List of works - Núria López-Bigas

A DNA methylation map of human cancer at single base-pair resolution.

scientific article published on 05 June 2017

A common frameshift mutation and other variants in GJB4 (connexin 30.3): Analysis of hearing impairment families

scientific article

A compendium of mutational cancer driver genes

scientific article published on 10 August 2020

A landscape of pharmacogenomic interactions in cancer.

scientific article published on 05 July 2016

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

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

scientific article published on 17 April 2018

A partially supervised classification approach to dominant and recessive human disease gene prediction

scientific article published on 26 January 2007

Altered oncomodules underlie chromatin regulatory factors driver mutations

scientific article

An intronic microRNA links Rb/E2F and EGFR signaling

scientific article

An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.).

scientific article

Are carcinogens direct mutagens?

scientific article published on 01 November 2020

Are splicing mutations the most frequent cause of hereditary disease?

scientific article

Author Correction: Reduced mutation rate in exons due to differential mismatch repair

scientific article published on 01 August 2018

Beyond 100 genomes

scientific article

BioMart Central Portal: an open database network for the biological community

scientific article

Biological convergence of cancer signatures

scientific article

Biological reprogramming in acquired resistance to endocrine therapy of breast cancer.

scientific article published on 16 August 2010

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

scientific article (publication date: 31 January 2017)

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

scientific article published on 28 March 2018

Chromatin-bound IκBα regulates a subset of polycomb target genes in differentiation and cancer

scientific article

Chromatin-wide profiling of DYRK1A reveals a role as a gene-specific RNA polymerase II CTD kinase.

scientific article

Co-regulation of histone-modifying enzymes in cancer

scientific article

CoGenT++: an extensive and extensible data environment for computational genomics

scientific article

Comparison of algorithms for the detection of cancer drivers at subgene resolution

scientific article published on 17 July 2017

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

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

scientific article

Connexin 31 (GJB3) is expressed in the peripheral and auditory nerves and causes neuropathy and hearing impairment

scientific article (publication date: 15 April 2001)

Connexin mutations in hearing loss, dermatological and neurological disorders.

scientific article

Cooperation between dE2F1 and Yki/Sd defines a distinct transcriptional program necessary to bypass cell cycle exit

scientific article (publication date: 15 February 2011)

Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation

scientific article

Corrigendum: Notch signal strength controls cell fate in the haemogenic endothelium

scientific article published on 4 March 2016

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

scientific article published in April 2015

Differences in the evolutionary history of disease genes affected by dominant or recessive mutations

scientific article

Discovering the drivers of clonal hematopoiesis

scientific article published in 2022

Distinct patterns in the regulation and evolution of human cancer genes

article

Drosophila GAGA factor is required for full activation of the dE2f1-Yki/Sd transcriptional program

scientific article

EU Pancreas: an integrated European platform for pancreas cancer research--from basic science to clinical and public health interventions for a rare disease

scientific article published in January 2013

Erratum: Comprehensive identification of mutational cancer driver genes across 12 tumor types

scientific article published in Scientific Reports

Erratum: Identification of five new mutations of PDS/SLC26A4 in Mediterranean families with hearing impairment.

scientific article published in July 2002

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

scientific article

Expression of polycomb targets predicts breast cancer prognosis

scientific article published on 05 August 2013

Expression profiles of the connexin genes, Gjb1 and Gjb3, in the developing mouse cochlea

scientific article published on November 2002

Expression profiles of the connexin genes, Gjb1 and Gjb3, in the developing mouse cochlea

scientific article published on December 2002

Fast randomization of large genomic datasets while preserving alteration counts

scientific article published on September 2014

Functional impact bias reveals cancer drivers

scientific article

Functional protein divergence in the evolution of Homo sapiens

scientific article

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation

scientific article

Genome-wide analysis using ChIP to identify isoform-specific gene targets

scientific article published on 7 July 2010

Genome-wide identification of genes likely to be involved in human genetic disease

scientific article

Genomic and evolutionary classification of lung cancer in never smokers

scientific article published on 06 September 2021

Gitools: analysis and visualisation of genomic data using interactive heat-maps

scientific article

HDAC7 is a repressor of myeloid genes whose downregulation is required for transdifferentiation of pre-B cells into macrophages.

scientific article

Highly consistent patterns for inherited human diseases at the molecular level.

scientific article published on 15 November 2005

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification of Cdca7 as a novel Notch transcriptional target involved in hematopoietic stem cell emergence.

scientific article

Identification of five new mutations of PDS/SLC26A4 in Mediterranean families with hearing impairment.

scientific article published in December 2001

Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression

scientific article published on 8 January 2013

Improving data and knowledge management to better integrate health care and research.

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

Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells.

scientific article

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes

scientific article published on 13 November 2014

Inhibition of specific NF-κB activity contributes to the tumor suppressor function of 14-3-3σ in breast cancer

scientific article

IntOGen-mutations identifies cancer drivers across tumor types.

scientific article

IntOGen: integration and data mining of multidimensional oncogenomic data

scientific article published in February 2010

Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets.

scientific article published on 14 August 2017

Integrative cancer genomics (IntOGen) in Biomart

scientific article

Jagged1 is the pathological link between Wnt and Notch pathways in colorectal cancer

scholarly article

Loss of dE2F compromises mitochondrial function

scientific article (publication date: 25 November 2013)

Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2.

scientific article

Molecular Diagnosis of Diffuse Gliomas through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid.

scientific article

Molecular basis of childhood deafness resulting from mutations in the GJB2 (connexin 26) gene

scientific article published in January 2000

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

scientific article

Mutations in GJB6 cause nonsyndromic autosomal dominant deafness at DFNA3 locus

scientific article (publication date: September 1999)

Mutations in the mitochondrial tRNA Ser(UCN) and in the GJB2 (connexin 26) gene are not modifiers of the age at onset or severity of hearing loss in Spanish patients with the 12S rRNA A1555G mutation

scientific article published on April 2000

NF-κB directly mediates epigenetic deregulation of common microRNAs in Epstein-Barr virus-mediated transformation of B-cells and in lymphomas.

scientific article

Non-coding recurrent mutations in chronic lymphocytic leukaemia

scientific article published in Nature

Notch signal strength controls cell fate in the haemogenic endothelium

scientific article

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

scientific article

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees

scientific article

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

scientific article published on 24 July 2013

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

Oncogenomics methods and resources

scientific article published on May 2012

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)

Patterns of evolutionary constraints on genes in humans

scientific article

Prioritization of candidate cancer genes--an aid to oncogenomic studies

scientific article published on 18 August 2008

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

Regulation of Plant Stem Cell Quiescence by a Brassinosteroid Signaling Module

article published in 2015

Regulation of Plant Stem Cell Quiescence by a Brassinosteroid Signaling Module

article

SNP and haplotype mapping for genetic analysis in the rat.

scientific article

SVGMap: configurable image browser for experimental data

scientific article

Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types

scientific article

Selective targeting of histone methylation

scientific article

Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer

scientific article published on 12 March 2021

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

scientific article published on 01 November 2018

Splice-site mutation in the PDS gene may result in intrafamilial variability for deafness in Pendred syndrome

scientific article published in January 1999

Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition.

scientific article

Structural and functional properties of genes involved in human cancer

scientific article

The A1555G mutation in the 12S rRNA gene of human mtDNA: recurrent origins and founder events in families affected by sensorineural deafness ⬇️

scientific article

The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion.

scientific article published on 15 January 2013

The Repertoire of Mutational Signatures in Human Cancer

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 road ahead in genetics and genomics

scientific article published on 24 August 2020

The transcriptional repressor HDAC7 promotes apoptosis and c-Myc downregulation in particular types of leukemia and lymphoma.

scientific article

Transcriptional activation of polycomb-repressed genes by ZRF1

scientific article

Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia

scientific article

Visualizing multidimensional cancer genomics data

scientific article

Whole genome analysis of p38 SAPK-mediated gene expression upon stress.

scientific article

Whole-genome landscapes of major melanoma subtypes.

scientific article published on 3 May 2017

jHeatmap: an interactive heatmap viewer for the web.

scientific article published on 23 February 2014

mir-11 limits the proapoptotic function of its host gene, dE2f1

scientific article

p27Kip1 represses transcription by direct interaction with p130/E2F4 at the promoters of target genes

scientific article published on 19 December 2011

List of works by Núria López-Bigas

A DNA methylation map of human cancer at single base-pair resolution.

A common frameshift mutation and other variants in GJB4 (connexin 30.3): Analysis of hearing impairment families

A compendium of mutational cancer driver genes

A landscape of pharmacogenomic interactions in cancer.

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

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

A partially supervised classification approach to dominant and recessive human disease gene prediction

Altered oncomodules underlie chromatin regulatory factors driver mutations

An intronic microRNA links Rb/E2F and EGFR signaling

An oligo-based microarray offers novel transcriptomic approaches for the analysis of pathogen resistance and fruit quality traits in melon (Cucumis melo L.).

Are carcinogens direct mutagens?

Are splicing mutations the most frequent cause of hereditary disease?

Author Correction: Reduced mutation rate in exons due to differential mismatch repair

Beyond 100 genomes

BioMart Central Portal: an open database network for the biological community

Biological convergence of cancer signatures

Biological reprogramming in acquired resistance to endocrine therapy of breast cancer.

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

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

Chromatin-bound IκBα regulates a subset of polycomb target genes in differentiation and cancer

Chromatin-wide profiling of DYRK1A reveals a role as a gene-specific RNA polymerase II CTD kinase.

Co-regulation of histone-modifying enzymes in cancer

CoGenT++: an extensive and extensible data environment for computational genomics

Comparison of algorithms for the detection of cancer drivers at subgene resolution

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

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.

Connexin 31 (GJB3) is expressed in the peripheral and auditory nerves and causes neuropathy and hearing impairment

Connexin mutations in hearing loss, dermatological and neurological disorders.

Cooperation between dE2F1 and Yki/Sd defines a distinct transcriptional program necessary to bypass cell cycle exit

Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation

Corrigendum: Notch signal strength controls cell fate in the haemogenic endothelium

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

Differences in the evolutionary history of disease genes affected by dominant or recessive mutations

Discovering the drivers of clonal hematopoiesis

Distinct patterns in the regulation and evolution of human cancer genes

Drosophila GAGA factor is required for full activation of the dE2f1-Yki/Sd transcriptional program

EU Pancreas: an integrated European platform for pancreas cancer research--from basic science to clinical and public health interventions for a rare disease

Erratum: Comprehensive identification of mutational cancer driver genes across 12 tumor types

Erratum: Identification of five new mutations of PDS/SLC26A4 in Mediterranean families with hearing impairment.

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

Expression of polycomb targets predicts breast cancer prognosis

Expression profiles of the connexin genes, Gjb1 and Gjb3, in the developing mouse cochlea

Expression profiles of the connexin genes, Gjb1 and Gjb3, in the developing mouse cochlea

Fast randomization of large genomic datasets while preserving alteration counts

Functional impact bias reveals cancer drivers

Functional protein divergence in the evolution of Homo sapiens

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation

Genome-wide analysis using ChIP to identify isoform-specific gene targets

Genome-wide identification of genes likely to be involved in human genetic disease

Genomic and evolutionary classification of lung cancer in never smokers

Gitools: analysis and visualisation of genomic data using interactive heat-maps

HDAC7 is a repressor of myeloid genes whose downregulation is required for transdifferentiation of pre-B cells into macrophages.

Highly consistent patterns for inherited human diseases at the molecular level.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Identification of Cdca7 as a novel Notch transcriptional target involved in hematopoietic stem cell emergence.

Identification of five new mutations of PDS/SLC26A4 in Mediterranean families with hearing impairment.

Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression

Improving data and knowledge management to better integrate health care and research.

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

Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells.

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes

Inhibition of specific NF-κB activity contributes to the tumor suppressor function of 14-3-3σ in breast cancer

IntOGen-mutations identifies cancer drivers across tumor types.

IntOGen: integration and data mining of multidimensional oncogenomic data

Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets.

Integrative cancer genomics (IntOGen) in Biomart

Jagged1 is the pathological link between Wnt and Notch pathways in colorectal cancer

Loss of dE2F compromises mitochondrial function

Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2.

Molecular Diagnosis of Diffuse Gliomas through Sequencing of Cell-Free Circulating Tumor DNA from Cerebrospinal Fluid.

Molecular basis of childhood deafness resulting from mutations in the GJB2 (connexin 26) gene

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

Mutations in GJB6 cause nonsyndromic autosomal dominant deafness at DFNA3 locus

Mutations in the mitochondrial tRNA Ser(UCN) and in the GJB2 (connexin 26) gene are not modifiers of the age at onset or severity of hearing loss in Spanish patients with the 12S rRNA A1555G mutation

NF-κB directly mediates epigenetic deregulation of common microRNAs in Epstein-Barr virus-mediated transformation of B-cells and in lymphomas.