List of works - Abel Gonzalez-Perez

A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT)

scientific article published in September 2018

A pan-cancer landscape of interactions between solid tumors and infiltrating immune cell populations

scientific article published on 17 April 2018

Altered oncomodules underlie chromatin regulatory factors driver mutations

scientific article

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Are carcinogens direct mutagens?

scientific article published on 01 November 2020

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

scientific article published on 28 March 2018

Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types.

scientific article

Comparative Studies of Transcriptional Regulation Mechanisms in a Group of Eight Gamma-proteobacterial Genomes

scientific article published on 04 October 2005

Comprehensive Characterization of Cancer Driver Genes and Mutations

scientific article published in April 2018

Comprehensive identification of mutational cancer driver genes across 12 tumor types

scientific article

Computational approaches to identify functional genetic variants in cancer genomes

scientific article published on August 2013

Conservation of key members in the course of the evolution of the insulin signaling pathway

scientific article published on 20 June 2008

Cytoplasmic accumulation of NCoR in malignant melanoma: consequences of altered gene repression and prognostic significance

scientific article published in April 2015

Discovering the drivers of clonal hematopoiesis

scientific article published in 2022

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Dynamic clonal remodelling in breast cancer metastases is associated with subtype conversion

scientific article published on 04 September 2019

Frequency and clinical impact of CDKN2A/ARF/CDKN2B gene deletions as assessed by in-depth genetic analyses in adult T cell acute lymphoblastic leukemia

scientific article published on 24 July 2018

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters

scientific article

Functional impact bias reveals cancer drivers ⬇️

scientific article published on August 16, 2012

Genomic and evolutionary classification of lung cancer in never smokers

scientific article published on 06 September 2021

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.

scientific article

Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.

scientific article

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

scientific article

In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities

scientific article

IntOGen-mutations identifies cancer drivers across tumor types.

scientific article

LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells

scientific article published on 28 August 2019

Local Determinants of the Mutational Landscape of the Human Genome

scientific article published on 01 March 2019

Manic Fringe deficiency imposes Jagged1 addiction to intestinal tumor cells

scientific article published in Nature Communications

Mutational landscape of RNA-binding proteins in human cancers

scientific article

NK Cell Infiltrates and HLA Class I Expression in Primary HER2+ Breast Cancer Predict and Uncouple Pathological Response and Disease-free Survival

scientific article published on 06 December 2018

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response

article

Non-canonical NF-κB pathway activation predicts outcome in borderline oestrogen receptor positive breast carcinoma

scientific article published on 12 July 2016

Nucleotide excision repair is impaired by binding of transcription factors to DNA.

scientific article

Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression

scientific article

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

scientific article published on 24 July 2013

OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers

scientific article published on 01 November 2019

OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations

scientific article published on 16 June 2016

OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action

scientific article

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

scientific article

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

scientific article

Pathway and network analysis of cancer genomes

scientific article (publication date: July 2015)

Prediction of TF target sites based on atomistic models of protein-DNA complexes

scientific article

Rational design of cancer gene panels with OncoPaD.

scientific article published on 03 October 2016

Reduced mutation rate in exons due to differential mismatch repair

scientific article

Somatic and Germline Mutation Periodicity Follow the Orientation of the DNA Minor Groove around Nucleosomes

scientific article published on 01 November 2018

TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes

scientific article

The evolution of hematopoietic cells under cancer therapy

scientific article published on 10 August 2021

The evolution of relapse of adult T cell acute lymphoblastic leukemia

scientific article published on 23 November 2020

The mutational footprints of cancer therapies

scientific article published on 18 November 2019

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples

scientific article

The ubiquity of the insulin superfamily across the eukaryotes detected using a bioinformatics approach

scientific article published on 16 March 2011

Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes

scientific article

Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing

scientific article published on 15 April 2016

Visualizing multidimensional cancer genomics data ⬇️

scientific article published on January 31, 2013

List of works by Abel Gonzalez-Perez

A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT)

A pan-cancer landscape of interactions between solid tumors and infiltrating immune cell populations

Altered oncomodules underlie chromatin regulatory factors driver mutations

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Are carcinogens direct mutagens?

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types.

Comparative Studies of Transcriptional Regulation Mechanisms in a Group of Eight Gamma-proteobacterial Genomes

Comprehensive Characterization of Cancer Driver Genes and Mutations

Comprehensive identification of mutational cancer driver genes across 12 tumor types

Computational approaches to identify functional genetic variants in cancer genomes

Conservation of key members in the course of the evolution of the insulin signaling pathway

Cytoplasmic accumulation of NCoR in malignant melanoma: consequences of altered gene repression and prognostic significance

Discovering the drivers of clonal hematopoiesis

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Dynamic clonal remodelling in breast cancer metastases is associated with subtype conversion

Frequency and clinical impact of CDKN2A/ARF/CDKN2B gene deletions as assessed by in-depth genetic analyses in adult T cell acute lymphoblastic leukemia

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters

Functional impact bias reveals cancer drivers ⬇️

Genomic and evolutionary classification of lung cancer in never smokers

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.

Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation

In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities

IntOGen-mutations identifies cancer drivers across tumor types.

LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells

Local Determinants of the Mutational Landscape of the Human Genome

Manic Fringe deficiency imposes Jagged1 addiction to intestinal tumor cells

Mutational landscape of RNA-binding proteins in human cancers

NK Cell Infiltrates and HLA Class I Expression in Primary HER2+ Breast Cancer Predict and Uncouple Pathological Response and Disease-free Survival

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response

Non-canonical NF-κB pathway activation predicts outcome in borderline oestrogen receptor positive breast carcinoma

Nucleotide excision repair is impaired by binding of transcription factors to DNA.

Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers

OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations

OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

Pathway and network analysis of cancer genomes

Prediction of TF target sites based on atomistic models of protein-DNA complexes

Rational design of cancer gene panels with OncoPaD.

Reduced mutation rate in exons due to differential mismatch repair

Somatic and Germline Mutation Periodicity Follow the Orientation of the DNA Minor Groove around Nucleosomes

TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes

The evolution of hematopoietic cells under cancer therapy

The evolution of relapse of adult T cell acute lymphoblastic leukemia

The mutational footprints of cancer therapies

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples

The ubiquity of the insulin superfamily across the eukaryotes detected using a bioinformatics approach

Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes

Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing

Visualizing multidimensional cancer genomics data ⬇️