List of works - Raúl Rabadán

A Case of T-cell Acute Lymphoblastic Leukemia Relapsed As Myeloid Acute Leukemia

scientific article published on 03 May 2016

A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk

scientific article (publication date: September 2013)

A Random Categorization Model for Hierarchical Taxonomies

scientific article

A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation

scientific article published on 23 December 2014

A recoding method to improve the humoral immune response to an HIV DNA vaccine

scientific article

A targetable GATA2-IGF2 axis confers aggressiveness in lethal prostate cancer

scientific article

Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas

scientific article published on 06 January 2017

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

scientific article

An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function. ⬇️

scientific article published in September 2017

An information theoretic method to identify combinations of genomic alterations that promote glioblastoma.

scientific article published on 4 May 2015

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

scientific article

Analysis of the coding genome of diffuse large B-cell lymphoma

scientific article

Anomalies in the influenza virus genome database: new biology or laboratory errors?

scientific article published on 25 June 2008

Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data

scientific article published on 12 September 2017

Author Correction: Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma

scientific article published on 01 June 2019

BRAF mutations in hairy-cell leukemia

scientific article

Beyond NPM-anaplastic lymphoma kinase driven lymphomagenesis: alternative drivers in anaplastic large cell lymphoma

scientific article published on July 2013

Biclustering of adverse drug events in the FDA's spontaneous reporting system.

scientific article published on 29 December 2010

Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia

scientific article

Clinical impact of small subclones harboring NOTCH1, SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia

scientific article published on 27 January 2016

Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia

scientific article published on 17 January 2018

Clonal evolution of glioblastoma under therapy.

scientific article

Clonality Analysis of Immunoglobulin Gene Rearrangement by Next-Generation Sequencing in Endemic Burkitt Lymphoma Suggests Antigen Drive Activation of BCR as Opposed to Sporadic Burkitt Lymphoma.

scientific article published on January 2016

Cluster analysis of the origins of the new influenza A(H1N1) virus

scientific article

Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

scientific article

Comparison of avian and human influenza A viruses reveals a mutational bias on the viral genomes.

scientific article

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

Convergent mutations and kinase fusions lead to oncogenic STAT3 activation in anaplastic large cell lymphoma.

scientific article

Copy number profiling across glioblastoma populations has implications for clinical trial design.

scientific article

CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining

scientific article published on 28 September 2020

Darwin or Lamarck? Future Challenges in Evolutionary Algorithms for Knowledge Discovery and Data Mining

Darwin, Lamarck, or Baldwin: Applying Evolutionary Algorithms to Machine Learning Techniques

scientific article published in August 2014

De novo transcriptome reconstruction and annotation of the Egyptian rousette bat.

scientific article published on 7 December 2015

Differences in patient age distribution between influenza A subtypes.

scientific article

Differential levels of transcription of p53-regulated genes by the arginine/proline polymorphism: p53 with arginine at codon 72 favors apoptosis.

scientific article

Discovering disease associations by integrating electronic clinical data and medical literature

scientific article (publication date: 2011)

Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities

scientific article

Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma

scientific article published on 15 October 2015

Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors

scientific article published on 01 November 2019

Drug-drug interaction through molecular structure similarity analysis.

scientific article published on 30 May 2012

E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells.

scientific article published on August 2013

Emergence of fatal avian influenza in New England harbor seals

scientific article published on 31 July 2012

Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration

scientific article

Evolutionary scalpels for dissecting tumor ecosystems

scientific article published on 3 December 2016

FBXW7 mutations in melanoma and a new therapeutic paradigm

scientific article

Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis.

scientific article published on 21 September 2011

Fractal-like distributions over the rational numbers in high-throughput biological and clinical data

scientific article

Frequency analysis techniques for identification of viral genetic data

scientific article

GAB2 induces tumor angiogenesis in NRAS-driven melanoma.

scientific article published on 27 August 2012

Generation of Live Attenuated Influenza Virus by Using Codon Usage Bias.

scientific article

Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia

scientific article published on 6 February 2012

Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness

scientific article published on 18 February 2014

Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome

scientific article published on 14 October 2013

Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes

scientific article published on 30 April 2015

Genetics of follicular lymphoma transformation

scientific article

Genomic Characterization of Dysplastic Nevi Unveils Implications for Diagnosis of Melanoma.

scientific article published on 24 November 2016

Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus

scientific article

Germ-Cell-Specific Inflammasome Component NLRP14 Negatively Regulates Cytosolic Nucleic Acid Sensing to Promote Fertilization

scientific article published on April 2017

Heart and skeletal muscle inflammation of farmed salmon is associated with infection with a novel reovirus

scientific article

High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants

scientific article published on 9 February 2015

Highly conserved regions of influenza a virus polymerase gene segments are critical for efficient viral RNA packaging.

scientific article

Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza.

scientific article

How many neutrophils are enough (redux, redux)? ⬇️

scientific article published on July 23, 2012

Identification of a new subclass of ALK-negative ALCL expressing aberrant levels of ERBB4 transcripts

scientific article

Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas

scientific article published on 3 October 2017

Identification of relevant genetic alterations in cancer using topological data analysis

scientific article published on 30 July 2020

Identifying hosts of families of viruses: a machine learning approach

scientific article (publication date: 2011)

Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma

scientific article published on 11 February 2019

Inactivating mutations of acetyltransferase genes in B-cell lymphoma

scientific article (publication date: 10 March 2011)

Inference of Ancestral Recombination Graphs through Topological Data Analysis ⬇️

scientific article (publication date: August 2016)

Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia

scientific article

Inter- and intra-patient clonal and subclonal heterogeneity of chronic lymphocytic leukaemia: evidences from circulating and lymph nodal compartments.

scientific article published on 24 November 2015

JAK-STAT in lymphoproliferative disorders

scientific article published on 11 August 2015

Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo-isomerase I inhibitors

scientific article published on 15 June 2016

Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts

scientific article

MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas

scientific article published on 04 August 2020

Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state

scientific article published on 19 October 2020

Mitochondrial DNA haplogroup D4a is a marker for extreme longevity in Japan

scientific article

Moduli Spaces of Phylogenetic Trees Describing Tumor Evolutionary Patterns

scholarly article by Sakellarios Zairis et al published 2014 in Lecture Notes in Computer Science

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

scientific article published on January 2016

Molecular characterization of severe and mild cases of influenza A (H1N1) 2009 strain from Argentina ⬇️

scientific article published on January 1, 2010

MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples

scientific article

Mutational and functional genetics mapping of chemotherapy resistance mechanisms in relapsed acute lymphoblastic leukemia

scientific article published on 19 October 2020

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

scientific article published on 21 September 2016

Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia

scientific article

Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness

scientific article (publication date: 28 October 2011)

Network analysis of global influenza spread

scientific article

Next generation syndromic surveillance: molecular epidemiology, electronic health records and the pandemic Influenza A (H1N1) virus.

scientific article

Non-random reassortment in human influenza A viruses

scientific article

Noncoding RNA transcription targets AID to divergently transcribed loci in B cells.

scientific article

Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry

scientific article published in April 2017

Oligonucleotide motifs that disappear during the evolution of influenza virus in humans increase alpha interferon secretion by plasmacytoid dendritic cells.

scientific article

On statistical modeling of sequencing noise in high depth data to assess tumor evolution

article by Raúl Rabadán et al published July 2018 in Journal of Statistical Physics

PHF6 mutations in T-cell acute lymphoblastic leukemia

scientific article (publication date: 14 March 2010)

Pan-cancer analysis identifies mutations in SUGP1 that recapitulate mutant SF3B1 splicing dysregulation

scientific article published on 24 April 2020

ParMap, an algorithm for the identification of small genomic insertions and deletions in nextgen sequencing data

scientific article

Patterns of evolution and host gene mimicry in influenza and other RNA viruses

scientific article

Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system

scientific article

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.

scientific article

Photon Regeneration from Pseudoscalars at X-Ray Laser Facilities

scientific article published on 24 March 2006

Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics

scientific article published in January 2018

Prognostic and therapeutic role of targetable lesions in B-lineage acute lymphoblastic leukemia without recurrent fusion genes

scientific article

Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4.

scientific article published in April 2012

Quantifying pathogen surveillance using temporal genomic data.

scientific article

RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity.

scientific article published on May 2015

Reassortment patterns in Swine influenza viruses

article published in 2009

Reassortment patterns in Swine influenza viruses.

scientific article

Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2

scientific article

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

scientific article published on 12 January 2014

Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches

scientific article published on 21 March 2016

Restoration of Replication Fork Stability in BRCA1- and BRCA2-Deficient Cells by Inactivation of SNF2-Family Fork Remodelers.

scientific article

SAVI: a statistical algorithm for variant frequency identification

scientific article

Signs of the 2009 influenza pandemic in the New York-Presbyterian Hospital electronic health records

scientific article

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development

scientific article published on May 2017

Somatic CLL mutations occur at multiple distinct hematopoietic maturation stages: documentation and cautionary note regarding cell fraction purity

scientific article published on 5 December 2017

Spatiotemporal genomic architecture informs precision oncology in glioblastoma

scientific article published on 6 March 2017

The 2019 mathematical oncology roadmap

scientific article published on 19 June 2019

The B-cell receptor controls fitness of MYC-driven lymphoma cells via GSK3β inhibition

scientific article published on 31 May 2017

The Contribution of the PB1-F2 Protein to the Fitness of Influenza A Viruses and its Recent Evolution in the 2009 Influenza A (H1N1) Pandemic Virus.

scientific article

The Emergence of 2009 H1N1 Pandemic Influenza

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

scientific article

The genetics of nodal marginal zone lymphoma

scientific article published on 22 June 2016

The integrated landscape of driver genomic alterations in glioblastoma

scientific article published on 05 August 2013

The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.

scientific article

The mutational landscape of cutaneous T cell lymphoma and Sézary syndrome

scientific article

Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination

scientific article

Topology of viral evolution

scientific article

Transcriptome reconstruction and annotation of cynomolgus and African green monkey

scientific article

Transcriptomics Identify CD9 as a Marker of Murine IL-10-Competent Regulatory B Cells

scientific article published on 27 October 2015

Transforming fusions of FGFR and TACC genes in human glioblastoma

scientific article

Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia

scientific article

Understanding Coronavirus

book edition from June 2020

Viral diversity and clonal evolution from unphased genomic data.

scientific article

Viral reassortment as an information exchange between viral segments

scientific article

Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype

scientific article

p53 Maintains Baseline Expression of Multiple Tumor Suppressor Genes

scientific article published on 8 May 2017

List of works by Raúl Rabadán

A Case of T-cell Acute Lymphoblastic Leukemia Relapsed As Myeloid Acute Leukemia

A Nondegenerate Code of Deleterious Variants in Mendelian Loci Contributes to Complex Disease Risk

A Random Categorization Model for Hierarchical Taxonomies

A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation

A recoding method to improve the humoral immune response to an HIV DNA vaccine

A targetable GATA2-IGF2 axis confers aggressiveness in lethal prostate cancer

Activating mutations and translocations in the guanine exchange factor VAV1 in peripheral T-cell lymphomas

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

An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function. ⬇️

An information theoretic method to identify combinations of genomic alterations that promote glioblastoma.

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

Analysis of the coding genome of diffuse large B-cell lymphoma

Anomalies in the influenza virus genome database: new biology or laboratory errors?

Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data

Author Correction: Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma

BRAF mutations in hairy-cell leukemia

Beyond NPM-anaplastic lymphoma kinase driven lymphomagenesis: alternative drivers in anaplastic large cell lymphoma

Biclustering of adverse drug events in the FDA's spontaneous reporting system.

Clinical impact of small TP53 mutated subclones in chronic lymphocytic leukemia

Clinical impact of small subclones harboring NOTCH1, SF3B1 or BIRC3 mutations in chronic lymphocytic leukemia

Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia

Clonal evolution of glioblastoma under therapy.

Clonality Analysis of Immunoglobulin Gene Rearrangement by Next-Generation Sequencing in Endemic Burkitt Lymphoma Suggests Antigen Drive Activation of BCR as Opposed to Sporadic Burkitt Lymphoma.

Cluster analysis of the origins of the new influenza A(H1N1) virus

Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

Comparison of avian and human influenza A viruses reveals a mutational bias on the viral genomes.

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

Convergent mutations and kinase fusions lead to oncogenic STAT3 activation in anaplastic large cell lymphoma.

Copy number profiling across glioblastoma populations has implications for clinical trial design.

CtIP-mediated DNA resection is dispensable for IgH class switch recombination by alternative end-joining

Darwin or Lamarck? Future Challenges in Evolutionary Algorithms for Knowledge Discovery and Data Mining

Darwin, Lamarck, or Baldwin: Applying Evolutionary Algorithms to Machine Learning Techniques

De novo transcriptome reconstruction and annotation of the Egyptian rousette bat.

Differences in patient age distribution between influenza A subtypes.

Differential levels of transcription of p53-regulated genes by the arginine/proline polymorphism: p53 with arginine at codon 72 favors apoptosis.

Discovering disease associations by integrating electronic clinical data and medical literature

Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities

Distinct Viral and Mutational Spectrum of Endemic Burkitt Lymphoma

Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors

Drug-drug interaction through molecular structure similarity analysis.

E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells.

Emergence of fatal avian influenza in New England harbor seals

Evolutionary Dynamics of Pandemic Methicillin-Sensitive Staphylococcus aureus ST398 and Its International Spread via Routes of Human Migration

Evolutionary scalpels for dissecting tumor ecosystems

FBXW7 mutations in melanoma and a new therapeutic paradigm

Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis.

Fractal-like distributions over the rational numbers in high-throughput biological and clinical data

Frequency analysis techniques for identification of viral genetic data

GAB2 induces tumor angiogenesis in NRAS-driven melanoma.

Generation of Live Attenuated Influenza Virus by Using Codon Usage Bias.

Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia

Genetic lesions associated with chronic lymphocytic leukemia chemo-refractoriness

Genetic lesions associated with chronic lymphocytic leukemia transformation to Richter syndrome

Genetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genes

Genetics of follicular lymphoma transformation

Genomic Characterization of Dysplastic Nevi Unveils Implications for Diagnosis of Melanoma.

Geographic dependence, surveillance, and origins of the 2009 influenza A (H1N1) virus

Germ-Cell-Specific Inflammasome Component NLRP14 Negatively Regulates Cytosolic Nucleic Acid Sensing to Promote Fertilization

Heart and skeletal muscle inflammation of farmed salmon is associated with infection with a novel reovirus

High-resolution Genomic Surveillance of 2014 Ebolavirus Using Shared Subclonal Variants

Highly conserved regions of influenza a virus polymerase gene segments are critical for efficient viral RNA packaging.

Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza.

How many neutrophils are enough (redux, redux)? ⬇️

Identification of a new subclass of ALK-negative ALCL expressing aberrant levels of ERBB4 transcripts

Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas

Identification of relevant genetic alterations in cancer using topological data analysis

Identifying hosts of families of viruses: a machine learning approach

Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma

Inactivating mutations of acetyltransferase genes in B-cell lymphoma

Inference of Ancestral Recombination Graphs through Topological Data Analysis ⬇️

Integrated mutational and cytogenetic analysis identifies new prognostic subgroups in chronic lymphocytic leukemia

Inter- and intra-patient clonal and subclonal heterogeneity of chronic lymphocytic leukaemia: evidences from circulating and lymph nodal compartments.

JAK-STAT in lymphoproliferative disorders

Kinase-dead ATM protein is highly oncogenic and can be preferentially targeted by Topo-isomerase I inhibitors

Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts

MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas

Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state

Mitochondrial DNA haplogroup D4a is a marker for extreme longevity in Japan

Moduli Spaces of Phylogenetic Trees Describing Tumor Evolutionary Patterns