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Juan Patiño-Galindo, Ioan Filip, Raul Rabadan .  2021.   Global Patterns of Recombination across Human Viruses.. Mol Biol Evol. 38 (6) :2520-2531 ▶ Go to Pubmed
Feixiong Cheng, Junfei Zhao, Yang Wang, Weiqiang Lu, Zehui Liu, Yadi Zhou, William Martin, Ruisheng Wang, Jin Huang, Tong Hao, Hong Yue, Jing Ma, Yuan Hou, Jessica Castrillon, Jiansong Fang, Justin Lathia, Ruth Keri, Felice Lightstone, Elliott Antman, Raul Rabadan, David Hill, Charis Eng, Marc Vidal, Joseph Loscalzo .  2021.   Comprehensive characterization of protein-protein interactions perturbed by disease mutations.. Nat Genet. 53 (3) :342-353 ▶ Go to Pubmed
Zhaoqi Liu, Raul Rabadan .  2021.   Computing the Role of Alternative Splicing in Cancer.. Trends Cancer. 7 (4) :347-358 ▶ Go to Pubmed
Hongxu Ding, Ying Yang, Yuanqing Xue, Lucas Seninge, Henry Gong, Rojin Safavi, Andrea Califano, Joshua Stuart .  2021.   Prioritizing transcriptional factors in gene regulatory networks with PageRank.. iScience. 24 (1) :102017 ▶ Go to Pubmed
Mehdi Damaghi, Jeffrey West, Mark Robertson-Tessi, Liping Xu, Meghan Ferrall-Fairbanks, Paul Stewart, Erez Persi, Brooke Fridley, Philipp Altrock, Robert Gatenby, Peter Sims, Alexander Anderson, Robert Gillies .  2021.   The harsh microenvironment in early breast cancer selects for a Warburg phenotype.. Proceedings of the National Academy of Sciences of the United States of America. 118 (3) ▶ Go to Pubmed
Yuan-Hung Lo, Kevin Kolahi, Yuhong Du, Chiung-Ying Chang, Andrey Krokhotin, Ajay Nair, Walter Sobba, Kasper Karlsson, Sunny Jones, Teri Longacre, Amanda Mah, Bahar Tercan, Alexandra Sockell, Hang Xu, Jose Seoane, Jin Chen, Ilya Shmulevich, Jonathan Weissman, Christina Curtis, Andrea Califano, Haian Fu, Gerald Crabtree, Calvin Kuo .  2021.   A CRISPR/Cas9-Engineered -Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation.. Cancer Discov. 11 (6) :1562-1581 ▶ Go to Pubmed
Evan Paull, Alvaro Aytes, Sunny Jones, Prem Subramaniam, Federico Giorgi, Eugene Douglass, Somnath Tagore, Brennan Chu, Alessandro Vasciaveo, Siyuan Zheng, Roel Verhaak, Cory Abate-Shen, Mariano Alvarez, Andrea Califano .  2021.   A modular master regulator landscape controls cancer transcriptional identity.. Cell. 184 (2) :334-351.e20 ▶ Go to Pubmed
Dinara Usmanova, Germán Plata, Dennis Vitkup .  2021.   The Relationship between the Misfolding Avoidance Hypothesis and Protein Evolutionary Rates in the Light of Empirical Evidence.. Genome Biol Evol. 13 (2) ▶ Go to Pubmed
Sung Yim, Ross McBee, Alan Song, Yiming Huang, Ravi Sheth, Harris Wang .  2021.   Robust direct digital-to-biological data storage in living cells.. Nature chemical biology. 17 (3) :246-253 ▶ Go to Pubmed
Wesley Tansey, Kathy Li, Haoran Zhang, Scott Linderman, Raul Rabadan, David Blei, Chris Wiggins .  2021.   Dose-response modeling in high-throughput cancer drug screenings: an end-to-end approach.. Biostatistics. ▶ Go to Pubmed
Mai Sato, Andrew Liebau, Zhaoqi Liu, Lizhi Liu, Raul Rabadan, Jean Gautier .  2021.   The UVSSA complex alleviates MYC-driven transcription stress.. J Cell Biol. 220 (2) ▶ Go to Pubmed
Matko Kalac, Michael Mangone, Alison Rinderspacher, Shi-Xian Deng, Luigi Scotto, Michael Markson, Mukesh Bansal, Andrea Califano, Donald Landry, Owen O'Connor .  2020.   -quinoline-benzenesulfonamide derivatives exert potent anti-lymphoma effect by targeting NF-κB.. iScience. 23 (12) :101884 ▶ Go to Pubmed
Doowon Huh, Maria Passarelli, Jenny Gao, Shahnoza Dusmatova, Clara Goin, Lisa Fish, Alexandra Pinzaru, Henrik Molina, Zhiji Ren, Elizabeth McMillan, Hosseinali Asgharian, Hani Goodarzi, Sohail Tavazoie .  2021.   A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression.. EMBO J. 40 (2) :e106696 ▶ Go to Pubmed
George Rosenberger, Moritz Heusel, Isabell Bludau, Ben Collins, Claudia Martelli, Evan Williams, Peng Xue, Yansheng Liu, Ruedi Aebersold, Andrea Califano .  2020.   SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles.. Cell Syst. 11 (6) :589-607.e8 ▶ Go to Pubmed
Karthik Arumugam, William Shin, Valentina Schiavone, Lukas Vlahos, Xiaochuan Tu, Davide Carnevali, Jordan Kesner, Evan Paull, Neus Romo, Prem Subramaniam, Jeremy Worley, Xiangtian Tan, Andrea Califano, Maria Cosma .  2020.   The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State.. Cell Rep. 33 (10) :108474 ▶ Go to Pubmed
Phuc Vo, Carlotta Ronda, Sanne Klompe, Ethan Chen, Christopher Acree, Harris Wang, Samuel Sternberg .  2021.   CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering.. Nature biotechnology. 39 (4) :480-489 ▶ Go to Pubmed
Phuc Vo, Carlotta Ronda, Sanne Klompe, Ethan Chen, Christopher Acree, Harris Wang, Samuel Sternberg .  2021.   CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering.. Nature biotechnology. 39 (4) :480-489 ▶ Go to Pubmed
Zhaoqi Liu, Ioan Filip, Karen Gomez, Dewaldt Engelbrecht, Shabnum Meer, Pooja Lalloo, Pareen Patel, Yvonne Perner, Junfei Zhao, Jiguang Wang, Laura Pasqualucci, Raul Rabadan, Pascale Willem .  2020.   Genomic characterization of HIV-associated plasmablastic lymphoma identifies pervasive mutations in the JAK-STAT pathway.. Blood Cancer Discov. 1 (1) :112-125 ▶ Go to Pubmed
Se-Jin Lee, Adam Lehar, Yewei Liu, Chi Ly, Quynh-Mai Pham, Michael Michaud, Renata Rydzik, Daniel Youngstrom, Michael Shen, Vesa Kaartinen, Emily Germain-Lee, Thomas Rando .  2020.   Functional redundancy of type I and type II receptors in the regulation of skeletal muscle growth by myostatin and activin A.. Proc Natl Acad Sci U S A. 117 (49) :30907-30917 ▶ Go to Pubmed
Luis Aparicio, Mykola Bordyuh, Andrew Blumberg, Raul Rabadan .  2020.   A Random Matrix Theory Approach to Denoise Single-Cell Data.. Patterns (N Y). 1 (3) :100035 ▶ Go to Pubmed
Maho Shibata, Nusrat Epsi, Shouhong Xuan, Antonina Mitrofanova, Michael Shen .  2020.   Bipotent Progenitors Do Not Require Androgen Receptor for Luminal Specification during Prostate Organogenesis.. Stem Cell Reports. 15 (5) :1026-1036 ▶ Go to Pubmed
Zhouzerui Liu, Jinzhou Yuan, Anna Lasorella, Antonio Iavarone, Jeffrey Bruce, Peter Canoll, Peter Sims .  2020.   Integrating single-cell RNA-seq and imaging with SCOPE-seq2.. Scientific reports. 10 (1) :19482 ▶ Go to Pubmed
Jamie Yang, Saeed Tavazoie .  2020.   Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.. PLoS One. 15 (11) :e0239528 ▶ Go to Pubmed
Francesca Caruso, Luciano Garofano, Fulvio D'Angelo, Kai Yu, Fuchou Tang, Jinzhou Yuan, Jing Zhang, Luigi Cerulo, Stefano Pagnotta, Davide Bedognetti, Peter Sims, Mario Suvà, Xiao-Dong Su, Anna Lasorella, Antonio Iavarone, Michele Ceccarelli .  2020.   A map of tumor-host interactions in glioma at single-cell resolution.. GigaScience. 9 (10) ▶ Go to Pubmed
Suji Han, Hyemi Shin, Jin-Ku Lee, Zhaoqi Liu, Raul Rabadan, Jeongwu Lee, Jihye Shin, Cheolju Lee, Heekyoung Yang, Donggeon Kim, Sung Kim, Jooyeon Kim, Jeong-Woo Oh, Doo-Sik Kong, Jung-Il Lee, Ho Seol, Jung Choi, Hyun Kang, Do-Hyun Nam .  2020.   Correction: Secretome analysis of patient-derived GBM tumorspheres identifies midkine as a potent therapeutic target.. Exp Mol Med. 52 (11) :1869 ▶ Go to Pubmed
Vartika Mishra, Diane Ré, Virginia Le Verche, Mariano Alvarez, Alessandro Vasciaveo, Arnaud Jacquier, Paschalis-Tomas Doulias, Todd Greco, Monica Nizzardo, Dimitra Papadimitriou, Tetsuya Nagata, Paola Rinchetti, Eduardo Perez-Torres, Kristin Politi, Burcin Ikiz, Kevin Clare, Manuel Than, Stefania Corti, Harry Ischiropoulos, Francesco Lotti, Andrea Califano, Serge Przedborski .  2020.   Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow.. Nat Commun. 11 (1) :5579 ▶ Go to Pubmed
Elena Anghileri, Natalia Di Ianni, Rosina Paterra, Tiziana Langella, Junfei Zhao, Marica Eoli, Monica Patanè, Bianca Pollo, Valeria Cuccarini, Antonio Iavarone, Raul Rabadan, Gaetano Finocchiaro, Serena Pellegatta .  2021.   High tumor mutational burden and T-cell activation are associated with long-term response to anti-PD1 therapy in Lynch syndrome recurrent glioblastoma patient.. Cancer Immunol Immunother. 70 (3) :831-842 ▶ Go to Pubmed
Andrew Chiang, Jonathan Chang, Jiayao Wang, Dennis Vitkup .  2021.   Exons as units of phenotypic impact for truncating mutations in autism.. Mol Psychiatry. 26 (5) :1685-1695 ▶ Go to Pubmed
Peter Szabo, Pranay Dogra, Joshua Gray, Steven Wells, Thomas Connors, Stuart Weisberg, Izabela Krupska, Rei Matsumoto, Maya Poon, Emma Idzikowski, Sinead Morris, Chloé Pasin, Andrew Yates, Amy Ku, Michael Chait, Julia Davis-Porada, Jing Zhou, Matthew Steinle, Sean Mackay, Anjali Saqi, Matthew Baldwin, Peter Sims, Donna Farber .  2020.   Analysis of respiratory and systemic immune responses in COVID-19 reveals mechanisms of disease pathogenesis.. medRxiv : the preprint server for health sciences. ▶ Go to Pubmed
Daniela Cerezo-Wallis, Marta Contreras-Alcalde, Kevin Troulé, Xavier Catena, Cynthia Mucientes, Tonantzin Calvo, Estela Cañón, Cristina Tejedo, Paula Pennacchi, Sabrina Hogan, Peter Kölblinger, Héctor Tejero, Andrew Chen, Nuria Ibarz, Osvaldo Graña-Castro, Lola Martinez, Javier Muñoz, Pablo Ortiz-Romero, José Rodriguez-Peralto, Gonzalo Gómez-López, Fátima Al-Shahrour, Raul Rabadan, Mitchell Levesque, David Olmeda, María Soengas .  2020.   Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state.. Nat Med. 26 (12) :1865-1877 ▶ Go to Pubmed
Paola Nicoletti, Daniel Carr, Sarah Barrett, Laurence McEvoy, Peter Friedmann, Neil Shear, Matthew Nelson, Anca Chiriac, Natalia Blanca-López, José Cornejo-García, Francesco Gaeta, Alla Nakonechna, Maria Torres, Cristiano Caruso, Rocco Valluzzi, Aris Floratos, Yufeng Shen, Rebecca Pavlos, Elizabeth Phillips, Pascal Demoly, Antonino Romano, Miguel Blanca, Munir Pirmohamed .  2021.   Beta-lactam-induced immediate hypersensitivity reactions: A genome-wide association study of a deeply phenotyped cohort.. The Journal of allergy and clinical immunology. 147 (5) :1830-1837.e15 ▶ Go to Pubmed
Gaojianyong Wang, Dimitris Anastassiou .  2020.   Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis.. Sci Rep. 10 (1) :17199 ▶ Go to Pubmed
Gorka Lasso, Barry Honig, Sagi Shapira .  2021.   A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease.. Cell Syst. 12 (1) :82-91.e3 ▶ Go to Pubmed
Bo Liu, Zhaoqi Liu, Sisi Chen, Michelle Ki, Caroline Erickson, Jorge Reis-Filho, Benjamin Durham, Qing Chang, Elisa de Stanchina, Yiwei Sun, Raul Rabadan, Omar Abdel-Wahab, Sarat Chandarlapaty .  2021.   Mutant SF3B1 promotes AKT- and NF-κB-driven mammary tumorigenesis.. J Clin Invest. 131 (1) ▶ Go to Pubmed
Md Bhuyan, Itsik Pe'er, Sohel Rahman .  2021.   SICaRiO: short indel call filtering with boosting.. Brief Bioinform. 22 (4) ▶ Go to Pubmed
Xiaobin Wang, Junfei Zhao, Foon Wu-Baer, Zhengping Shao, Brian Lee, Olivia Cupo, Raul Rabadan, Jean Gautier, Richard Baer, Shan Zha .  2020.   CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining.. Proc Natl Acad Sci U S A. 117 (41) :25700-25711 ▶ Go to Pubmed
Huize Pan, Chenyi Xue, Benjamin Auerbach, Jiaxin Fan, Alexander Bashore, Jian Cui, Dina Yang, Sarah Trignano, Wen Liu, Jianting Shi, Chinyere Ihuegbu, Erin Bush, Jeremy Worley, Lukas Vlahos, Pasquale Laise, Robert Solomon, Edward Connolly, Andrea Califano, Peter Sims, Hanrui Zhang, Mingyao Li, Muredach Reilly .  2020.   Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human.. Circulation. 142 (21) :2060-2075 ▶ Go to Pubmed
Huize Pan, Chenyi Xue, Benjamin Auerbach, Jiaxin Fan, Alexander Bashore, Jian Cui, Dina Yang, Sarah Trignano, Wen Liu, Jianting Shi, Chinyere Ihuegbu, Erin Bush, Jeremy Worley, Lukas Vlahos, Pasquale Laise, Robert Solomon, Edward Connolly, Andrea Califano, Peter Sims, Hanrui Zhang, Mingyao Li, Muredach Reilly .  2020.   Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human.. Circulation. 142 (21) :2060-2075 ▶ Go to Pubmed
Jennifer Diaz, Mehmet Ahsen, Thomas Schaffter, Xintong Chen, Ronald Realubit, Charles Karan, Andrea Califano, Bojan Losic, Gustavo Stolovitzky .  2020.   The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies.. Elife. 9 ▶ Go to Pubmed
Cai Bowen, Maho Shibata, Hailan Zhang, Sarah Bergren, Michael Shen, Edward Gelmann .  2020.   CRISPR/Cas9-Mediated Point Mutation in Prolongs Protein Half-Life and Reverses Effects Allelic Loss.. Cancer Res. 80 (21) :4805-4814 ▶ Go to Pubmed
Joshua Broyde, David Simpson, Diana Murray, Evan Paull, Brennan Chu, Somnath Tagore, Sunny Jones, Aaron Griffin, Federico Giorgi, Alexander Lachmann, Peter Jackson, Alejandro Sweet-Cordero, Barry Honig, Andrea Califano .  2021.   Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.. Nat Biotechnol. 39 (2) :215-224 ▶ Go to Pubmed
Sung Yim, Nathan Johns, Vincent Noireaux, Harris Wang .  2020.   Protecting Linear DNA Templates in Cell-Free Expression Systems from Diverse Bacteria.. ACS synthetic biology. 9 (10) :2851-2855 ▶ Go to Pubmed
Laura Crowley, Francesco Cambuli, Luis Aparicio, Maho Shibata, Brian Robinson, Shouhong Xuan, Weiping Li, Hanina Hibshoosh, Massimo Loda, Raul Rabadan, Michael Shen .  2020.   A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors.. Elife. 9 ▶ Go to Pubmed
An-Phi Nguyen, Paola Nicoletti, Damien Arnol, Andrea Califano, María Martínez .  2020.   Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN.. Front Bioeng Biotechnol. 8 :798 ▶ Go to Pubmed
Benjamin Hobson, Linghao Kong, Erik Hartwick, Ruben Gonzalez, Peter Sims .  2020.   Elongation inhibitors do not prevent the release of puromycylated nascent polypeptide chains from ribosomes.. eLife. 9 ▶ Go to Pubmed
Barbara Oldrini, Nuria Vaquero-Siguero, Quanhua Mu, Paula Kroon, Ying Zhang, Marcos Galán-Ganga, Zhaoshi Bao, Zheng Wang, Hanjie Liu, Jason Sa, Junfei Zhao, Hoon Kim, Sandra Rodriguez-Perales, Do-Hyun Nam, Roel Verhaak, Raul Rabadan, Tao Jiang, Jiguang Wang, Massimo Squatrito .  2020.   MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas.. Nat Commun. 11 (1) :3883 ▶ Go to Pubmed
Raul Rabadan, Yamina Mohamedi, Udi Rubin, Tim Chu, Adam Alghalith, Oliver Elliott, Luis Arnes, Santiago Cal, Álvaro Obaya, Arnold Levine, Pablo Camara .  2020.   Identification of relevant genetic alterations in cancer using topological data analysis.. Nat Commun. 11 (1) :3808 ▶ Go to Pubmed
Claudia Capdevila, Ruben Calderon, Erin Bush, Kismet Sheldon-Collins, Peter Sims, Kelley Yan .  2020.   Single-Cell Transcriptional Profiling of the Intestinal Epithelium.. Methods in molecular biology (Clifton, N.J.). 2171 :129-153 ▶ Go to Pubmed
Daniel Freedberg, Megan Messina, Elissa Lynch, Monika Tess, Elizabeth Miracle, David Chong, Romina Wahab, Julian Abrams, Harris Wang, Christian Munck .  2020.   Impact of Fiber-Based Enteral Nutrition on the Gut Microbiome of ICU Patients Receiving Broad-Spectrum Antibiotics: A Randomized Pilot Trial.. Critical care explorations. 2 (6) :e0135 ▶ Go to Pubmed
Hsing-I Ho, Jennifer Fang, Jacky Cheung, Harris Wang .  2020.   Programmable CRISPR-Cas transcriptional activation in bacteria.. Molecular systems biology. 16 (7) :e9427 ▶ Go to Pubmed
Christian Munck, Ravi Sheth, Edward Cuaresma, Jessica Weidler, Stephania Stump, Philip Zachariah, David Chong, Anne-Catrin Uhlemann, Julian Abrams, Harris Wang, Daniel Freedberg .  2020.   The effect of short-course antibiotics on the resistance profile of colonizing gut bacteria in the ICU: a prospective cohort study.. Critical care (London, England). 24 (1) :404 ▶ Go to Pubmed
Luigi Scotto, Cristina Kinahan, Beatrice Casadei, Michael Mangone, Eugene Douglass, Vundavalli Murty V, Enrica Marchi, Helen Ma, Changchun George, Francesca Montanari, Andrea Califano, Owen O'Connor .  2020.   Generation of pralatrexate resistant T-cell lymphoma lines reveals two patterns of acquired drug resistance that is overcome with epigenetic modifiers.. Genes Chromosomes Cancer. 59 (11) :639-651 ▶ Go to Pubmed
Michael Stokes, Jonnell Small, Alessandro Vasciaveo, Kenichi Shimada, Tal Hirschhorn, Andrea Califano, Brent Stockwell .  2020.   Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation.. Sci Rep. 10 (1) :10748 ▶ Go to Pubmed
Dogukan Mizrak, Sumru Bayin, Jinzhou Yuan, Zhouzerui Liu, Radu Suciu, Micah Niphakis, Nhi Ngo, Kenneth Lum, Benjamin Cravatt, Alexandra Joyner, Peter Sims .  2020.   Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator.. Cell reports. 31 (12) :107805 ▶ Go to Pubmed
Danilo Fiore, Luca Cappelli, Paul Zumbo, Jude Phillips, Zhaoqi Liu, Shuhua Cheng, Liron Yoffe, Paola Ghione, Federica Di Maggio, Ahmet Dogan, Inna Khodos, Elisa de Stanchina, Joseph Casano, Clarisse Kayembe, Wayne Tam, Doron Betel, Robin Foa', Leandro Cerchietti, Raul Rabadan, Steven Horwitz, David Weinstock, Giorgio Inghirami .  2020.   A Novel JAK1 Mutant Breast Implant-Associated Anaplastic Large Cell Lymphoma Patient-Derived Xenograft Fostering Pre-Clinical Discoveries.. Cancers (Basel). 12 (6) ▶ Go to Pubmed
Orr Comay, Oz Ben Yehuda, Dubi Benyamini, Racheli Schwartz-Tzachor, Israel Pe'er, Tal Melochna, Guy Pe'er .  2020.   Analysis of monitoring data where butterflies fly year-round.. Ecol Appl. 30 (8) :e02196 ▶ Go to Pubmed
Mythily Ganapathi, Loukas Argyriou, Francisco Martínez-Azorín, Susanne Morlot, Gökhan Yigit, Teresa Lee, Bernd Auber, Alexander von Gise, Donald Petrey, Holger Thiele, Lukas Cyganek, María Sabater-Molina, Priyanka Ahimaz, Juan Cabezas-Herrera, Moisés Sorlí-García, Arne Zibat, Markus Siegelin, Peter Burfeind, Christie Buchovecky, Gerd Hasenfuss, Barry Honig, Yun Li, Alejandro Iglesias, Bernd Wollnik .  2020.   Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenesis.. Hum Genet. 139 (11) :1443-1454 ▶ Go to Pubmed
Antonio Gomes, Nathan Johns, Anthony Yang, Florencia Velez-Cortes, Christopher Smillie, Mark Smith, Eric Alm, Harris Wang .  2020.   Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria.. The ISME journal. 14 (9) :2347-2357 ▶ Go to Pubmed
Pasquale Laise, Gideon Bosker, Xiaoyun Sun, Yao Shen, Eugene Douglass, Charles Karan, Ronald Realubit, Sergey Pampou, Andrea Califano, Mariano Alvarez .  2020.   The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States.. bioRxiv. ▶ Go to Pubmed
Juan Patiño-Galindo, Ioan Filip, Ratul Chowdhury, Costas Maranas, Peter Sorger, Mohammed AlQuraishi, Raul Rabadan .  2021.   Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2.. bioRxiv. ▶ Go to Pubmed
Sydney Blattman, Wenyan Jiang, Panos Oikonomou, Saeed Tavazoie .  2020.   Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing.. Nat Microbiol. 5 (10) :1192-1201 ▶ Go to Pubmed
Joshua Kane, Junfei Zhao, Takashi Tsujiuchi, Brice Laffleur, Víctor Arrieta, Aayushi Mahajan, Ganesh Rao, Angeliki Mela, Crismita Dmello, Li Chen, Daniel Zhang, Edgar González-Buendia, Catalina Lee-Chang, Ting Xiao, Gerson Rothschild, Uttiya Basu, Craig Horbinski, Maciej Lesniak, Amy Heimberger, Raul Rabadan, Peter Canoll, Adam Sonabend .  2020.   CD8 T-cell-Mediated Immunoediting Influences Genomic Evolution and Immune Evasion in Murine Gliomas.. Clin Cancer Res. 26 (16) :4390-4401 ▶ Go to Pubmed
Marta Galanti, Devon Comito, Chanel Ligon, Benjamin Lane, Nelsa Matienzo, Sadiat Ibrahim, Atinuke Shittu, Eudosie Tagne, Ruthie Birger, Minhaz Ud-Dean, Ioan Filip, Haruka Morita, Raul Rabadan, Simon Anthony, Greg Freyer, Peter Dayan, Bo Shopsin, Jeffrey Shaman .  2020.   Active surveillance documents rates of clinical care seeking due to respiratory illness.. Influenza Other Respir Viruses. 14 (5) :499-506 ▶ Go to Pubmed
Barry Honig, Lawrence Shapiro .  2020.   Adhesion Protein Structure, Molecular Affinities, and Principles of Cell-Cell Recognition.. Cell. 181 (3) :520-535 ▶ Go to Pubmed
Alina Sergeeva, Phinikoula Katsamba, Filip Cosmanescu, Joshua Brewer, Goran Ahlsen, Seetha Mannepalli, Lawrence Shapiro, Barry Honig .  2020.   DIP/Dpr interactions and the evolutionary design of specificity in protein families.. Nat Commun. 11 (1) :2125 ▶ Go to Pubmed
Zhaoqi Liu, Jian Zhang, Yiwei Sun, Tomin Perea-Chamblee, James Manley, Raul Rabadan .  2020.   Pan-cancer analysis identifies mutations in that recapitulate mutant SF3B1 splicing dysregulation.. Proc Natl Acad Sci U S A. 117 (19) :10305-10312 ▶ Go to Pubmed
Qin Yuan, Yuan He, Pan-Yin Xiang, Sheng-Peng Wang, Zheng-Wen Cao, Tao Gou, Miao-Miao Shen, Li Zhao, Wen Qin, Ren-You Gan, Ding-Tao Wu .  2020.   Effects of simulated saliva-gastrointestinal digestion on the physicochemical properties and bioactivities of okra polysaccharides.. Carbohydr Polym. 238 :116183 ▶ Go to Pubmed
Brian Ji, Ravi Sheth, Purushottam Dixit, Konstantine Tchourine, Dennis Vitkup .  2020.   Macroecological dynamics of gut microbiota.. Nat Microbiol. 5 (5) :768-775 ▶ Go to Pubmed
Zhaoqi Liu, Akihide Yoshimi, Jiguang Wang, Hana Cho, Stanley Lee, Michelle Ki, Lillian Bitner, Timothy Chu, Harshal Shah, Bo Liu, Anthony Mato, Peter Ruvolo, Giulia Fabbri, Laura Pasqualucci, Omar Abdel-Wahab, Raul Rabadan .  2020.   Mutations in the RNA Splicing Factor SF3B1 Promote Tumorigenesis through MYC Stabilization.. Cancer Discov. 10 (6) :806-821 ▶ Go to Pubmed
Rose Orenbuch, Ioan Filip, Raul Rabadan .  2020.   HLA Typing from RNA Sequencing and Applications to Cancer.. Methods Mol Biol. 2120 :71-92 ▶ Go to Pubmed
Wenyan Jiang, Panos Oikonomou, Saeed Tavazoie .  2020.   Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity.. Cell. 180 (5) :1002-1017.e31 ▶ Go to Pubmed
Kaiyi Zhu, Dimitris Anastassiou .  2020.   2DImpute: imputation in single-cell RNA-seq data from correlations in two dimensions.. Bioinformatics. 36 (11) :3588-3589 ▶ Go to Pubmed
Indrajyoti Indra, Regina Troyanovsky, Lawrence Shapiro, Barry Honig, Sergey Troyanovsky .  2020.   Sensing Actin Dynamics through Adherens Junctions.. Cell Rep. 30 (8) :2820-2833.e3 ▶ Go to Pubmed
Oliver Harrison, Julia Brasch, Phinikoula Katsamba, Goran Ahlsen, Alex Noble, Hanbin Dan, Rosemary Sampogna V, Clinton Potter, Bridget Carragher, Barry Honig, Lawrence Shapiro .  2020.   Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins.. Cell Rep. 30 (8) :2655-2671.e7 ▶ Go to Pubmed
Oyetunji Ogundijo, Kaiyi Zhu, Xiaodong Wang, Dimitris Anastassiou .  2021.   Characterizing Intra-Tumor Heterogeneity From Somatic Mutations Without Copy-Neutral Assumption.. IEEE/ACM Trans Comput Biol Bioinform. 18 (6) :2271-2280 ▶ Go to Pubmed
Eugenia Lyashenko, Mario Niepel, Purushottam Dixit, Sang Lim, Peter Sorger, Dennis Vitkup .  2020.   Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks.. Elife. 9 ▶ Go to Pubmed
K Öberg, A Califano, J Strosberg, S Ma, U Pape, L Bodei, G Kaltsas, C Toumpanakis, J Goldenring, A Frilling, S Paulson .  2020.   A meta-analysis of the accuracy of a neuroendocrine tumor mRNA genomic biomarker (NETest) in blood.. Ann Oncol. 31 (2) :202-212 ▶ Go to Pubmed
Robyn Gartrell-Corrado, Andrew Chen, Emanuelle Rizk, Douglas Marks, Margaret Bogardus, Thomas Hart, Andrew Silverman, Claire -Audrey Y Bayan, Grace Finkel, Luke Barker, Kimberly Komatsubara, Richard Carvajal, Basil Horst, Rui Chang, Anthea Monod, Raul Rabadan, Yvonne Saenger .  2020.   Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma.. Cancer Res. 80 (5) :1078-1087 ▶ Go to Pubmed
Christian Munck, Ravi Sheth, Daniel Freedberg, Harris Wang .  2020.   Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR-Cas spacer acquisition platform.. Nature communications. 11 (1) :95 ▶ Go to Pubmed
Yiming Huang, Ravi Sheth, Andrew Kaufman, Harris Wang .  2020.   Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics.. Nucleic acids research. 48 (4) :e20 ▶ Go to Pubmed
Purushottam Dixit, Eugenia Lyashenko, Mario Niepel, Dennis Vitkup .  2020.   Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks.. Cell Syst. 10 (2) :204-212.e8 ▶ Go to Pubmed
Rachael Vaubel, Shulan Tian, Dioval Remonde, Mark Schroeder, Ann Mladek, Gaspar Kitange, Alissa Caron, Thomas Kollmeyer, Rebecca Grove, Sen Peng, Brett Carlson, Daniel Ma, Gobinda Sarkar, Lisa Evers, Paul Decker, Huihuang Yan, Harshil Dhruv, Michael Berens, Qianghu Wang, Bianca Marin, Eric Klee, Andrea Califano, Daniel LaChance, Jeanette Eckel-Passow, Roel Verhaak, Erik Sulman, Terry Burns, Fredrick Meyer, Brian O'Neill, Nhan Tran, Caterina Giannini, Robert Jenkins, Ian Parney, Jann Sarkaria .  2020.   Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma.. Clin Cancer Res. 26 (5) :1094-1104 ▶ Go to Pubmed
Regina Martuscello, Chloë Kerridge, Debotri Chatterjee, Whitney Hartstone, Sheng-Han Kuo, Peter Sims, Elan Louis, Phyllis Faust .  2020.   Gene expression analysis of the cerebellar cortex in essential tremor.. Neuroscience letters. 721 :134540 ▶ Go to Pubmed
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