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2020

2020 Publications

Juan Arriaga, Sukanya Panja, Mohammed Alshalalfa, Junfei Zhao, Min Zou, Arianna Giacobbe, Chioma Madubata, Jaime Kim, Antonio Rodriguez, Ilsa Coleman, Renu Virk, Hanina Hibshoosh, Onur Ertunc, Büşra Ozbek, Julia Fountain, Jeffrey Karnes, Jun Luo, Emmanuel Antonarakis, Peter Nelson, Felix Feng, Mark Rubin, Angelo De Marzo, Raul Rabadan, Peter Sims, Antonina Mitrofanova, Cory Abate-Shen .  2020.   A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance.. Nat Cancer. 1 (11) :1082-1096 ▶ Go to Pubmed
Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie Brown, Juan Patiño-Galindo, Timothy Chu, Aidan Quinn, Thomas Gunning, Laura Belver, Alberto Ambesi-Impiombato, Valeria Tosello, Zhengqiang Wang, Maria Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Milagros Balbin, Concepción Nicolas, Julie Gastier-Foster, Meenakshi Devidas, Mignon Loh, Elisabeth Paietta, Martin Tallman, Jacob Rowe, Mark Litzow, Mark Minden, Jules Meijerink, Raul Rabadan, Adolfo Ferrando .  2020.   Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia.. Nat Cancer. 1 (11) :1113-1127 ▶ 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
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
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
Jamie Yang, Saeed Tavazoie .  2020.   Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress.. PLoS One. 15 (11) :e0239528 ▶ 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
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
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
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
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
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
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
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
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
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
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
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
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