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2019

2019 Publications

Brian Ji, Ravi Sheth, Purushottam Dixit, Yiming Huang, Andrew Kaufman, Harris Wang, Dennis Vitkup .  2019.   Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.. Nat Methods. 16 (8) :731-736 ▶ Go to Pubmed
Judith Kribelbauer, Chaitanya Rastogi, Harmen Bussemaker, Richard Mann .  2019.   Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.. Annu Rev Cell Dev Biol. 35 :357-379 ▶ Go to Pubmed
Steven Cook, Travis Jarrell, Christopher Brittin, Yi Wang, Adam Bloniarz, Maksim Yakovlev, Ken Nguyen, Leo Tang, Emily Bayer, Janet Duerr, Hannes Bülow, Oliver Hobert, David Hall, Scott Emmons .  2019.   Whole-animal connectomes of both Caenorhabditis elegans sexes.. Nature. 571 (7763) :63-71 ▶ Go to Pubmed
Anna Nam, Kyu-Tae Kim, Ronan Chaligne, Franco Izzo, Chelston Ang, Justin Taylor, Robert Myers, Ghaith Abu-Zeinah, Ryan Brand, Nathaniel Omans, Alicia Alonso, Caroline Sheridan, Marisa Mariani, Xiaoguang Dai, Eoghan Harrington, Alessandro Pastore, Juan Cubillos-Ruiz, Wayne Tam, Ronald Hoffman, Raul Rabadan, Joseph Scandura, Omar Abdel-Wahab, Peter Smibert, Dan Landau .  2019.   Somatic mutations and cell identity linked by Genotyping of Transcriptomes.. Nature. 571 (7765) :355-360 ▶ Go to Pubmed
Tyler Joseph, Itsik Pe'er .  2019.   Inference of Population Structure from Time-Series Genotype Data.. Am J Hum Genet. 105 (2) :317-333 ▶ Go to Pubmed
Joris van Arensbergen, Ludo Pagie, Vincent FitzPatrick, Marcel de Haas, Marijke Baltissen, Federico Comoglio, Robin van der Weide, Hans Teunissen, Urmo Võsa, Lude Franke, Elzo de Wit, Michiel Vermeulen, Harmen Bussemaker, Bas van Steensel .  2019.   High-throughput identification of human SNPs affecting regulatory element activity.. Nat Genet. 51 (7) :1160-1169 ▶ Go to Pubmed
Wenji Ma, Jaeyop Lee, Daniel Backenroth, Yu Zhou, Erin Bush, Peter Sims, Kang Liu, Yufeng Shen .  2019.   Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose.. BMC Mol Cell Biol. 20 (1) :20 ▶ Go to Pubmed
Huijuan Feng, Suying Bao, Mohammad Rahman, Sebastien Weyn-Vanhentenryck, Aziz Khan, Justin Wong, Ankeeta Shah, Elise Flynn, Adrian Krainer, Chaolin Zhang .  2019.   Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites.. Mol Cell. 74 (6) :1189-1204.e6 ▶ Go to Pubmed
Benjamin Glicksberg, Boris Oskotsky, Phyllis Thangaraj, Nicholas Giangreco, Marcus Badgeley, Kipp Johnson, Debajyoti Datta, Vivek Rudrapatna, Nadav Rappoport, Mark Shervey, Riccardo Miotto, Theodore Goldstein, Eugenia Rutenberg, Remi Frazier, Nelson Lee, Sharat Israni, Rick Larsen, Bethany Percha, Li Li, Joel Dudley, Nicholas Tatonetti, Atul Butte .  2019.   PatientExploreR: an extensible application for dynamic visualization of patient clinical history from Electronic Health Records in the OMOP Common Data Model Title.. Bioinformatics. ▶ Go to Pubmed
Ela Elyada, Mohan Bolisetty, Pasquale Laise, William Flynn, Elise Courtois, Richard Burkhart, Jonathan Teinor, Pascal Belleau, Giulia Biffi, Matthew Lucito, Santhosh Sivajothi, Todd Armstrong, Dannielle Engle, Kenneth Yu, Yuan Hao, Christopher Wolfgang, Youngkyu Park, Jonathan Preall, Elizabeth Jaffee, Andrea Califano, Paul Robson, David Tuveson .  2019.   Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts.. Cancer Discov. 9 (8) :1102-1123 ▶ Go to Pubmed
Liat Shenhav, Mike Thompson, Tyler Joseph, Leah Briscoe, Ori Furman, David Bogumil, Itzhak Mizrahi, Itsik Pe'er, Eran Halperin .  2019.   FEAST: fast expectation-maximization for microbial source tracking.. Nat Methods. 16 (7) :627-632 ▶ Go to Pubmed
R Orenbuch, I Filip, D Comito, J Shaman, I Pe'er, R Rabadan .  2019.   arcasHLA: high resolution HLA typing from RNAseq.. Bioinformatics. ▶ Go to Pubmed
Maher Hanoun, Anna Arnal-Estapé, Maria Maryanovich, Ali Zahalka, Sarah Bergren, Chee Chua, Avigdor Leftin, Patrik Brodin, Michael Shen, Chandan Guha, Paul Frenette .  2019.   NestinNG2 Cells Form a Reserve Stem Cell Population in the Mouse Prostate.. Stem Cell Reports. 12 (6) :1201-1211 ▶ Go to Pubmed
Donna Farber, Peter Sims .  2019.   Dissecting lung development and fibrosis at single-cell resolution.. Genome Med. 11 (1) :33 ▶ Go to Pubmed
Benjamin Hobson, Peter Sims .  2019.   Critical Analysis of Particle Detection Artifacts in Synaptosome Flow Cytometry.. eNeuro. 6 (3) ▶ Go to Pubmed
Leslie Beh, Galia Debelouchina, Derek Clay, Robert Thompson, Kelsi Lindblad, Elizabeth Hutton, John Bracht, Robert Sebra, Tom Muir, Laura Landweber .  2019.   Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.. Cell. 177 (7) :1781-1796.e25 ▶ Go to Pubmed
Stanley Ahalt, Christopher Chute, Karamarie Fecho, Gustavo Glusman, Jennifer Hadlock, Casey Taylor, Emily Pfaff, Peter Robinson, Harold Solbrig, Casey Ta, Nicholas Tatonetti, Chunhua Weng, Biomedical Consortium .  2019.   Clinical Data: Sources and Types, Regulatory Constraints, Applications.. Clin Transl Sci. 12 (4) :329-333 ▶ Go to Pubmed
Paola Nicoletti, Sarah Barrett, Laurence McEvoy, Ann Daly, Guruprasad Aithal, Isabel Lucena, Raul Andrade, Mia Wadelius, Pär Hallberg, Camilla Stephens, Einar Bjornsson, Peter Friedmann, Kati Kainu, Tarja Laitinen, Anthony Marson, Mariam Molokhia, Elizabeth Phillips, Werner Pichler, Antonino Romano, Neil Shear, Graeme Sills, Luciana Tanno, Ashley Swale, Aris Floratos, Yufeng Shen, Matthew Nelson, Paul Watkins, Mark Daly, Andrew Morris, Ana Alfirevic, Munir Pirmohamed .  2019.   Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.. Clin Pharmacol Ther. 106 (5) :1028-1036 ▶ Go to Pubmed
Paola Nicoletti, Sarah Barrett, Laurence McEvoy, Ann Daly, Guruprasad Aithal, Isabel Lucena, Raul Andrade, Mia Wadelius, Pär Hallberg, Camilla Stephens, Einar Bjornsson, Peter Friedmann, Kati Kainu, Tarja Laitinen, Anthony Marson, Mariam Molokhia, Elizabeth Phillips, Werner Pichler, Antonino Romano, Neil Shear, Graeme Sills, Luciana Tanno, Ashley Swale, Aris Floratos, Yufeng Shen, Matthew Nelson, Paul Watkins, Mark Daly, Andrew Morris, Ana Alfirevic, Munir Pirmohamed .  2019.   Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.. Clinical pharmacology and therapeutics. 106 (5) :1028-1036 ▶ Go to Pubmed
Jing Zhang, Francesca Caruso, Jason Sa, Sune Justesen, Do-Hyun Nam, Peter Sims, Michele Ceccarelli, Anna Lasorella, Antonio Iavarone .  2019.   The combination of neoantigen quality and T lymphocyte infiltrates identifies glioblastomas with the longest survival.. Commun Biol. 2 :135 ▶ Go to Pubmed
Ziyue Gao, Priya Moorjani, Thomas Sasani, Brent Pedersen, Aaron Quinlan, Lynn Jorde, Guy Amster, Molly Przeworski .  2019.   Overlooked roles of DNA damage and maternal age in generating human germline mutations.. Proc Natl Acad Sci U S A. 116 (19) :9491-9500 ▶ Go to Pubmed
Luciano Cascione, Andrea Rinaldi, Alessio Bruscaggin, Chiara Tarantelli, Alberto Arribas, Ivo Kwee, Lorenza Pecciarini, Afua Mensah, Valeria Spina, Elaine Chung, Lodovico di Bergamo, Stephan Dirnhofer, Alexandar Tzankov, Roberto Miranda, Kenneth Young, Alexandra Traverse-Glehen, Gianluca Gaidano, Steven Swerdlow, Randy Gascoyne, Raul Rabadan, Maurilio Ponzoni, Govind Bhagat, Davide Rossi, Emanuele Zucca, Francesco Bertoni .  2019.   Novel insights into the genetics and epigenetics of MALT lymphoma unveiled by next generation sequencing analyses.. Haematologica. ▶ Go to Pubmed
Gloria Echeverria V, Zhongqi Ge, Sahil Seth, Xiaomei Zhang, Sabrina Jeter-Jones, Xinhui Zhou, Shirong Cai, Yizheng Tu, Aaron McCoy, Michael Peoples, Yuting Sun, Huan Qiu, Qing Chang, Christopher Bristow, Alessandro Carugo, Jiansu Shao, Xiaoyan Ma, Angela Harris, Prabhjot Mundi, Rosanna Lau, Vandhana Ramamoorthy, Yun Wu, Mariano Alvarez, Andrea Califano, Stacy Moulder, William Symmans, Joseph Marszalek, Timothy Heffernan, Jeffrey Chang, Helen Piwnica-Worms .  2019.   Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state.. Sci Transl Med. 11 (488) ▶ Go to Pubmed
María Blasco, Carolina Navas, Guillermo Martín-Serrano, Osvaldo Graña-Castro, Carmen Lechuga, Laura Martín-Díaz, Magdolna Djurec, Jing Li, Lucia Morales-Cacho, Laura Esteban-Burgos, Javier Perales-Patón, Emilie Bousquet-Mur, Eva Castellano, Harrys Jacob, Lavinia Cabras, Monica Musteanu, Matthias Drosten, Sagrario Ortega, Francisca Mulero, Bruno Sainz, Nelson Dusetti, Juan Iovanna, Francisco Sanchez-Bueno, Manuel Hidalgo, Hossein Khiabanian, Raul Rabadan, Fátima Al-Shahrour, Carmen Guerra, Mariano Barbacid .  2019.   Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF.. Cancer Cell. 35 (4) :573-587.e6 ▶ Go to Pubmed
David Zeevi, Tal Korem, Anastasia Godneva, Noam Bar, Alexander Kurilshikov, Maya Lotan-Pompan, Adina Weinberger, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Segal .  2019.   Structural variation in the gut microbiome associates with host health.. Nature. 568 (7750) :43-48 ▶ Go to Pubmed
Sohani Sharma, Jordan Metz, Hongyu Li, Benjamin Hobson, Nicholas Hornstein, David Sulzer, Guomei Tang, Peter Sims .  2019.   Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice.. Cell Rep. 26 (12) :3313-3322.e5 ▶ Go to Pubmed
Emily Slotkin, Daniel Diolaiti, Neerav Shukla, Filemon Cruz, Jennifer Clark, Gunes Gundem, Venkata Yellapantula, Max Levine, Daoqi You, Peilin Ma, Sagarika Pachhal, Glorymar Sanchez, Ryma Benayed, Achim Jungbluth, Lillian Smyth, Audrey Mauguen, Irena Gushterova, Hongxu Ding, Lee Spraggon, Robert Darnell, Andrea Califano, Marc Ladanyi, Elli Papaemmanuil, Andrew Kung, David Hyman, Stephen Roberts .  2019.   Patient-driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-driven Cancer.. Cancer Discov. ▶ Go to Pubmed
Mark Snyder, Michael Finlayson, Thomas Connors, Pranay Dogra, Takashi Senda, Erin Bush, Dustin Carpenter, Charles Marboe, Luke Benvenuto, Lori Shah, Hilary Robbins, Jaime Hook, Megan Sykes, Frank D'Ovidio, Matthew Bacchetta, Joshua Sonett, David Lederer, Selim Arcasoy, Peter Sims, Donna Farber .  2019.   Generation and persistence of human tissue-resident memory T cells in lung transplantation.. Sci Immunol. 4 (33) ▶ Go to Pubmed
Lalanti Venkatasubramanian, Richard Mann .  2019.   The development and assembly of the Drosophila adult ventral nerve cord.. Curr Opin Neurobiol. 56 :135-143 ▶ Go to Pubmed
Chen Wang, Oliver Hobert .  2019.   Sex-specific pheromone responses in .. EMBO Rep. 20 (3) ▶ Go to Pubmed
Marta Galanti, Ruthie Birger, Minhaz Ud-Dean, Ioan Filip, Haruka Morita, Devon Comito, Simon Anthony, Greg Freyer, Sadiat Ibrahim, Benjamin Lane, Chanel Ligon, Raul Rabadan, Atinuke Shittu, Eudosie Tagne, Jeffrey Shaman .  2019.   Longitudinal active sampling for respiratory viral infections across age groups.. Influenza Other Respir Viruses. ▶ Go to Pubmed
Junfei Zhao, Andrew Chen, Robyn Gartrell, Andrew Silverman, Luis Aparicio, Tim Chu, Darius Bordbar, David Shan, Jorge Samanamud, Aayushi Mahajan, Ioan Filip, Rose Orenbuch, Morgan Goetz, Jonathan Yamaguchi, Michael Cloney, Craig Horbinski, Rimas Lukas V, Jeffrey Raizer, Ali Rae, Jinzhou Yuan, Peter Canoll, Jeffrey Bruce, Yvonne Saenger, Peter Sims, Fabio Iwamoto, Adam Sonabend, Raul Rabadan .  2019.   Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.. Nat Med. 25 (3) :462-469 ▶ Go to Pubmed
Andrew Anzalone V, Sakellarios Zairis, Annie Lin, Raul Rabadan, Virginia Cornish .  2019.   Interrogation of Eukaryotic Stop Codon Readthrough Signals by in Vitro RNA Selection.. Biochemistry. 58 (8) :1167-1178 ▶ Go to Pubmed
Abhishek Bhattacharya, Ulkar Aghayeva, Emily Berghoff, Oliver Hobert .  2019.   Plasticity of the Electrical Connectome of C. elegans.. Cell. 176 (5) :1174-1189.e16 ▶ Go to Pubmed
Mythily Ganapathi, Leah Padgett, Kentaro Yamada, Orrin Devinsky, Rebecca Willaert, Richard Person, Ping-Yee Au, Julia Tagoe, Marie McDonald, Danielle Karlowicz, Barry Wolf, Joanna Lee, Yufeng Shen, Volkan Okur, Liyong Deng, Charles Leduc, Jiayao Wang, Ashleigh Hanner, Raghavendra Mirmira, Myung Park, Teresa Mastracci, Wendy Chung .  2019.   Recessive Rare Variants in Deoxyhypusine Synthase, an Enzyme Involved in the Synthesis of Hypusine, Are Associated with a Neurodevelopmental Disorder.. Am J Hum Genet. 104 (2) :287-298 ▶ Go to Pubmed
Carlo Maurer, Sam Holmstrom, Jing He, Pasquale Laise, Tao Su, Aqeel Ahmed, Hanina Hibshoosh, John Chabot, Paul Oberstein, Antonia Sepulveda, Jeanine Genkinger, Jiapeng Zhang, Alina Iuga, Mukesh Bansal, Andrea Califano, Kenneth Olive .  2019.   Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes.. Gut. ▶ Go to Pubmed
Hannah Klein, Giedrė Bačinskaja, Jun Che, Anais Cheblal, Rajula Elango, Anastasiya Epshtein, Devon Fitzgerald, Belén Gómez-González, Sharik Khan, Sandeep Kumar, Bryan Leland, Léa Marie, Qian Mei, Judith Miné-Hattab, Alicja Piotrowska, Erica Polleys, Christopher Putnam, Elina Radchenko, Anissia Saada, Cynthia Sakofsky, Eun Shim, Mathew Stracy, Jun Xia, Zhenxin Yan, Yi Yin, Andrés Aguilera, Juan Argueso, Catherine Freudenreich, Susan Gasser, Dmitry Gordenin, James Haber, Grzegorz Ira, Sue Jinks-Robertson, Megan King, Richard Kolodner, Andrei Kuzminov, Sarah Lambert, Sang Lee, Kyle Miller, Sergei Mirkin, Thomas Petes, Susan Rosenberg, Rodney Rothstein, Lorraine Symington, Pawel Zawadzki, Nayun Kim, Michael Lisby, Anna Malkova .  2019.   Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways.. Microb Cell. 6 (1) :1-64 ▶ Go to Pubmed
Mukesh Bansal, Jing He, Michael Peyton, Manjunath Kustagi, Archana Iyer, Michael Comb, Michael White, John Minna, Andrea Califano .  2019.   Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis.. PLoS One. 14 (1) :e0208646 ▶ Go to Pubmed