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List of works by José M. Fernández

A FAIRification roadmap for ELIXIR Software Management Plans

scientific article published in 2022

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

BioHackEU23: FAIR Workflow Execution with WfExS and Workflow Run Crate

Bioinformatic Software Developments in Spain

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

scientific article

CARGO: a web portal to integrate customized biological information

scientific article published on 5 May 2007

COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain

publication published on 30 November 2021

ELIXIR Software Management Plan for Life Sciences

FUN-L: gene prioritization for RNAi screens

scientific article published on 08 February 2015

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

scientific article published on 26 January 2017

Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation

scientific article

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

scientific article

Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships

scientific article published on 05 June 2020

Packaging research artefacts with RO-Crate

scientific article published on 20 July 2022

RD-Connect: Data sharing and analysis for rare disease research within the integrated platform and through GA4GH beacon and matchmaker exchange

article

RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data

scientific article

RUbioSeq+: An Application that Executes Parallelized Pipelines to Analyse Next-Generation Sequencing Data

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses

scientific article published on 28 April 2013

Recommendations for the FAIRification of genomic track metadata

scientific article published in 2021

Recording provenance of workflow runs with RO-Crate

scientific article published on 10 September 2024

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

scientific article

The BLUEPRINT Data Analysis Portal.

scientific article

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

scientific article published on 19 November 2019

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

scientific article (publication date: 21 August 2010)

The EMBRACE web service collection

scientific article (publication date: July 2010)

The Quest for Orthologs benchmark service and consensus calls in 2020

scientific article published on 06 May 2020

The REGIA database (RegiaDB): status, limitations and future developments

scientific article published on January 2002

Unveiling the molecular basis of disease co-occurrence: towards personalized comorbidity profiles

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

scientific article published in December 2023

YAdumper: extracting and translating large information volumes from relational databases to structured flat files

scientific article

iHOP Web Services Family

iHOP web services

scientific article (publication date: July 2007)

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