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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
Sarah Kim-Hellmuth, Matthias Bechheim, Benno Pütz, Pejman Mohammadi, Yohann Nédélec, Nicholas Giangreco, Jessica Becker, Vera Kaiser, Nadine Fricker, Esther Beier, Peter Boor, Stephane Castel, Markus Nöthen, Luis Barreiro, Joseph Pickrell, Bertram Müller-Myhsok, Tuuli Lappalainen, Johannes Schumacher, Veit Hornung .  2017.   Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations.. Nat Commun. 8 (1) :266 ▶ Go to Pubmed
Logan Walsh, Mariano Alvarez, Erich Sabio, Marsha Reyngold, Vladimir Makarov, Suranjit Mukherjee, Ken-Wing Lee, Alexis Desrichard, Şevin Turcan, Martin Dalin, Vinagolu Rajasekhar, Shuibing Chen, Linda Vahdat, Andrea Califano, Timothy Chan .  2017.   An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis.. Cell Rep. 20 (7) :1623-1640 ▶ Go to Pubmed
Rotem Rubinstein, Kerry Goodman, Tom Maniatis, Lawrence Shapiro, Barry Honig .  2017.   Structural origins of clustered protocadherin-mediated neuronal barcoding.. Semin Cell Dev Biol. 69 :140-150 ▶ Go to Pubmed
Erin Bush, Forest Ray, Mariano Alvarez, Ronald Realubit, Hai Li, Charles Karan, Andrea Califano, Peter Sims .  2017.   PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens.. Nat Commun. 8 (1) :105 ▶ Go to Pubmed
Chen Chen, Hongjian Qi, Yufeng Shen, Joseph Pickrell, Molly Przeworski .  2017.   Contrasting Determinants of Mutation Rates in Germline and Soma.. Genetics. 207 (1) :255-267 ▶ Go to Pubmed
Evgeni Efimenko, Utpal Davé, Irina Lebedeva V, Yao Shen, Maria Sanchez-Quintero, Daniel Diolaiti, Andrew Kung, Andrea Califano, Brian Lannutti, Jianchung Chen, Ronald Realubit, Zoya Niatsetskaya, Vadim Ten, Charles Karan, Xi Chen, Thomas Diacovo .  2017.   PI3Kγ/δ and NOTCH1 Cross-Regulate Pathways That Define the T-cell Acute Lymphoblastic Leukemia Disease Signature.. Mol Cancer Ther. 16 (10) :2069-2082 ▶ Go to Pubmed
Cameron Palmer, Itsik Pe'er .  2017.   Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies.. PLoS Genet. 13 (7) :e1006916 ▶ Go to Pubmed
Mary Boland, Pradipta Parhi, Pierre Gentine, Nicholas Tatonetti .  2017.   Climate Classification is an Important Factor in Assessing Quality-of-Care Across Hospitals.. Sci Rep. 7 (1) :4948 ▶ Go to Pubmed
Harmen Bussemaker, Helen Causton, Mina Fazlollahi, Eunjee Lee, Ivor Muroff .  2017.   Network-based approaches that exploit inferred transcription factor activity to analyze the impact of genetic variation on gene expression.. Curr Opin Syst Biol. 2 :98-102 ▶ Go to Pubmed
James Russell, Julie Theriot, Pranidhi Sood, Wallace Marshall, Laura Landweber, Lillian Fritz-Laylin, Jessica Polka, Snezhana Oliferenko, Therese Gerbich, Amy Gladfelter, James Umen, Magdalena Bezanilla, Madeline Lancaster, Shuonan He, Matthew Gibson, Bob Goldstein, Elly Tanaka, Chi-Kuo Hu, Anne Brunet .  2017.   Non-model model organisms.. BMC Biol. 15 (1) :55 ▶ Go to Pubmed
Jaeyop Lee, Yu Zhou, Wenji Ma, Wanwei Zhang, Arafat Aljoufi, Thomas Luh, Kimberly Lucero, Deguang Liang, Matthew Thomsen, Govind Bhagat, Yufeng Shen, Kang Liu .  2017.   Lineage specification of human dendritic cells is marked by IRF8 expression in hematopoietic stem cells and multipotent progenitors.. Nat Immunol. 18 (8) :877-888 ▶ Go to Pubmed
Judith Kribelbauer, Oleg Laptenko, Siying Chen, Gabriella Martini, William Freed-Pastor, Carol Prives, Richard Mann, Harmen Bussemaker .  2017.   Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes.. Cell Rep. 19 (11) :2383-2395 ▶ Go to Pubmed
Sung-Cheol Kim, Benjamin Wunsch, Huan Hu, Joshua Smith, Robert Austin, Gustavo Stolovitzky .  2017.   Broken flow symmetry explains the dynamics of small particles in deterministic lateral displacement arrays.. Proc Natl Acad Sci U S A. 114 (26) :E5034-E5041 ▶ Go to Pubmed
Zachary Baker, Molly Schumer, Yuki Haba, Lisa Bashkirova, Chris Holland, Gil Rosenthal, Molly Przeworski .  2017.   Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates.. Elife. 6 ▶ Go to Pubmed
Gabriele Varano, Simon Raffel, Martina Sormani, Federica Zanardi, Silvia Lonardi, Christin Zasada, Laura Perucho, Valentina Petrocelli, Andrea Haake, Albert Lee, Mattia Bugatti, Ulrike Paul, Eelco Van Anken, Laura Pasqualucci, Raul Rabadan, Reiner Siebert, Stefan Kempa, Maurilio Ponzoni, Fabio Facchetti, Klaus Rajewsky, Stefano Casola .  2017.   The B-cell receptor controls fitness of MYC-driven lymphoma cells via GSK3β inhibition.. Nature. 546 (7657) :302-306 ▶ Go to Pubmed
Hua-Sheng Chiu, María Martínez, Mukesh Bansal, Aravind Subramanian, Todd Golub, Xuerui Yang, Pavel Sumazin, Andrea Califano .  2017.   High-throughput validation of ceRNA regulatory networks.. BMC Genomics. 18 (1) :418 ▶ Go to Pubmed
Tuuli Lappalainen, John Greally .  2017.   Associating cellular epigenetic models with human phenotypes.. Nat Rev Genet. 18 (7) :441-451 ▶ Go to Pubmed
Vita Fedele, Fangping Dai, Anie Masilamani, Dieter Heiland, Eva Kling, Ana Gätjens-Sanchez, Roberto Ferrarese, Leonardo Platania, Doostkam Soroush, Hyunsoo Kim, Sven Nelander, Astrid Weyerbrock, Marco Prinz, Andrea Califano, Antonio Iavarone, Markus Bredel, Maria Carro .  2017.   Epigenetic Regulation of ZBTB18 Promotes Glioblastoma Progression.. Mol Cancer Res. 15 (8) :998-1011 ▶ Go to Pubmed
Ida Larsen, Yoshiki Narimatsu, Hiren Joshi, Zhang Yang, Oliver Harrison, Julia Brasch, Lawrence Shapiro, Barry Honig, Sergey Vakhrushev, Henrik Clausen, Adnan Halim .  2017.   Mammalian O-mannosylation of cadherins and plexins is independent of protein O-mannosyltransferases 1 and 2.. J Biol Chem. 292 (27) :11586-11598 ▶ Go to Pubmed
Kyrie Pappas, Jia Xu, Sakellarios Zairis, Lois Resnick-Silverman, Francesco Abate, Nicole Steinbach, Sait Ozturk, Lao Saal, Tao Su, Pamela Cheung, Hank Schmidt, Stuart Aaronson, Hanina Hibshoosh, James Manfredi, Raul Rabadan, Ramon Parsons .  2017.   p53 Maintains Baseline Expression of Multiple Tumor Suppressor Genes.. Mol Cancer Res. 15 (8) :1051-1062 ▶ Go to Pubmed
Abbas Rizvi, Pablo Camara, Elena Kandror, Thomas Roberts, Ira Schieren, Tom Maniatis, Raul Rabadan .  2017.   Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development.. Nat Biotechnol. 35 (6) :551-560 ▶ Go to Pubmed
Kelsi Lindblad, John Bracht, April Williams, Laura Landweber .  2017.   Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development.. RNA. 23 (8) :1200-1208 ▶ Go to Pubmed
Junghyun Lim, Pankaj Giri, David Kazadi, Brice Laffleur, Wanwei Zhang, Veronika Grinstein, Evangelos Pefanis, Lewis Brown, Erik Ladewig, Ophélie Martin, Yuling Chen, Raul Rabadan, François Boyer, Gerson Rothschild, Michel Cogné, Eric Pinaud, Haiteng Deng, Uttiya Basu .  2017.   Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry.. Cell. 169 (3) :523-537.e15 ▶ Go to Pubmed
Flaminia Talos, Antonina Mitrofanova, Sarah Bergren, Andrea Califano, Michael Shen .  2017.   A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue.. Nat Commun. 8 :14662 ▶ Go to Pubmed
Takayuki Abe, Albert Lee, Ramaswami Sitharam, Jordan Kesner, Raul Rabadan, Sagi Shapira .  2017.   Germ-Cell-Specific Inflammasome Component NLRP14 Negatively Regulates Cytosolic Nucleic Acid Sensing to Promote Fertilization.. Immunity. 46 (4) :621-634 ▶ Go to Pubmed
Min Zou, Roxanne Toivanen, Antonina Mitrofanova, Nicolas Floch, Sheida Hayati, Yanping Sun, Clémentine Le Magnen, Daniel Chester, Elahe Mostaghel, Andrea Califano, Mark Rubin, Michael Shen, Cory Abate-Shen .  2017.   Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer.. Cancer Discov. 7 (7) :736-749 ▶ Go to Pubmed
Roxanne Toivanen, Michael Shen .  2017.   Prostate organogenesis: tissue induction, hormonal regulation and cell type specification.. Development. 144 (8) :1382-1398 ▶ Go to Pubmed
Aditya Dutta, Sukanya Panja, Renu Virk, Jaime Kim, Roseann Zott, Serge Cremers, David Golombos, Deli Liu, Juan Mosquera, Elahe Mostaghel, Christopher Barbieri, Antonina Mitrofanova, Cory Abate-Shen .  2017.   Co-clinical Analysis of a Genetically Engineered Mouse Model and Human Prostate Cancer Reveals Significance of NKX3.1 Expression for Response to 5α-reductase Inhibition.. Eur Urol. 72 (4) :499-506 ▶ Go to Pubmed
Tal Lorberbaum, Nicholas Tatonetti .  2017.   Reply: Combination Therapy With Ceftriaxone and Lansoprazole, Acquired Long QT Syndrome and Torsades de Pointes Risk.. J Am Coll Cardiol. 69 (14) :1877-1878 ▶ Go to Pubmed
James Xue, Todd Lencz, Ariel Darvasi, Itsik Pe'er, Shai Carmi .  2017.   The time and place of European admixture in Ashkenazi Jewish history.. PLoS Genet. 13 (4) :e1006644 ▶ Go to Pubmed
Xu Zhang, Tapan Maity, Manoj Kashyap, Mukesh Bansal, Abhilash Venugopalan, Sahib Singh, Shivangi Awasthi, Arivusudar Marimuthu, Harrys Jacob, Natalya Belkina, Stephanie Pitts, Constance Cultraro, Shaojian Gao, Guldal Kirkali, Romi Biswas, Raghothama Chaerkady, Andrea Califano, Akhilesh Pandey, Udayan Guha .  2017.   Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response.. Mol Cell Proteomics. 16 (5) :891-910 ▶ Go to Pubmed
Mauro Longoni, Frances High, Hongjian Qi, Maliackal Joy, Regis Hila, Caroline Coletti, Julia Wynn, Maria Loscertales, Linshan Shan, Carol Bult, Jay Wilson, Yufeng Shen, Wendy Chung, Patricia Donahoe .  2017.   Genome-wide enrichment of damaging de novo variants in patients with isolated and complex congenital diaphragmatic hernia.. Hum Genet. 136 (6) :679-691 ▶ Go to Pubmed
Dmytro Ustianenko, Sebastien Weyn-Vanhentenryck, Chaolin Zhang .  2017.   Microexons: discovery, regulation, and function.. Wiley Interdiscip Rev RNA. 8 (4) ▶ Go to Pubmed
Alexandre Fort, Nikolaos Panousis, Marco Garieri, Stylianos Antonarakis, Tuuli Lappalainen, Emmanouil Dermitzakis, Olivier Delaneau .  2017.   MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets.. Bioinformatics. 33 (12) :1895-1897 ▶ Go to Pubmed
Peter Kwong, Gwo-Yu Chuang, Brandon DeKosky, Tatyana Gindin, Ivelin Georgiev, Thomas Lemmin, Chaim Schramm, Zizhang Sheng, Cinque Soto, An-Suei Yang, John Mascola, Lawrence Shapiro .  2017.   Antibodyomics: bioinformatics technologies for understanding B-cell immunity to HIV-1.. Immunol Rev. 275 (1) :108-128 ▶ Go to Pubmed
Esther Lopez-Rivera, Yangfan Liu, Miguel Verbitsky, Blair Anderson, Valentina Capone, Edgar Otto, Zhonghai Yan, Adele Mitrotti, Jeremiah Martino, Nicholas Steers, David Fasel, Katarina Vukojevic, Rong Deng, Silvia Racedo, Qingxue Liu, Max Werth, Rik Westland, Asaf Vivante, Gabriel Makar, Monica Bodria, Matthew Sampson, Christopher Gillies, Virginia Vega-Warner, Mariarosa Maiorana, Donald Petrey, Barry Honig, Vladimir Lozanovski, Rémi Salomon, Laurence Heidet, Wassila Carpentier, Dominique Gaillard, Alba Carrea, Loreto Gesualdo, Daniele Cusi, Claudia Izzi, Francesco Scolari, Joanna van Wijk, Adela Arapovic, Mirna Saraga-Babic, Marijan Saraga, Nenad Kunac, Ali Samii, Donna McDonald-McGinn, Terrence Crowley, Elaine Zackai, Dorota Drozdz, Monika Miklaszewska, Marcin Tkaczyk, Przemyslaw Sikora, Maria Szczepanska, Malgorzata Mizerska-Wasiak, Grazyna Krzemien, Agnieszka Szmigielska, Marcin Zaniew, John Darlow, Prem Puri, David Barton, Emilio Casolari, Susan Furth, Bradley Warady, Zoran Gucev, Hakon Hakonarson, Hana Flogelova, Velibor Tasic, Anna Latos-Bielenska, Anna Materna-Kiryluk, Landino Allegri, Craig Wong, Iain Drummond, Vivette D'Agati, Akira Imamoto, Jonathan Barasch, Friedhelm Hildebrandt, Krzysztof Kiryluk, Richard Lifton, Bernice Morrow, Cecile Jeanpierre, Virginia Papaioannou, Gian Ghiggeri, Ali Gharavi, Nicholas Katsanis, Simone Sanna-Cherchi .  2017.   Genetic Drivers of Kidney Defects in the DiGeorge Syndrome.. N Engl J Med. ▶ Go to Pubmed
Roumen Voutev, Richard Mann .  2017.   Bxb1 phage recombinase assists genome engineering in Drosophila melanogaster.. Biotechniques. 62 (1) :37-38 ▶ Go to Pubmed
Marta Sanchez-Martin, Adolfo Ferrando .  2017.   The NOTCH1-MYC highway towards T-cell acute lymphoblastic leukemia.. Blood. ▶ Go to Pubmed
Mary Boland, Konrad Karczewski, Nicholas Tatonetti .  2017.   Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing.. PLoS Comput Biol. 13 (1) :e1005278 ▶ Go to Pubmed
Rivkah Rogawski, Ivan Sergeyev V, Yongjun Li, Maria Ottaviani, Virginia Cornish, Ann McDermott .  2017.   Dynamic Nuclear Polarization Signal Enhancement with High-Affinity Biradical Tags.. J Phys Chem B. ▶ Go to Pubmed
Anne-Catrin Uhlemann, Paul McAdam, Sean Sullivan, Justin Knox, Hossein Khiabanian, Raul Rabadan, Peter Davies, Ross Fitzgerald, Franklin Lowy .  2017.   Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration.. MBio. 8 (1) ▶ Go to Pubmed
Jimmy Liu, Yaniv Erlich, Joseph Pickrell .  2017.   Case-control association mapping by proxy using family history of disease.. Nat Genet. ▶ Go to Pubmed
Tomasz Owczarek, Takashi Kobayashi, Ricardo Ramirez, Lijie Rong, Anna Puzio-Kuter, Gopa Iyer, Min Teo, Francisco Sanchez-Vega, Jingqiang Wang, Nikolaus Schultz, Tian Zheng, David Solit, Hikmat Al-Ahmadie, Cory Abate-Shen .  2017.   ARF confers a context-dependent response to chemotherapy in muscle invasive bladder cancer.. Cancer Res. ▶ Go to Pubmed
Nicolas Christoforou, Syandan Chakraborty, Robert Kirkton, Andrew Adler, Russell Addis, Kam Leong .  2017.   Core Transcription Factors, MicroRNAs, and Small Molecules Drive Transdifferentiation of Human Fibroblasts Towards The Cardiac Cell Lineage.. Sci Rep. 7 :40285 ▶ Go to Pubmed
Esther Serrano-Saiz, Meital Oren-Suissa, Emily Bayer, Oliver Hobert .  2017.   Sexually Dimorphic Differentiation of a C. elegans Hub Neuron Is Cell Autonomously Controlled by a Conserved Transcription Factor.. Curr Biol. ▶ Go to Pubmed
Francesco Abate, Ana da Silva-Almeida, Sakellarios Zairis, Javier Robles-Valero, Lucile Couronné, Hossein Khiabanian, Aidan Quinn, Mi-Yeon Kim, Maria Laginestra, Christine Kim, Danilo Fiore, Govind Bhagat, Miguel Piris, Elias Campo, Izidore Lossos, Olivier Bernard, Giorgio Inghirami, Stefano Pileri, Xosé Bustelo, Raul Rabadan, Adolfo Ferrando, Teresa Palomero .  2017.   Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas.. Proc Natl Acad Sci U S A. ▶ Go to Pubmed
Kai Wang, Kam Leong, Yong Yang .  2016.   Expanding Nanopatterned Substrates Using Stitch Technique for Nanotopographical Modulation of Cell Behavior.. J Vis Exp. (118) ▶ Go to Pubmed
Sze Kerk, Paschalis Kratsios, Michael Hart, Romulo Mourao, Oliver Hobert .  2017.   Diversification of C. elegans Motor Neuron Identity via Selective Effector Gene Repression.. Neuron. 93 (1) :80-98 ▶ Go to Pubmed
Jaewoo Lee, Jennifer Jackman, Jean Kwun, Miriam Manook, Angelo Moreno, Eric Elster, Allan Kirk, Kam Leong, Bruce Sullenger .  2016.   Nucleic acid scavenging microfiber mesh inhibits trauma-induced inflammation and thrombosis.. Biomaterials. 120 :94-102 ▶ Go to Pubmed