Selected
Publications
Our main scientific interests lie in modeling and understanding the dynamics of biological
systems through the lens of genomics. Our work focuses on three distinct topics:
Cancer, Infectious Diseases, and Electronic Health Records.
This page contains links to Selected Publications. We also have a full Publications Archive.
“ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma.”
AUTHORS: Víctor A. Arrieta*, Andrew X. Chen*, J. Robert Kane, Seong Jae Kang, Cynthia Kassab, Crismita Dmello, Junfei Zhao, Kirsten B. Burdett, Pavan S. Upadhyayula, Catalina Lee-Chang, Joseph Shilati, Dinesh Jaishankar, Li Chen, Andrew Gould, Daniel Zhang, Jinzhou Yuan, Wenting Zhao, Xiaoyang Ling, Jared K. Burks, Brice Laffleur, Christina Amidei, Jeffrey N. Bruce, Rimas V. Lukas, Jonathan T. Yamaguchi, David Cieremans, Gerson Rothschild, Uttiya Basu, Matthew McCord, Daniel J. Brat, Hui Zhang, Lee A. D. Cooper, Bin Zhang, Peter Sims, Tim F. Cloughesy, Robert Prins, Peter Canoll, Roger Stupp, Amy B. Heimberger, Craig Horbinski, Fabio M. Iwamoto+, Raul Rabadan+, Adam M. Sonabend+.
*These authors have contributed equally to this work. +Corresponding authors.
Nature Cancer. 2021 November 29. doi:0.1038/s43018-021-00260-2
“Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2.”
AUTHORS: Juan Ángel Patiño-Galindo, Ioan Filip, Ratul Chowdhury, Costas D. Maranas, Peter K. Sorger, Mohammed AlQuraishi, Raul Rabadan+.
*These authors have contributed equally to this work. +Corresponding authors.
"A Phase I Study of the Combination of Pexidartinib and Sirolimus to Target Tumor-Associated Macrophages in Unresectable Sarcoma and Malignant Peripheral Nerve Sheath Tumors."
AUTHORS: Gulam A. Manji, Brian A. Van Tine, Shing M. Lee, Alexander G. Raufi, Ilenia Pellicciotta, Angela C. Hirbe, Jaya Pradhan, Andrew Chen, Raul Rabadan, Gary K. Schwartz.
American Association for Cancer Research. 2021 Sept 7. doi: 10.1158/1078-0432.CCR-21-1779
“Transcriptional control of CBX5 by the RNA-binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia”
AUTHORS: Camila Prieto, Diu T. T. Nguyen, Zhaoqi Liu, Justin Wheat, Alexendar Perez, Saroj Gourkanti, Timothy Chou, Ersilia Barin, Anthony Velleca, Thomas Rohwetter, Arthur Chow, James Taggart, Angela M. Savino, Katerina Hoskova, Meera Dhodapkar, Alexandra Schurer, Trevor S. Barlowe, Ly P. Vu, Christina Leslie, Ulrich Steidl, Raul Rabadan, Michael G. Kharas.
“Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma”
AUTHORS: Marco Fangazio, Erik Ladewig, Karen Gomez, Laura Garcia-Ibanez, Rahul Kumar, Julie Teruya-Feldstein, Davide Rossi, Ioan Filip, Qiang Pan-Hammarström, Giorgio Inghirami, Renzo Boldorini, German Ott, Annette M. Staiger, Björn Chapuy, Gianluca Gaidano, Govind Bhagat, Katia Basso, Raul Rabadan, Laura Pasqualucci, Riccardo Dalla-Favera.
Proc Natl Acad Sci U S A. 2021 June 1. doi: 10.1073/pnas.2104504118
“Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker”
AUTHORS: Andrew X. Chen, Robyn D. Gartrell, Junfei Zhao, Pavan S. Upadhyayula, Wenting Zhao, Jinzhou Yuan, Hanna E. Minns, Athanassios Dovas, Jeffrey N. Bruce, Anna Lasorella, Antonio Iavarone, Peter Canoll, Peter A. Sims, Raul Rabadan.
“Pregnancy Specific Glycoproteins: A Possible Mediator of Immune Tolerance of Cancers”
AUTHORS: Junfei Zhao, Raul Rabadan, Arnold J. Levine.
“Global Patterns Of Recombination Across Human Viruses”
AUTHORS: Juan Ángel Patiño-Galindo, Ioan Filip, Raul Rabadan.
Molecular Biology and Evolution. 2021 Feb 15. doi: 10.1093/molbev/msab046
“Computing The Role Of Alternative Splicing In Cancer”
AUTHORS: Zhaoqi Liu, Raul Rabadan.
Trends In Cancer. 2021 Jan 23. doi: 10.1016/j.trecan.2020.12.015
“Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia”
AUTHORS: 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+.
Nature Cancer. 2020 Oct 19. doi: 10.1038/s43018-020-00124-1.
“A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors”
AUTHORS: 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.
“Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis.”
AUTHORS: 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.
Nature Commun. 2020 July 30. doi: 10.1038/s41467-020-17659-7.
“Topological Data Analysis for Genomics and Evolution: Topology in Biology.”
AUTHORS: Raul Rabadan and Andrew J. Blumberg.
“A Random Matrix Theory Approach to Denoise Single-Cell Data”
AUTHORS: Luis Aparicio, Mykola Bordyuh, Andrew Blumberg, Raul Rabadan.