2020 Publications
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Double Empirical Bayes Testing
Wesley Tansey, Yixin Wang, Raul Rabadan, David Blei.

High Tumor Mutational Burden and T-cell Activation are Associated with Long-Term Response to Anti-PD1 Therapy in Lynch Syndrome Recurrent Glioblastoma Patient
Elena Anghileri, Natalia Di Ianni, Rosina Paterra, Tiziana Langella, Junfei Zhao, Marica Eoli, Monica Patane, Bianca Pollo, Valeria Cuccarini, Antonio Iavarone, Raul Rabadan, Gaetano Finocchiaro, Serena Pellegatta.

Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia
Koichi Oshima, Junfei Zhao, Pablo Pérez-Durán, Jessie A. Brown, Juan Angel Patiño-Galindo, Timothy Chu, Aidan Quinn, Thomas Gunning, Laura Belver, Alberto Ambesi-Impiombato, Valeria Tosello, Zhengqiang Wang, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Milagros Balbin, Concepcion Nicolas, Julie M. Gastier-Foster, Meenakshi Devidas, Mignon L. Loh, Elisabeth Paietta, Martin S. Tallman, Jacob M. Rowe, Mark Litzow, Mark D. Minden, Jules Meijerink, Raul Rabadan+, Adolfo Ferrando+.
*These authors have contributed equally to this work. +Corresponding authors.

Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state
Daniela Cerezo-Wallis, Marta Contreras-Alcalde, Kevin Troulé, Xavier Catena, Cynthia Mucientes, Tonantzin G. Calvo, Estela Cañón, Cristina Tejedo, Paula C. Pennacchi, Sabrina Hogan, Peter Kölblinger, Héctor Tejero, Andrew X. Chen, Nuria Ibarz, Osvaldo Graña-Castro, Lola Martinez, Javier Muñoz, Pablo Ortiz-Romero, José L. Rodriguez-Peralto, Gonzalo Gómez-López, Fátima Al-Shahrour, Raúl Rabadán, Mitchell P. Levesque, David Olmeda, María S. Soengas.

A MYC and RAS co-activation signature in localized prostate cancer drives bone metastasis and castration resistance
Juan M. Arriaga, Sukanya Panja, Mohammed Alshalalfa, Junfei Zhao, Min Zou, Arianna Giacobbe, Chioma J. Madubata, Jaime Yeji Kim, Antonio Rodriguez, Ilsa Coleman, Renu K. Virk, Hanina Hibshoosh, Onur Ertunc, Büşra Ozbek, Julia Fountain, R. Jeffrey Karnes, Jun Luo, Emmanuel S. Antonarakis, Peter S. Nelson, Felix Y. Feng, Mark A. Rubin, Angelo M. De Marzo, Raul Rabadan, Peter A. Sims, Antonina Mitrofanova, Cory Abate-Shen.

A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors
Laura Crowley, Francesco Cambuli, Luis Aparicio, Maho Shibata, Brian D Robinson, Shouhong Xuan, Weiping Li, Hanina Hibshoosh, Massimo Loda, Raul Rabadan+, Michael M Shen+.
*These authors have contributed equally to this work. +Corresponding authors.

Mutant SF3B1 promotes AKT and NF-kB driven mammary tumorigenesis
Bo Liu, Zhaoqi Liu, Sisi Chen, Michelle Ki, Caroline Erickson, Jorge S. Reis-Filho, Benjamin H. Durham, Qing Chang, Elisa de Stanchina, Yiwei Sun, Raul Rabadan, Omar Abdel-Wahab, Sarat Chandarlapaty.

CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining
Xiaobin S. Wang, Junfei Zhao, Foon Wu-Baer, Zhengping Shao, Brian J. Lee, Olivia M. Cupo, Raul Rabadan, Jean Gautier, Richard Baer, Shan Zha.

A Novel JAK1 Mutant Breast Implant-Associated Anaplastic Large Cell Lymphoma Patient-Derived Xenograft Fostering Pre-Clinical Discoveries
Danilo Fiore, Luca Vincenzo Cappelli, Paul Zumbo, Jude M. 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 M. Weinstock, Giorgio Inghirami.

A Random Matrix Theory Approach to Denoise Single-Cell Data
Luis Aparicio, Mykola Bordyuh, Andrew Blumberg, Raul Rabadan.

Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway.
Zhaoqi Liu, Ioan Filip, Karen Gomez, Dewaldt Engelbrecht, Shabnum Meer, Pooja N. Lalloo, Pareen Patel, Yvonne Perner, Junfei Zhao, Jiguang Wang, Laura Pasqualucci, Raul Rabadan and Pascale Willem.

Understanding Coronavirus (Understanding Life)
Raul Rabadan.

Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation.
Liu Z, Zhang J, Sun Y, Perea-Chamblee TE, Manley JL, Rabadan R.

Mutations in the RNA splicing factor SF3B1 promote tumorigenesis through MYC stabilization.
Liu Z, Yoshimi A, Wang J, Cho H, Chun-Wei Lee S, Ki M, Bitner L, Chu T, Shah H, Liu B, Mato AR, Ruvolo P, Fabbri G, Pasqualucci L, Abdel-Wahab O, Rabadan R.

MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas.
Barbara Oldrini, Nuria Vaquero-Siguero, Quanhua Mu, Paula Kroon, Ying Zhang, Marcos Galán-Ganga, Zhaoshi Bao, Zheng Wang, Hanjie Liu, Jason K Sa, Junfei Zhao, Hoon Kim, Sandra Rodriguez-Perales, Do-Hyun Nam, Roel GW Verhaak, Raul Rabadan, Tao Jiang, Jiguang Wang, Massimo Squatrito.

HLA Typing from RNA Sequencing and Applications to Cancer.
Rose Orenbuch, Ioan Filip, Raul Rabadan+.
*These authors have contributed equally to this work. +Corresponding authors.

Linking Transcriptomic and Imaging Data Defines Features of a Favorable Tumor Immune Microenvironment and Identifies a Combination Biomarker for Primary Melanoma.
Gartrell-Corrado RD, Chen AX, Rizk EM, Marks DK, Bogardus MH, Hart TD, Silverman AM, Bayan CY, Finkel GG, Barker LW, Komatsubara KM, Carvajal RD, Horst BA, Chang R, Monod A, Rabadan R, Saenger YM.

MREC: a fast and versatile framework for aligning and matching point clouds with applications to single cell molecular data.
Andrew J. Blumberg, Mathieu Carriere, Michael A. Mandell, Raul Rabadan, Soledad Villar.

Abstract P3-03-01: Double PIK3CA mutations in cis drive oncogene addiction and enhance sensitivity to PI3K alpha inhibitors in breast cancer.
Neil Vasan, Pedram Razavi, Jared L Johnson, Hong Shao, Timothy Wilson, Frauke Schimmoller, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Ting-Yu Lin, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T Chang, Barry S. Taylor, Maura N. Dickler, Komal Jhaveri, Sarat Chandarlapaty, Raul Rabadan, Ed Reznik, Melissa L Smith, Robert Sebra, Lori Friedman, Lewis C Cantley, Maurizio Scaltriti and José Baselga.

Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2.
Juan Ángel Patiño-Galindo, Ioan Filip, Mohammed AlQuraishi, Raul Rabadan+.
*These authors have contributed equally to this work. +Corresponding authors.

Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis.
Raúl Rabadán+, Yamina Mohamedi, Udi Rubin, Tim Chu, Oliver Elliott, Luis Arnés, Santiago Cal, Álvaro J. Obaya, Arnold J. Levine+, Pablo G. Cámara+.
*These authors have contributed equally to this work. +Corresponding authors.