Javier Herrero

发表

Ensembl 2008

Andreas Prlic, Andrew M. Jenkinson, Damian Smedley, 2007, Nucleic Acids Res..

TranscriptSNPView: a genome-wide catalog of mouse coding variation

E. Birney, F. Cunningham, P. Flicek, 2006, Nature Genetics.

The Common Marmoset Genome Provides Insight into Primate Biology and Evolution

Albert J. Vilella, Charles E. Vejnar, Matthew W. Hahn, 2014, Nature Genetics.

Comparative and demographic analysis of orang-utan genomes

Albert J. Vilella, Zhengyuan O. Wang, Matthew W. Hahn, 2011, Nature.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

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

E. Birney, B. Paten, Kathryn Beal, 2008, Genome research.

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2011, PLoS biology.

RNAcentral: A vision for an international database of RNA sequences.

Anton J. Enright, Albert J. Vilella, Mathew W. Wright, 2011, RNA.

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

Gabor T. Marth, Uday S. Evani, H. Kang, 2013, Science.

Comparing bacterial genomes through conservation profiles.

Maria J Martin, Javier Herrero, Joaquin Dopazo, 2003, Genome research.

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

Joaquín Dopazo, Javier Herrero, J. Dopazo, 2002, Journal of proteome research.

A comparative encyclopedia of DNA elements in the mouse genome

Shane J. Neph, Dmitri D. Pervouchine, Matthew D. Rasmussen, 2014, Nature.

Alignathon: a competitive assessment of whole-genome alignment methods

David Haussler, Inna Dubchak, Ngan Nguyen, 2014, bioRxiv.

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

Gautier Koscielny, Manolis Kellis, Ewan Birney, 2012, Genome Biology.

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

Kathryn Beal, Olgert Denas, Ross C Hardison, 2014, BMC Genomics.

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

Albert J. Vilella, Matthew D. Rasmussen, André L. Martins, 2011, Nature.

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

Yoshiyuki Sakaki, Sumio Sugano, Anthony T Papenfuss, 2011, Genome Biology.

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

S. Searle, G. Weinstock, R. Gibbs, 2013, Genome Biology.

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

Matthieu Muffato, Manuel Gil, Christophe Dessimoz, 2015, Systematic biology.

The zebrafish reference genome sequence and its relationship to the human genome

Anton J. Enright, James D. Cooper, N. Carter, 2013, Nature.

Aequatus: An open-source homology browser

Anil S. Thanki, Robert P. Davey, Javier Herrero, 2016, bioRxiv.

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

Albert J. Vilella, Steven G. Schroeder, Edward J. Smith, 2010, PLoS biology.

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

S. Searle, Jun Wang, Yingrui Li, 2013, Nature Genetics.

The draft genomes of softshell turtle and green sea turtle yield insights into the development and evolution of the turtlespecific body plan

Bronwen L. Aken, A. Zadissa, S. Searle, 2013 .

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

Bronwen L. Aken, A. Zadissa, S. Searle, 2013, Nature Genetics.

Genome-wide nucleotide-level mammalian ancestor reconstruction.

E. Birney, P. Flicek, I. Holmes, 2008, Genome research.

Ensembl comparative genomics resources

Albert J. Vilella, Andrew D. Yates, S. Searle, 2016, Database : the journal of biological databases and curation.

Phylogenetic Identification and Functional Characterization of Orthologs and Paralogs across Human, Mouse, Fly, and Worm

Matthew D. Rasmussen, Manolis Kellis, Javier Herrero, 2014, bioRxiv.

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

Albert J. Vilella, E. Birney, P. Flicek, 2011, Genome Biology.

Insights into hominid evolution from the gorilla genome sequence

Albert J. Vilella, Gregory E. Jordan, Petra C. Schwalie, 2012, Nature.

Gibbon genome and the fast karyotype evolution of small apes

August E. Woerner, Matthew W. Hahn, Miriam K. Konkel, 2014 .

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

Alexander S. Garruss, Alexander S Garruss, Bronwen L. Aken, 2013, Nature Genetics.

Consortium, G.P A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073

Ken Chen, Joshua M. Korn, Afidalina Tumian, 2010 .

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

Joaquín Dopazo, Christian Blaschke, Javier Herrero, 2002, Journal of biotechnology.

Ensembl comparative genomics resources

Albert J. Vilella, Andrew D. Yates, S. Searle, 2016, Database J. Biol. Databases Curation.

Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma.

A. Dopazo, M. Piris, J. Dopazo, 2002, The American journal of pathology.

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

Anton J. Enright, James D. Cooper, N. Carter, 2013, Nature.

Construction of a high density linkage map in Oil Palm using SPET markers

Javier Herrero, E. Ritter, A. Herrán, 2020, Scientific Reports.

Development of a molecular marker system to distinguish shell thickness in oil palm genotypes

Javier Herrero, E. Ritter, D. Asmono, 2015, Euphytica.

Ensembl comparative genomics resources

Albert J. Vilella, Andrew D. Yates, S. Searle, 2016, Database J. Biol. Databases Curation.

Next station in microarray data analysis: GEPAS

Joaquín Dopazo, Joaquín Tárraga, Javier Herrero, 2006, Nucleic Acids Res..

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

Joaquín Dopazo, Ramón Díaz-Uriarte, Javier Herrero, 2005, Nucleic Acids Res..

Evaluation of root biomass, rubber and inulincontents in nine Taraxacum koksaghyz Rodin populations

Javier Herrero, E. Ritter, M. Arias, 2016 .

Toward community standards in the quest for orthologs

Javier Herrero, David S. Roos, Erik L. L. Sonnhammer, 2012, Bioinform..

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

Arcadi Navarro, Joel Armstrong, Benedict Paten, 2017, GigaScience.

An integrated map of genetic variation from 1,092 human genomes

Kenny Q. Ye, Mauricio O. Carneiro, Francisco M. De La Vega, 2012, Nature.

Ensembl 2014

Daniel R. Zerbino, Laurent Gil, Ewan Birney, 2013, Nucleic Acids Res..

Ensembl 2012

Gautier Koscielny, Laurent Gil, Ewan Birney, 2011, Nucleic Acids Res..

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

Kathryn Beal, William Chow, Kerstin Howe, 2014, bioRxiv.

Salinibacter ruber: genomics and biogeography

R. Amann, F. Glöckner, J. Dopazo, 2005 .

Ensembl 2013

Laurent Gil, Paul Flicek, Fiona Cunningham, 2012, Nucleic Acids Res..

A hierarchical unsupervised growing neural network for clustering gene expression patterns

Alfonso Valencia, Joaquín Dopazo, Javier Herrero, 2001, Bioinform..

Supplemental Section S1 – Genome Sequencing and Assembly........................................... 2 Supplemental Section S2 – Indel Assessment with the Neutral Indel Model ................11 Supplemental Section S3 – Great Ape Divergence Estimate via Wgs Read Mapping..11 Supplemental Section S7 –

Albert J. Vilella, Zhengyuan O. Wang, Miriam K. Konkel, 2022 .

An Approach to Inferring Transcriptional Regulation Among Genes From Large-Scale Expression Data

Joaquín Dopazo, Ramón Díaz-Uriarte, Javier Herrero, 2003, Comparative and functional genomics.

Ensembl 2009

Andrew M. Jenkinson, Sarah C. Ayling, Damian Smedley, 2008, Nucleic Acids Res..

Ensembl 2006

Andreas Prlic, Damian Smedley, Daniel Rios, 2005, Nucleic Acids Res..

Extending reference assembly models

Richard Durbin, Michael M Hoffman, Gabor T Marth, 2015, Genome Biology.

Ensembl 2005

Damian Smedley, Ewan Birney, Javier Herrero, 2004, Nucleic Acids Res..

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

Olivier Gascuel, Paolo Di Tommaso, Jia-Ming Chang, 2019, Bioinform..

ncRNA orthologies in the vertebrate lineage

Paul Flicek, Miguel Pignatelli, Albert J. Vilella, 2016, Database J. Biol. Databases Curation.

Database: The Journal of Biological Databases and Curation

Miguel Pignatelli, Albert J. Vilella, Matthieu Muffato, 2016 .

Ensembl 2007

Andreas Prlic, Damian Smedley, Ewan Birney, 2006, Nucleic Acids Res..

Construction of a high density linkage map in Oil Palm using SPET markers

Javier Herrero, E. Ritter, A. Herrán, 2020, Scientific Reports.

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

R. Sandstrom, Olgert Denas, R. Hardison, 2014, bioRxiv.

Ensembl 2011

Daniel Rios, Yuan Chen, Paul Flicek, 2010, Nucleic Acids Res..

Ensembl Genomes: Extending Ensembl across the taxonomic space

Gautier Koscielny, Uma Maheswari, Paul J. Kersey, 2009, Nucleic Acids Res..

Aequatus: an open-source homology browser

Anil S. Thanki, Anil S Thanki, Nicola Soranzo, 2016, bioRxiv.

Gene expression data preprocessing

Joaquín Dopazo, Javier Herrero, Ramón Díaz-Uriarte, 2003, Bioinform..

eHive: An Artificial Intelligence workflow system for genomic analysis

Paul Flicek, Albert J. Vilella, Leo Gordon, 2010, BMC Bioinformatics.

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

Joaquín Dopazo, Ramón Díaz-Uriarte, Javier Herrero, 2003, Nucleic Acids Res..

Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma.

A. Dopazo, M. Piris, J. Dopazo, 2002, The American journal of pathology.

Ensembl’s 10th year

Gautier Koscielny, Andrew M. Jenkinson, Damian Smedley, 2009, Nucleic Acids Res..

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

Benedict Paten, Javier Herrero, Ewan Birney, 2009, Bioinform..

New Challenges in Gene Expression Data Analysis and the Extended GEPAS

Joaquín Dopazo, Ramón Díaz-Uriarte, Javier Herrero, 2004, Spanish Bioinformatics Conference.

Analysis of genetic diversity and discrimination of Oil Palm DxP populations based on the origins of pisifera elite parents

Javier Herrero, E. Ritter, D. Asmono, 2021, Breeding science.

Development of a molecular marker system to distinguish shell thickness in oil palm genotypes

Javier Herrero, E. Ritter, D. Asmono, 2015, Euphytica.

Using a Genetic Algorithm and a Perceptron for Feature Selection and Supervised Class Learning in DNA Microarray Data

Joaquín Dopazo, Javier Herrero, Álvaro Mateos, 2003, Artificial Intelligence Review.

The common marmoset genome provides insight into primate biology and evolution

Albert J. Vilella, Charles E. Vejnar, Miriam K. Konkel, 2014, Nature Genetics.

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

China, S. Searle, R. Webster, 2014 .

A comparative encyclopedia of DNA elements in the mouse genome

Mukul S. Bansal, Shane J. Neph, Dmitri D. Pervouchine, 2014, Nature.

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

Gabor T. Marth, Uday S. Evani, H. Kang, 2013, Science.

Gibbon genome and the fast karyotype evolution of small apes

August E. Woerner, Matthew W. Hahn, Miriam K. Konkel, 2014, Nature.

Digital Commons@Becker

Gabor T. Marth, Bronwen L. Aken, R. Durbin, 2022 .

Supervised Neural Networks for Clustering Conditions in DNA Array Data After Reducing Noise by Clustering Gene Expression Profiles

Joaquín Dopazo, Javier Herrero, Álvaro Mateos, 2002 .

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

E. Birney, B. Paten, Javier Herrero, 2009, Bioinform..