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.”
 

 

“Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma.”
THE RABADAN LAB THE RABADAN LAB

“Pervasive mutations of JAK-STAT pathway genes in classical Hodgkin lymphoma.”

AUTHORS: Enrico Tiacci, Erik Ladewig, Gianluca Schiavoni, Alex Penson, Elisabetta Fortini, Valentina Pettirossi, Yuchun Wang, Ariele Rosseto, Alessandra Venanzi, Sofija Vlasevska, Roberta Pacini, Simonetta Piattoni, Alessia Tabarrini, Alessandra Pucciarini, Barbara Bigerna, Alessia Santi, Alessandro M Gianni, Simonetta Viviani, Antonello Cabras, Stefano Ascani, Barbara Crescenzi, Cristina Mecucci, Laura Pasqualucci, Raul Rabadan, Brunangelo Falini.

Blood [12 Apr 2018, 131(22):2454-2465]. doi:10.1182/blood-2017-11-814913.

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“Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia.”
THE RABADAN LAB THE RABADAN LAB

“Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia.”

AUTHORS: Gannie Tzoneva, Chelsea L Dieck, Koichi Oshima, Alberto Ambesi-Impiombato, Marta Sánchez-Martín, Chioma J Madubata, Hossein Khiabanian, Jiangyan Yu, Esme Waanders, Ilaria Iacobucci, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Julie M Gastier-Foster, Mignon L Loh, Renate Kirschner-Schwabe, Charles G Mullighan, Raul Rabadan, Adolfo A Ferrando.

Nature volume 553, pages 511–514 (25 January 2018) doi:10.1038/nature25186.

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“Spatiotemporal genomic architecture informs precision oncology in glioblastoma.”
THE RABADAN LAB THE RABADAN LAB

“Spatiotemporal genomic architecture informs precision oncology in glioblastoma.”

AUTHORS: Lee JK*, Wang J*, Sa JK*, Ladewig E*, Lee HO, Lee IH, Kang HJ, Rosenbloom DS, Camara PG, Liu Z, van Nieuwenhuizen P, Jung SW, Choi SW, Kim J, Chen A, Kim KT, Shin S, Seo YJ, Oh JM, Shin YJ, Park CK, Kong DS, Seol HJ, Blumberg A, Lee JI, Iavarone A, Park WY+, Rabadan R+, Nam DH+.

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

Nat Genet. 2017 Apr. doi: 10.1038/ng.3806.

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“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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