List of works - Javier Herrero

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0).

scientific article published on 30 October 2017

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

scientific article

A Human IPS Model Implicates Embryonic B-Myeloid Fate Restriction as Developmental Susceptibility to B Acute Lymphoblastic Leukemia-Associated ETV6-RUNX1.

scientific article published on 27 December 2017

A clonal expression biomarker associates with lung cancer mortality

scientific article published on 07 October 2019

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

A hierarchical unsupervised growing neural network for clustering gene expression patterns

scientific article

A high-resolution map of human evolutionary constraint using 29 mammals

scientific article

A novel requirement for DROSHA in maintenance of mammalian CG methylation

scientific article published in September 2017

A novel requirement for DROSHA in maintenance of mammalian CG methylation

scientific article

Aequatus: An open-source homology browser

Alignathon: a competitive assessment of whole-genome alignment methods

scientific article

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution

scientific article published on 21 October 2017

An approach to inferring transcriptional regulation among genes from large-scale expression data.

scientific article

Analysis of variation at transcription factor binding sites in Drosophila and humans

scientific article published in 2012

Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate

scientific article

Author Correction: G-tract RNA removes Polycomb repressive complex 2 from genes

scientific article published on 01 December 2019

Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction

scientific article

CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening

scientific article

Chemotherapy induces canalization of cell state in childhood B-cell precursor acute lymphoblastic leukemia

scientific article published on 05 July 2021

Clonal Evolutionary Analysis during HER2 Blockade in HER2-Positive Inflammatory Breast Cancer: A Phase II Open-Label Clinical Trial of Afatinib +/- Vinorelbine

scientific article

Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns

scientific article published in September 2002

Comparative and demographic analysis of orang-utan genomes

scientific article

Comparing bacterial genomes through conservation profiles.

scientific article published on 14 April 2003

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses ⬇️

scientific article published on February 21, 2011

Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

scientific article published in Nature

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

scientific article

DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

scientific article published on 22 February 2016

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

scientific article published on 11 April 2018

EZH2 deficient T-cell acute lymphoblastic leukemia is sensitized to CHK1 inhibition through enhanced replication stress

scientific article published on 29 April 2020

Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology

scientific article published on 02 July 2019

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs

scientific article

Ensembl 2005

scientific article

Ensembl 2006.

scientific article

Ensembl 2007

scientific article

Ensembl 2008

scientific article

Ensembl 2011

scientific article

Ensembl 2012

scientific article

Ensembl 2013

scientific article

Ensembl 2014

scientific article

Ensembl Genomes: extending Ensembl across the taxonomic space

scientific article

Ensembl comparative genomics resources

scientific article published on 20 February 2016

Ensembl comparative genomics resources

scientific article published on 2 May 2016

Ensembl's 10th year

scientific article

Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

scientific article published in Nature

Escape from nonsense-mediated decay associates with anti-tumor immunogenicity

scientific article published on 30 July 2020

Expression profiles and biological function

scientific article published on January 1, 2000

Extending reference assembly models

scientific article

G-tract RNA removes Polycomb repressive complex 2 from genes

scientific article published on 23 September 2019

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data

scientific article

GEPAS: A web-based resource for microarray gene expression data analysis

scientific article

Gene expression data preprocessing.

scientific article

Generation of a cancer testis antigen mCherry reporter HCT116 colorectal carcinoma cell line

Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease.

scientific article

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

scientific article

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

scientific article

Genome-wide nucleotide-level mammalian ancestor reconstruction

scientific article (publication date: November 2008)

Gibbon genome and the fast karyotype evolution of small apes

scientific article

Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion

scientific article published on 14 April 2021

H3.3K27M Cooperates with Trp53 Loss and PDGFRA Gain in Mouse Embryonic Neural Progenitor Cells to Induce Invasive High-Grade Gliomas.

scientific article

Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs

scientific article published on 24 August 2017

Improved Class Prediction in DNA Microarray Gene Expression Data by Unsupervised Reduction of the Dimensionality followed by Supervised Learning with a Perceptron

article

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

scientific article published on 06 February 2019

Insights into hominid evolution from the gorilla genome sequence

scientific article

Integrative annotation of variants from 1092 humans: application to cancer genomics

scientific article

Intratumoural evolutionary landscape of high-risk prostate cancer: the PROGENY study of genomic and immune parameters

scientific article published in October 2017

KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control

scientific article published on 30 July 2018

Marrow infiltrating regulatory T cells correlate with the presence of dysfunctional CD4+PD-1+ cells and inferior survival in patients with newly diagnosed multiple myeloma

scientific article published on 27 March 2020

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

scientific article published on 27 January 2021

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

scientific article published in 2010

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

scientific article

Publisher Correction: A clonal expression biomarker associates with lung cancer mortality

scientific article published on 03 June 2020

Publisher Correction: Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

scientific article published on 03 June 2020

Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection.

scientific article

RNA-seq of newly diagnosed patients in the PADIMAC study leads to a bortezomib/lenalidomide decision signature

scientific article published on 04 September 2018

RNAcentral: A vision for an international database of RNA sequences

scientific article (publication date: November 2011)

Saturation analysis for whole-genome bisulfite sequencing data

scientific article

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

scientific article

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

scientific article

Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

scientific article published on 07 October 2019

The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes.

scientific article published on 4 May 2018

The Personal Genome Project-UK, an open access resource of human multi-omics data

scientific article published on 31 October 2019

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan ⬇️

scientific article published on April 28, 2013

The duck genome and transcriptome provide insight into an avian influenza virus reservoir species

scientific article

The pig X and Y Chromosomes: structure, sequence, and evolution

scientific article published on 11 November 2015

Toward community standards in the quest for orthologs ⬇️

scientific article (publication date: 15 March 2012)

Tracking the Evolution of Non-Small-Cell Lung Cancer

scientific article published on 26 April 2017

TranscriptSNPView: a genome-wide catalog of mouse coding variation

scientific article published on August 2006

Whole-genome sequencing of single circulating tumor cells from neuroendocrine neoplasms

scientific article published on 11 August 2021

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

scientific article

eHive: an artificial intelligence workflow system for genomic analysis

scientific article

ncRNA orthologies in the vertebrate lineage

scientific article published on 15 March 2016

List of works by Javier Herrero

A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0).

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

A Human IPS Model Implicates Embryonic B-Myeloid Fate Restriction as Developmental Susceptibility to B Acute Lymphoblastic Leukemia-Associated ETV6-RUNX1.

A clonal expression biomarker associates with lung cancer mortality

A comparative encyclopedia of DNA elements in the mouse genome

A hierarchical unsupervised growing neural network for clustering gene expression patterns

A high-resolution map of human evolutionary constraint using 29 mammals

A novel requirement for DROSHA in maintenance of mammalian CG methylation

A novel requirement for DROSHA in maintenance of mammalian CG methylation

Aequatus: An open-source homology browser

Aequatus: An open-source homology browser

Alignathon: a competitive assessment of whole-genome alignment methods

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution

An approach to inferring transcriptional regulation among genes from large-scale expression data.

Analysis of variation at transcription factor binding sites in Drosophila and humans

Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate

Author Correction: G-tract RNA removes Polycomb repressive complex 2 from genes

Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction

CORALINA: a universal method for the generation of gRNA libraries for CRISPR-based screening

Chemotherapy induces canalization of cell state in childhood B-cell precursor acute lymphoblastic leukemia

Clonal Evolutionary Analysis during HER2 Blockade in HER2-Positive Inflammatory Breast Cancer: A Phase II Open-Label Clinical Trial of Afatinib +/- Vinorelbine

Combining hierarchical clustering and self-organizing maps for exploratory analysis of gene expression patterns

Comparative and demographic analysis of orang-utan genomes

Comparing bacterial genomes through conservation profiles.

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses ⬇️

Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference.

DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

EZH2 deficient T-cell acute lymphoblastic leukemia is sensitized to CHK1 inhibition through enhanced replication stress

Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs

Ensembl 2005

Ensembl 2006.

Ensembl 2007

Ensembl 2008

Ensembl 2011

Ensembl 2012

Ensembl 2013

Ensembl 2014

Ensembl Genomes: extending Ensembl across the taxonomic space

Ensembl comparative genomics resources

Ensembl comparative genomics resources

Ensembl's 10th year

Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

Escape from nonsense-mediated decay associates with anti-tumor immunogenicity

Expression profiles and biological function

Extending reference assembly models

G-tract RNA removes Polycomb repressive complex 2 from genes

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data

GEPAS: A web-based resource for microarray gene expression data analysis

Gene expression data preprocessing.

Generation of a cancer testis antigen mCherry reporter HCT116 colorectal carcinoma cell line

Genetic variants alter T-bet binding and gene expression in mucosal inflammatory disease.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

Genome-wide nucleotide-level mammalian ancestor reconstruction

Gibbon genome and the fast karyotype evolution of small apes

Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion

H3.3K27M Cooperates with Trp53 Loss and PDGFRA Gain in Mouse Embryonic Neural Progenitor Cells to Induce Invasive High-Grade Gliomas.

Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs

Improved Class Prediction in DNA Microarray Gene Expression Data by Unsupervised Reduction of the Dimensionality followed by Supervised Learning with a Perceptron

Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability

Insights into hominid evolution from the gorilla genome sequence

Integrative annotation of variants from 1092 humans: application to cancer genomics

Intratumoural evolutionary landscape of high-risk prostate cancer: the PROGENY study of genomic and immune parameters

KAP1 regulates endogenous retroviruses in adult human cells and contributes to innate immune control

Marrow infiltrating regulatory T cells correlate with the presence of dysfunctional CD4+PD-1+ cells and inferior survival in patients with newly diagnosed multiple myeloma

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

Publisher Correction: A clonal expression biomarker associates with lung cancer mortality

Publisher Correction: Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection.

RNA-seq of newly diagnosed patients in the PADIMAC study leads to a bortezomib/lenalidomide decision signature

RNAcentral: A vision for an international database of RNA sequences

Saturation analysis for whole-genome bisulfite sequencing data

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution