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:
Illuminating the Noncoding Genome in Cancer using Artificial Intelligence
Illuminating the Noncoding Genome in Cancer using Artificial Intelligence
Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer
Meta-analyses of mouse and human prostate single-cell transcriptomes reveal widespread epithelial plasticity in tissue regression, regeneration, and cancer
A foundation model of transcription across human cell types
A foundation model of transcription across human cell types
Understanding variants of unknown significance: the computational frontier
Understanding variants of unknown significance: the computational frontier
Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
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.”
 

 

A foundation model of transcription across human cell types
THE RABADAN LAB THE RABADAN LAB

A foundation model of transcription across human cell types

AUTHORS: Xi Fu, Shentong Mo, Alejandro Buendia, Anouchka P. Laurent, Anqi Shao, Maria del Mar Alvarez-Torres, Tianji Yu, Jimin Tan, Jiayu Su, Romella Sagatelian, Adolfo A. Ferrando, Alberto Ciccia, Yanyan Lan, David M. Owens, Teresa Palomero, Eric P. Xing, Raul Rabadan.

*These authors have contributed equally to this work. +Corresponding authors.

https://www.nature.com/articles/s41586-024-08391-z

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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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