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.

 
SELECTED PUBLICATIONS:
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.
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.
GET: a foundation model of transcription across human cell types.
GET: a foundation model of transcription across human cell types.
Disentangling interpretable factors with supervised independent subspace principal component analysis
Disentangling interpretable factors with supervised independent subspace principal component analysis
Pervasiveness of HLA allele-specific expression loss across tumor types.
Pervasiveness of HLA allele-specific expression loss across tumor types.
Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data.
Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data.
Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma
Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma
“ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma.”
“ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma.”
“A persistent look at how tumours evade therapy.”
“A persistent look at how tumours evade therapy.”
“Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2.”
“Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2.”
“Transcriptional control of CBX5 by the RNA-binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia”
“Transcriptional control of CBX5 by the RNA-binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia”
“Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma”
“Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma”
“Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker”
“Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker”
“Pregnancy Specific Glycoproteins: A Possible Mediator of Immune Tolerance of Cancers”
“Pregnancy Specific Glycoproteins: A Possible Mediator of Immune Tolerance of Cancers”
“Global Patterns Of Recombination Across Human Viruses”
“Global Patterns Of Recombination Across Human Viruses”
“Computing The Role Of Alternative Splicing In Cancer”
“Computing The Role Of Alternative Splicing In Cancer”
“Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia”
“Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia”
“A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors”
“A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors”
“Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis.”
“Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis.”
“Topological Data Analysis for Genomics and Evolution: Topology in Biology.”
“Topological Data Analysis for Genomics and Evolution: Topology in Biology.”
“A Random Matrix Theory Approach to Denoise Single-Cell Data”
“A Random Matrix Theory Approach to Denoise Single-Cell Data”
“Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway.”
“Genomic Characterization of HIV-Associated Plasmablastic Lymphoma Identifies Pervasive Mutations in the JAK–STAT Pathway.”
“Understanding Coronavirus (Understanding Life)”
“Understanding Coronavirus (Understanding Life)”
“Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation.”
“Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation.”
“Mutations in the RNA splicing factor SF3B1 promote tumorigenesis through MYC stabilization.”
“Mutations in the RNA splicing factor SF3B1 promote tumorigenesis through MYC stabilization.”
“HLA Typing from RNA Sequencing and Applications to Cancer.”
“HLA Typing from RNA Sequencing and Applications to Cancer.”
“arcasHLA: high resolution HLA typing from RNAseq.”
“arcasHLA: high resolution HLA typing from RNAseq.”
“Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.”
“Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma.”
“Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy.”
“Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy.”
“Black Box FDR.”
“Black Box FDR.”
“Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma.”
“Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma.”
 

 

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.
THE RABADAN LAB THE RABADAN LAB

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

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Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma
THE RABADAN LAB THE RABADAN LAB

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.

Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma - March 01, 2019

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“ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma.”
THE RABADAN LAB THE RABADAN LAB

“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

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“Transcriptional control of CBX5 by the RNA-binding proteins RBMX and RBMXL1 maintains chromatin state in myeloid leukemia”
THE RABADAN LAB THE RABADAN LAB

“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.

Nature Cancer. 2021 July 5. doi: 10.1038/s43018-021-00220-w

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“Genetic mechanisms of HLA-I loss and immune escape in diffuse large B cell lymphoma”
THE RABADAN LAB THE RABADAN LAB

“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

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