J. Rodríguez

发表

GENCODE: The reference human genome annotation for The ENCODE Project

Bronwen L. Aken, Michael F. Lin, D. Haussler, 2012, Genome research.

De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

J. Rodriguez, D. Pisano, A. Muñoz-Mérida, 2013, DNA research : an international journal for rapid publication of reports on genes and genomes.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

Alfonso Valencia, Jennifer Harrow, Michael L. Tress, 2012, Molecular biology and evolution.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

APPRIS: annotation of principal and alternative splice isoforms

Alfonso Valencia, Michael L. Tress, Gonzalo López, 2012, Nucleic Acids Res..

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level

Alfonso Valencia, Michael L. Tress, Jose Manuel Rodriguez, 2015, PLoS Comput. Biol..

Most highly expressed protein-coding genes have a single dominant isoform.

Alfonso Valencia, Jose Manuel Rodriguez, Iakes Ezkurdia, 2015, Journal of proteome research.

APPRIS 2017: principal isoforms for multiple gene sets

Alfonso Valencia, Tomás Di Domenico, Michael L. Tress, 2017, Nucleic Acids Res..

Loose ends: almost one in five human genes still have unresolved coding status

Laura Martinez, Jose Manuel Rodriguez, David Juan, 2018, Nucleic acids research.

Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

J. Harrow, A. Frankish, M. Diekhans, 2014, Human molecular genetics.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

M. Tress, J. Rodriguez, A. Valencia, 2016, Genome Biology.

Unbiased plasma proteomics discovery of biomarkers for improved detection of subclinical atherosclerosis

J. Rodriguez, J. Ordovás, B. Ibáñez, 2022, EBioMedicine.

Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene

J. Rodriguez, E. Ganko, J. McDonald, 2002, BMC Evolutionary Biology.

Clinical variant interpretation and biologically relevant reference transcripts

M. Tress, J. Rodriguez, Jesús Vázquez, 2022, npj Genomic Medicine.

APPRIS principal isoforms and MANE Select transcripts in clinical variant interpretation

M. Tress, J. Rodriguez, Jesús Vázquez, 2021, bioRxiv.

An analysis of tissue-specific alternative splicing at the protein level

M. Tress, J. Rodriguez, Jesús Vázquez, 2020, PLoS Comput. Biol..

PanDrugs: a novel method to prioritize anticancer drug treatments according to individual genomic data

J. Rodriguez, A. Valencia, M. Hidalgo, 2018, Genome Medicine.

APPRIS WebServer and WebServices

Alfonso Valencia, Michael L. Tress, Jose Manuel Rodriguez, 2015, Nucleic Acids Res..

firestar—advances in the prediction of functionally important residues

Alfonso Valencia, Michael L. Tress, Gonzalo López, 2011, Nucleic Acids Res..

Assessing the functional relevance of splice isoforms

M. Tress, J. Rodriguez, F. Abascal, 2021, NAR genomics and bioinformatics.

The EMBRACE web service collection

Terri K. Attwood, Jon C. Ison, Vincent Breton, 2010, Nucleic Acids Res..

iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data

J. López, E. Camafeita, I. Jorge, 2023, bioRxiv.

SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments

Jose Manuel Rodriguez, Iakes Ezkurdia, Marco Trevisan-Herraz, 2018, Bioinform..

Comprehensive quantification of the modified proteome reveals oxidative heart damage in mitochondrial heteroplasmy

Spiros Michalakopoulos, Jesús Vázquez, Iakes Ezkurdia, 2018, bioRxiv.

The shrinking human protein coding complement: are there now fewer than 20,000 genes?

Alfonso Valencia, Mark Diekhans, Jennifer Harrow, 2013, bioRxiv.

TurboPutative: A web server for data handling and metabolite classification in untargeted metabolomics

J. Rodriguez, A. Ferrarini, Jesús Vázquez, 2022, Frontiers in Molecular Biosciences.

Resource GENCODE : The reference human genome annotation for The ENCODE Project

Bronwen L. Aken, J. Harrow, A. Frankish, 2012 .

Hierarchical analyses of genetic variation of samples from breeding and feeding grounds confirm the genetic partitioning of northwest Atlantic and South Atlantic populations of swordfish (Xiphias gladius L.)

J. Rodriguez, J. Mejuto, J. Viñas, 2005 .