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.”
 

 

“Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia.”
THE RABADAN LAB THE RABADAN LAB

“Mutational landscape, clonal evolution patterns, and role of RAS mutations in relapsed acute lymphoblastic leukemia.”

AUTHORS: Koichi Oshima*, Hossein Khiabanian*, Ana C. da Silva-Almeida, Gannie Tzoneva, Francesco Abate, Alberto Ambesi-Impiombato, Marta Sanchez-Martin, Zachary Carpenter, Alex Penson, Arianne Perez-Garcia, Cornelia Eckert, Concepción Nicolas, Milagros Balbin, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Julie M. Gastier-Foster, Meenakshi Devidas, Mignon L. Loh, Renate Kirschner-Schwabe, Teresa Palomero+, Raul Rabadan+, and Adolfo A. Ferrando+.

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

PNAS. 2016 August. doi: 10.1073/pnas.1608420113.

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“RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity.”
THE RABADAN LAB THE RABADAN LAB

“RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity.”

AUTHORS: Evangelos Pefanis*, Jiguang Wang*, Gerson Rothschild*, Junghyun Lim*, David Kazadi, Jianbo Sun, Alexander Federation, Jaime Chao, Oliver Elliott, Zhi-Ping Liu, Aris N. Economides, James E. Bradner, Raul Rabadan+, Uttiya Basu+.

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

Cell 2015 May; doi: 10.1016/j.cell.2015.04.034.

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“Convergent Mutations and Kinase Fusions Lead to Oncogenic STAT3 Activation in Anaplastic Large Cell Lymphoma.”
THE RABADAN LAB THE RABADAN LAB

“Convergent Mutations and Kinase Fusions Lead to Oncogenic STAT3 Activation in Anaplastic Large Cell Lymphoma.”

AUTHORS: Ramona Crescenzo*, Francesco Abate*, Elena Lasorsa*, Fabrizio Tabbo, Marcello Gaudiano, Nicoletta Chiesa, Filomena Di Giacomo, Elisa Spaccarotella, Luigi Barbarossa, Elisabetta Ercole, Maria Todaro, Michela Boi, Andrea Acquaviva, Elisa Ficarra, Domenico Novero, Andrea Rinaldi, Thomas Tousseyn, Andreas Rosenwald, Lukas Kenner, Lorenzo Cerroni, Alexander Tzankov, Maurilio Ponzoni, Marco Paulli, Dennis Weisenburger, Wing C. Chan, Javeed Iqbal, Miguel A. Piris, Alberto Zamo, Carmela Ciardullo, Davide Rossi, Gianluca Gaidano, Stefano Pileri, Enrico Tiacci, Brunangelo Falini, Leonard D. Shultz, Laurence Mevellec, Jorge E. Vialard, Roberto Piva, Francesco Bertoni, Raul Rabadan‡, Giorgio Inghirami‡.

* These authors have contributed equally to this work. ‡ These authors have contributed equally to this work.

Cancer Cell 2015 April 13; doi:10.1016/j.ccell.2015.03.006.

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“Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas.”
THE RABADAN LAB THE RABADAN LAB

“Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas.”

AUTHORS: Palomero T*, Couronné L*, Khiabanian H*, Kim MY, Ambesi-Impiombato A, Perez-Garcia A, Carpenter Z, Abate F, Allegretta M, Haydu JE, Jiang X, Lossos IS, Nicolas C, Balbin M, Bastard C, Bhagat G, Piris MA, Campo E, Bernard OA, Rabadan R‡, Ferrando AA‡.

* These authors have contributed equally to this work. ‡ These authors have contributed equally to this work.

Nat Genet. 2014 Feb;46(2):166-70. doi: 10.1038/ng.2873.

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“The integrated landscape of driver genomic alterations in glioblastoma.”
THE RABADAN LAB THE RABADAN LAB

“The integrated landscape of driver genomic alterations in glioblastoma.”

AUTHORS: Frattini V, Trifonov V, Chan JM, Castano A, Lia M, Abate F, Keir ST, Ji AX, Zoppoli P, Niola F, Danussi C, Dolgalev I, Porrati P, Pellegatta S, Heguy A, Gupta G, Pisapia DJ, Canoll P, Bruce JN, McLendon RE, Yan H, Aldape K, Finocchiaro G, Mikkelsen T, Privé GG, Bigner DD, Lasorella A*, Rabadan R*, Iavarone A*.

* These authors have contributed equally to this work.

Nature Genetics 2013 Aug 05. doi:10.1038/ng.2734.

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