuart Schreiber, Daniela Gerhard, Leandro Hermida, Subhashini Jagu, Chris Sander, Aris Floratos, Paul Clemons .  2017.   CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network.. Database : the journal of biological databases and curation. 2017 ▶ Go to Pubmed
Bülent Aksoy, Vlado Dancik, Kenneth Smith, Jessica Mazerik, Zhou Ji, Benjamin Gross, Olga Nikolova, Nadia Jaber, Andrea Califano, Stuart Schreiber, Daniela Gerhard, Leandro Hermida, Subhashini Jagu, Chris Sander, Aris Floratos, Paul Clemons .  2017.   CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network.. Database (Oxford). 2017 ▶ Go to Pubmed
Xintong Chen, Sander Houten, Kimaada Allette, Robert Sebra, Gustavo Stolovitzky, Bojan Losic .  2018.   Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology.. Pac Symp Biocomput. 23 :8-19 ▶ Go to Pubmed
Guido D'Amico, Raul Rabadan, Matthew Kleban .  2017.   A Random Categorization Model for Hierarchical Taxonomies.. Sci Rep. 7 (1) :17051 ▶ Go to Pubmed
S Marsilio, H Khiabanian, G Fabbri, S Vergani, C Scuoppo, E Montserrat, E Shpall, M Hadigol, P Marin, K Rai, R Rabadan, S Devereux, L Pasqualucci, N Chiorazzi .  2017.   Somatic CLL mutations occur at multiple distinct hematopoietic maturation stages: documentation and cautionary note regarding cell fraction purity.. Leukemia. ▶ Go to Pubmed
Xiaowei Chen, Huan Deng, Michael Churchill, Larry Luchsinger, Xing Du, Timothy Chu, Andrea Califano, Richard Friedman, Moritz Middelhoff, Hongxu Ding, Yagnesh Tailor, Alexander Wang, Haibo Liu, Zhengchuan Niu, Hongshan Wang, Zhenyu Jiang, Simon Renders, Siu-Hong Ho, Spandan Shah V, Pavel Tishchenko, Wenju Chang, Theresa Swayne, Laura Munteanu, Ryota Takahashi, Karan Nagar, Bernhard Renz, Daniel Worthley, Benedikt Westphalen, Yoku Hayakawa, Samuel Asfaha, Florence Borot, Chyuan-Sheng Lin, Hans-Willem Snoeck, Siddhartha Mukherjee, Timothy Wang .  2017.   Bone Marrow Myeloid Cells Regulate Myeloid-Biased Hematopoietic Stem Cells via a Histamine-Dependent Feedback Loop.. Cell Stem Cell. 21 (6) :747-760.e7 ▶ Go to Pubmed
Liyang Zhang, Gabriella Martini, Tomas Rube, Judith Kribelbauer, Chaitanya Rastogi, Vincent FitzPatrick, Jon Houtman, Harmen Bussemaker, Miles Pufall .  2018.   SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site.. Genome Res. 28 (1) :111-121 ▶ Go to Pubmed
Jinzhou Yuan, Peter Sims .  2017.   SPOTs fill a major gap in RNA quantification.. Nat Methods. 14 (12) :1137-1138 ▶ Go to Pubmed
Weston Jackson, Ipsita Agarwal, Itsik Pe'er .  2017.   2-Way k-Means as a Model for Microbiome Samples.. J Healthc Eng. 2017 :5284145 ▶ Go to Pubmed
Ravi Sheth, Sung Yim, Felix Wu, Harris Wang .  2017.   Multiplex recording of cellular events over time on CRISPR biological tape.. Science. ▶ Go to Pubmed
Surapon Charoensook, Damian Williams, Syandan Chakraborty, Kam Leong, Gordana Vunjak-Novakovic .  2017.   Bioreactor model of neuromuscular junction with electrical stimulation for pharmacological potency testing.. Integr Biol (Camb). 9 (12) :956-967 ▶ Go to Pubmed
Rebecca Delker, Richard Mann .  2017.   From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering.. Adv Exp Med Biol. 1016 :45-74 ▶ Go to Pubmed
Kerry Goodman, Rotem Rubinstein, Hanbin Dan, Fabiana Bahna, Seetha Mannepalli, Goran Ahlsen, Chan Thu, Rosemary Sampogna V, Tom Maniatis, Barry Honig, Lawrence Shapiro .  2017.   Protocadherin cis-dimer architecture and recognition unit diversity.. Proc Natl Acad Sci U S A. 114 (46) :E9829-E9837 ▶ Go to Pubmed
Jaspreet Khurana, Derek Clay, Sandrine Moreira, Xing Wang, Laura Landweber .  2018.   Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha.. RNA. 24 (1) :18-29 ▶ Go to Pubmed
Angelo Taglialatela, Silvia Alvarez, Giuseppe Leuzzi, Vincenzo Sannino, Lepakshi Ranjha, Jen-Wei Huang, Chioma Madubata, Roopesh Anand, Brynn Levy, Raul Rabadan, Petr Cejka, Vincenzo Costanzo, Alberto Ciccia .  2017.   Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers.. Mol Cell. 68 (2) :414-430.e8 ▶ Go to Pubmed
Tsu-Pei Chiu, Satyanarayan Rao, Richard Mann, Barry Honig, Remo Rohs .  2017.   Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding.. Nucleic Acids Res. 45 (21) :12565-12576 ▶ Go to Pubmed
Mary Boland, Pradipta Parhi, Li Li, Riccardo Miotto, Robert Carroll, Usman Iqbal, Phung-Anh Nguyen, Martijn Schuemie, Seng You, Donahue Smith, Sean Mooney, Patrick Ryan, Yu-Chuan Li, Rae Park, Josh Denny, Joel Dudley, George Hripcsak, Pierre Gentine, Nicholas Tatonetti .  2017.   Uncovering exposures responsible for birth season - disease effects: a global study.. J Am Med Inform Assoc. ▶ Go to Pubmed
Zeljko Tomljanovic, Mitesh Patel, William Shin, Andrea Califano, Andrew Teich .  2018.   ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease.. Bioinformatics. 34 (3) :367-371 ▶ Go to Pubmed
Yao Shen, Mariano Alvarez, Brygida Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano .  2017.   Systematic, network-based characterization of therapeutic target inhibitors.. PLoS Comput Biol. 13 (10) :e1005599 ▶ Go to Pubmed
Taru Tukiainen, Alexandra-Chloé Villani, Tuuli Lappalainen, Angela Yen, Manuel Rivas, Jamie Marshall, Rahul Satija, Matt Aguirre, Laura Gauthier, Mark Fleharty, Andrew Kirby, Beryl Cummings, Stephane Castel, Konrad Karczewski, François Aguet, Andrea Byrnes, GTEx Consortium, Data Laboratory, Statistical Group, Enhancing groups, NIH Fund, NIH /NCI, NIH /NHGRI, NIH /NIMH, NIH /NIDA, Biospecimen Site—NDRI, Biospecimen Site—RPCI, Biospecimen Resource—VARI, Brain Bank, Leidos Management, ELSI Study, Genome Visualization—EBI, University Institute, Aviv Regev, Kristin Ardlie, Nir Hacohen, Daniel MacArthur .  2017.   Landscape of X chromosome inactivation across human tissues.. Nature. 550 (7675) :244-248 ▶ Go to Pubmed
GTEx Consortium, Data Laboratory, Statistical Group, Enhancing groups, NIH Fund, NIH /NCI, NIH /NHGRI, NIH /NIMH, NIH /NIDA, Biospecimen Site—NDRI, Biospecimen Site—RPCI, Biospecimen Resource—VARI, Brain Bank, Leidos Management, ELSI Study, Genome Visualization—EBI, University Institute, Lead analysts:, Data Laboratory, NIH management:, Biospecimen collection:, Pathology :, eQTL group:, Alexis Battle, Christopher Brown, Barbara Engelhardt, Stephen Montgomery .  2017.   Genetic effects on gene expression across human tissues.. Nature. 550 (7675) :204-213 ▶ Go to Pubmed
Pejman Mohammadi, Stephane Castel, Andrew Brown, Tuuli Lappalainen .  2017.   Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change.. Genome Res. 27 (11) :1872-1884 ▶ Go to Pubmed
Mary Boland, Fernanda Polubriaginof, Nicholas Tatonetti .  2017.   Development of A Machine Learning Algorithm to Classify Drugs Of Unknown Fetal Effect.. Sci Rep. 7 (1) :12839 ▶ Go to Pubmed
Mehmet Gönen, Barbara Weir, Glenn Cowley, Francisca Vazquez, Yuanfang Guan, Alok Jaiswal, Masayuki Karasuyama, Vladislav Uzunangelov, Tao Wang, Aviad Tsherniak, Sara Howell, Daniel Marbach, Bruce Hoff, Thea Norman, Antti Airola, Adrian Bivol, Kerstin Bunte, Daniel Carlin, Sahil Chopra, Alden Deran, Kyle Ellrott, Peddinti Gopalacharyulu, Kiley Graim, Samuel Kaski, Suleiman Khan, Yulia Newton, Sam Ng, Tapio Pahikkala, Evan Paull, Artem Sokolov, Hao Tang, Jing Tang, Krister Wennerberg, Yang Xie, Xiaowei Zhan, Fan Zhu, Broad-DREAM Community, Tero Aittokallio, Hiroshi Mamitsuka, Joshua Stuart, Jesse Boehm, David Root, Guanghua Xiao, Gustavo Stolovitzky, William Hahn, Adam Margolin .  2017.   A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.. Cell Syst. 5 (5) :485-497.e3 ▶ Go to Pubmed
Ida Larsen, Yoshiki Narimatsu, Hiren Joshi, Lina Siukstaite, Oliver Harrison, Julia Brasch, Kerry Goodman, Lars Hansen, Lawrence Shapiro, Barry Honig, Sergey Vakhrushev, Henrik Clausen, Adnan Halim .  2017.   Discovery of an O-mannosylation pathway selectively serving cadherins and protocadherins.. Proc Natl Acad Sci U S A. 114 (42) :11163-11168 ▶ Go to Pubmed
Chloé-Agathe Azencott, Tero Aittokallio, Sushmita Roy, DREAM Consortium, Thea Norman, Stephen Friend, Gustavo Stolovitzky, Anna Goldenberg .  2017.   The inconvenience of data of convenience: computational research beyond post-mortem analyses.. Nat Methods. 14 (10) :937-938 ▶ Go to Pubmed
Carlos Amorim, Ziyue Gao, Zachary Baker, José Diesel, Yuval Simons, Imran Haque, Joseph Pickrell, Molly Przeworski .  2017.   The population genetics of human disease: The case of recessive, lethal mutations.. PLoS Genet. 13 (9) :e1006915 ▶ Go to Pubmed
Jing He, Zhou Zhou, Michael Reed, Andrea Califano .  2017.   Accelerated parallel algorithm for gene network reverse engineering.. BMC Syst Biol. 11 (Suppl 4) :83 ▶ Go to Pubmed
Brahma Kumar V, Yufeng Shen, Wenji Ma, Michelle Miron, Tomer Granot, Rebecca Guyer, Dustin Carpenter, Takashi Senda, Xiaoyun Sun, Siu-Hong Ho, Harvey Lerner, Amy Friedman, Donna Farber .  2017.   Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites.. Cell Rep. 20 (12) :2921-2934 ▶ Go to Pubmed
I Del Giudice, G Rigolin, S Raponi, L Cafforio, C Ilari, J Wang, M Bordyuh, A Piciocchi, M Marinelli, M Nanni, S Tavolaro, M Filetti, A Bardi, E Tammiso, E Volta, M Negrini, E Saccenti, F Mauro, D Rossi, G Gaidano, A Guarini, R Rabadan, A Cuneo, R Foà .  2017.   Refined karyotype-based prognostic stratification of chronic lymphocytic leukemia with a low- and very-low-risk genetic profile.. Leukemia. ▶ Go to Pubmed
Nenad Macesic, Fernanda Polubriaginof, Nicholas Tatonetti .  2017.   Machine learning: novel bioinformatics approaches for combating antimicrobial resistance.. Curr Opin Infect Dis. 30 (6) :511-517 ▶ Go to Pubmed
Noam Rudnick, Christopher Griffey, Paolo Guarnieri, Valeria Gerbino, Xueyong Wang, Jason Piersaint, Juan Tapia, Mark Rich, Tom Maniatis .  2017.   Distinct roles for motor neuron autophagy early and late in the SOD1(G93A) mouse model of ALS.. Proc Natl Acad Sci U S A. 114 (39) :E8294-E8303 ▶ Go to Pubmed
Qiang Gong, Chao Wang, Weiwei Zhang, Javeed Iqbal, Yang Hu, Timothy Greiner, Adam Cornish, Jo-Heon Kim, Raul Rabadan, Francesco Abate, Xin Wang, Giorgio Inghirami, Timothy McKeithan, Wing Chan .  2017.   Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data.. Sci Rep. 7 (1) :11301 ▶ Go to Pubmed
Hyunju Oh, Yenkel Grinberg-Bleyer, Will Liao, Dillon Maloney, Pingzhang Wang, Zikai Wu, Jiguang Wang, Dev Bhatt, Nicole Heise, Roland Schmid, Matthew Hayden, Ulf Klein, Raul Rabadan, Sankar Ghosh .  2017.   An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function.. Immunity. 47 (3) :450-465.e5 ▶ Go to Pubmed
Yuan Pan, Erin Bush, Joseph Toonen, Yu Ma, Anne Solga, Peter Sims, David Gutmann .  2017.   Whole tumor RNA-sequencing and deconvolution reveal a clinically-prognostic PTEN/PI3K-regulated glioma transcriptional signature.. Oncotarget. 8 (32) :52474-52487 ▶ Go to Pubmed
Hakhamanesh Mostafavi, Tomaz Berisa, Felix Day, John Perry, Molly Przeworski, Joseph Pickrell .  2017.   Identifying genetic variants that affect viability in large cohorts.. PLoS Biol. 15 (9) :e2002458 ▶ Go to Pubmed
Yao Ng, Pedro Baldera-Aguayo, Virginia Cornish .  2017.   Fluorescence Polarization Assay for Small Molecule Screening of FK506 Biosynthesized in 96-Well Microtiter Plates.. Biochemistry. ▶ Go to Pubmed
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