J. Rodriguez

发表

GENCODE: The reference human genome annotation for The ENCODE Project

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

An Integrated Encyclopedia of DNA Elements in the Human Genome

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

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

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

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

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

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

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

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

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

APPRIS: selecting functionally important isoforms

M. Tress, J. Rodriguez, Jesús Vázquez, 2021, Nucleic Acids Res..

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

J. Rodriguez, I. Ezkurdia, J. Enríquez, 2018, 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.

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 define reference splice variants

M. Tress, J. Rodriguez, Jesús Vázquez, 2022, Bioinformatics.

Frequency of HLA‐C alleles in differentiated thyroid carcinoma in southeastern Spain

J. Rodriguez, P. Parrilla, A. Ríos, 2004, Cancer.

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..

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.

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.

Assessing the functional relevance of splice isoforms

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

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.

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

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

APPRIS: annotation of principal and alternative splice isoforms

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

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.

CARGO: a web portal to integrate customized biological information

Alfonso Valencia, Jose Manuel Rodriguez, David G. Pisano, 2007, Nucleic Acids Res..

APPRIS principal isoforms and MANE Select transcripts in clinical variant interpretation

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

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

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

Perspectives on ENCODE

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

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.

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

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

APPRIS 2017: principal isoforms for multiple gene sets

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

APPRIS WebServer and WebServices

Alfonso Valencia, Michael L. Tress, Jose Manuel Rodriguez, 2015, 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.

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

J. Rodriguez, M. Hidalgo, F. Al-Shahrour, 2018, Genome Medicine.

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

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

firestar—advances in the prediction of functionally important residues

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

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 .

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..

The EMBRACE web service collection

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