Lista de obras - Javier Herrero - Dominio Público Uruguay

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

artículo científico publicado en 2017

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

artículo científico publicado en 2008

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

artículo científico publicado en 2017

A clonal expression biomarker associates with lung cancer mortality

artículo científico publicado en 2019

A comparative encyclopedia of DNA elements in the mouse genome

artículo científico publicado en 2014

A hierarchical unsupervised growing neural network for clustering gene expression patterns

artículo científico publicado en 2001

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

artículo científico publicado en 2011

A novel requirement for DROSHA in maintenance of mammalian CG methylation

artículo científico publicado en 2017

A novel requirement for DROSHA in maintenance of mammalian CG methylation

artículo científico publicado en 2017

Aequatus: An open-source homology browser

Alignathon: a competitive assessment of whole-genome alignment methods

artículo científico publicado en 2014

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

artículo científico publicado en 2017

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

artículo científico publicado en 2003

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

artículo científico publicado en 2012

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

artículo científico publicado en 2001

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

artículo científico publicado en 2002

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

artículo científico publicado en 2016

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

artículo científico publicado en 2021

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

artículo científico publicado en 2016

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

artículo científico publicado en 2002

Comparative and demographic analysis of orang-utan genomes

artículo científico publicado en 2011

Comparing bacterial genomes through conservation profiles.

artículo científico publicado en 2003

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

artículo científico publicado el 21 de febrero de 2011

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

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2016

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.

artículo científico publicado en 2018

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

artículo científico publicado en 2020

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

artículo científico publicado en 2019

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

artículo científico publicado en 2008

Ensembl 2005

artículo científico publicado en 2005

Ensembl 2006.

artículo científico publicado en 2006

Ensembl 2007

artículo científico publicado en 2007

Ensembl 2008

artículo científico publicado en 2008

Ensembl 2011

artículo científico publicado en 2011

Ensembl 2012

artículo científico publicado en 2012

Ensembl 2013

artículo científico publicado en 2013

Ensembl 2014

artículo científico publicado en 2014

Ensembl Genomes: extending Ensembl across the taxonomic space

artículo científico publicado en 2009

Ensembl comparative genomics resources

artículo científico publicado en 2016

Ensembl comparative genomics resources

artículo científico publicado en 2016

Ensembl's 10th year

artículo científico publicado en 2010

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

artículo científico publicado en 2020

Extending reference assembly models

artículo científico publicado en 2015

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

artículo científico publicado en 2005

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

artículo científico publicado en 2003

Gene expression data preprocessing.

artículo científico publicado en 2003

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.

artículo científico publicado en 2017

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

artículo científico publicado en 2011

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

artículo científico publicado en 2015

Genome-wide nucleotide-level mammalian ancestor reconstruction

artículo científico publicado en 2008

Gibbon genome and the fast karyotype evolution of small apes

artículo científico publicado en 2014

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

artículo científico publicado en 2021

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

artículo científico publicado en 2017

Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs

artículo científico

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

artículo científico publicado en 2012

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

artículo científico publicado en 2013

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

artículo científico publicado en 2017

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

artículo científico publicado en 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

artículo científico publicado en 2010

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

artículo científico publicado en 2017

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.

artículo científico publicado en 2017

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

artículo científico publicado en 2011

Saturation analysis for whole-genome bisulfite sequencing data

artículo científico publicado en 2016

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

artículo científico publicado en 2008

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

artículo científico publicado en 2013

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

artículo científico publicado en 2019

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

artículo científico publicado en 2018

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

scientific article published on 31 October 2019

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

artículo científico publicado en 2013

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

artículo científico publicado en 2015

Toward community standards in the quest for orthologs

artículo científico publicado en 2012

Tracking the Evolution of Non-Small-Cell Lung Cancer

artículo científico publicado en 2017

TranscriptSNPView: a genome-wide catalog of mouse coding variation

artículo científico publicado en 2006

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

artículo científico publicado en 2021

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

artículo científico publicado en 2016

eHive: an artificial intelligence workflow system for genomic analysis

artículo científico publicado en 2010

ncRNA orthologies in the vertebrate lineage

artículo científico publicado en 2016

Lista de obras de 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

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

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