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.
Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people.
AUTHORS: Marta Galanti, Eudosie Tagne, Atinuke Shittu, Oliver Elliot, Tomin Perea-Chamblee, Sanjay Natesan, Daniel Scholes Rosenbloom, Jeffrey Shaman, Raul Rabadan.
*These authors have contributed equally to this work. +Corresponding authors.
PLOS Biology. 2024 January 18. doi.org/10.1371/journal.pbio.3002089
GET: a foundation model of transcription across human cell types.
AUTHORS: Xi Fu, Shentong Mo, Anqi Shao, Anouchka Laurent, Alejandro Buendia, Adolfo A Ferrando, Alberto Ciccia, Yanyan Lan, Teresa Palomero, David M Owens, Eric P Xing, Raul Rabadan.
*These authors have contributed equally to this work. +Corresponding authors.
Disentangling interpretable factors with supervised independent subspace principal component analysis
AUTHORS: Jiayu Su, David A Knowles, Raul Rabadan.
*These authors have contributed equally to this work. +Corresponding authors.
TBD
Pervasiveness of HLA allele-specific expression loss across tumor types.
AUTHORS: 1. Ioan Philip, Anqi Wang, Oleksandr Kravets, Rose Orenbuch, Junfei Zhao, Tomin E. Perea- Chamblee, Gulam A. Manji, Evangelina López de Maturana, Nuria Malats, Kenneth P. Olive, Raul Rabadan.
*These authors have contributed equally to this work. +Corresponding authors.
Genome Medicine. 2023 January 9. doi.org/10.1186/s13073-023-01154-x
Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data.
AUTHORS: Jiayu Su, Jean-Baptiste Reynier, Xi Fu, Guojie Zhong, Jiahao Jiang, Rydberg Supo Escalante, Yiping Wang, Luis Aparicio, Benjamin Izar, David A Knowles, Raul Rabadan.
*These authors have contributed equally to this work. +Corresponding authors.
Genome Biology. 2023 December 18. doi.org/10.1186/s13059-023-03138-x
Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma
AUTHORS: Luis Arnes, Zhaoqi Liu, Jiguang Wang, Carlo Maurer, Irina Sagalovskiy, Marta Sanchez-Martin, Nikhil Bommakanti, Diana C Garofalo, Dina A Balderes, Lori Sussel, Kenneth P Olive, Rabadan R
*These authors have contributed equally to this work. +Corresponding authors.
“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