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.”
 

 

“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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“BRAF Mutations in Hairy-Cell Leukemia.”
THE RABADAN LAB THE RABADAN LAB

“BRAF Mutations in Hairy-Cell Leukemia.”

AUTHORS: Tiacci E, Trifonov V, Schiavoni G, Holmes A, Kern W, Martelli MP, Pucciarini A, Bigerna B, Pacini R, Wells VA, Sportoletti P, Pettirossi V, Mannucci R, Elliott O, Liso A, Ambrosetti A, Pulsoni A, Forconi F, Trentin L, Semenzato G, Inghirami G, Capponi M, Di Raimondo F, Patti C, Arcaini L, Musto P, Pileri S, Haferlach C, Schnittger S, Pizzolo G, Foà R, Farinelli L, Haferlach T, Pasqualucci L, Rabadan R*, Falini B*.

* These authors have contributed equally to this work.

The New England Journal of Medicine 2011 Jun 16;364(24):2305-15.

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“Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation.”
THE RABADAN LAB THE RABADAN LAB

“Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation.”

AUTHORS: Fabbri G, Rasi S, Rossi D, Trifonov V, Khiabanian H, Ma J, Grunn A, Fangazio M, Capello D, Monti S, Cresta S, Gargiulo E, Forconi F, Guarini A, Arcaini L, Paulli M, Laurenti L, Larocca LM, Marasca R, Gattei V, Oscier D, Bertoni F, Mullighan CG, Foá R, Pasqualucci L*, Rabadan R*, Dalla-Favera R*, Gaidano G*.

* These authors have contributed equally to this work.

The Journal of Experimental Medicine 2011 Jun 13;208:1389-1401.

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