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.”
 

 

“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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“Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL.”
THE RABADAN LAB THE RABADAN LAB

“Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL.”

AUTHORS: Tzoneva G*, Perez-Garcia A*, Carpenter Z*, Khiabanian H, Tosello V, Allegretta M, Paietta E, Racevskis J, Rowe J, Tallman M, Paganin M, Basso G, Hof J, Kirschner-Schwabe R, Palomero T‡, Rabadan R‡, Ferrando A.‡

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

Nature Medicine 2013 February 03. doi:10.1038/nm.3078.

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“The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development.”
THE RABADAN LAB THE RABADAN LAB

“The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development.”

AUTHORS: Davide Rossi*, Vladimir Trifonov*, Marco Fangazio*, Alessio Bruscaggin, Silvia Rasi, Valeria Spina, Sara Monti, Tiziana Vaisitti, Francesca Arruga, Rosella Famà, Carmela Ciardullo, Mariangela Greco, Stefania Cresta, Daniela Piranda, Antony Holmes, Giulia Fabbri, Monica Messina, Andrea Rinaldi, Jiguang Wang, Claudio Agostinelli, Pier Paolo Piccaluga, Marco Lucioni, Fabrizio Tabbò, Roberto Serra, Silvia Franceschetti, Clara Deambrogi, Giulia Daniele, Valter Gattei, Roberto Marasca, Fabio Facchetti, Luca Arcaini, Giorgio Inghirami, Francesco Bertoni, Stefano A. Pileri, Silvia Deaglio, Robin Foà, Riccardo Dalla-Favera‡, Laura Pasqualucci‡, Raul Rabadan‡, and Gianluca Gaidano‡.

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

The Journal of Experimental Medicine 2012 August. doi: 10.1084/jem.20120904.

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“Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma.”
THE RABADAN LAB THE RABADAN LAB

“Transforming Fusions of FGFR and TACC Genes in Human Glioblastoma.”

AUTHORS: Devendra Singh*, Joseph Minhow Chan*, Pietro Zoppoli*, Francesco Niola*, Ryan Sullivan, Angelica Castano, Eric Minwei Liu, Jonathan Reichel, Paola Porrati, Serena Pellegatta, Kunlong Qiu, Zhibo Gao, Michele Ceccarelli, Riccardo Riccardi, Daniel J. Brat, Abhijit Guha, Ken Aldape, John G. Golfinos, David Zagzag, Tom Mikkelsen, Gaetano Finocchiaro, Anna Lasorella‡, Raul Rabadan‡, Antonio Iavarone‡.

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

Science 2012 10.1126/science.1220834.

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