Alfonso Valencia
Orcid: 0000-0002-8937-6789Affiliations:
- Barcelona Supercomputing Centre, Life Sciences Department, Spain
According to our database1,
Alfonso Valencia
authored at least 158 papers
between 1994 and 2023.
Collaborative distances:
Collaborative distances:
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Online presence:
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on orcid.org
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on id.loc.gov
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Bibliography
2023
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations.
Database J. Biol. Databases Curation, 2023
Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation.
Proceedings of the Platform for Advanced Scientific Computing Conference, 2023
2022
PLoS Comput. Biol., 2022
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools.
Bioinform., 2022
Proceedings of the 21st Workshop on Biomedical Language Processing, 2022
2021
Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment.
npj Digit. Medicine, 2021
Proceedings of the Computational Methods in Systems Biology, 2021
2020
Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare.
npj Digit. Medicine, 2020
Nucleic Acids Res., 2020
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research.
F1000Research, 2020
Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning (DCTL).
Bioinform., 2020
On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models.
Bioinform., 2020
Bioinform., 2020
Proceedings of the High Performance Computing, 2020
2019
IEEE Technol. Soc. Mag., 2019
PLoS Comput. Biol., 2019
Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm.
J. Cheminformatics, 2019
Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention.
Bioinform., 2019
Bioinform., 2019
BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications.
Bioinform., 2019
Briefings Bioinform., 2019
2018
2017
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes.
Nucleic Acids Res., 2017
CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.
Bioinform., 2017
ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.
Bioinform., 2017
The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts.
Proceedings of the Second Workshop on Evaluation of Human Language Technologies for Iberian Languages (IberEval 2017) co-located with 33th Conference of the Spanish Society for Natural Language Processing (SEPLN 2017), 2017
2016
ISCB's Initial Reaction to <i>The New England Journal of Medicine</i> Editorial on Data Sharing.
PLoS Comput. Biol., 2016
A computational approach inspired by simulated annealing to study the stability of protein interaction networks in cancer and neurological disorders.
Data Min. Knowl. Discov., 2016
The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge.
Database J. Biol. Databases Curation, 2016
Annotation Process, Guidelines and Text Corpus of Small Non-Coding RNA Molecules: the MiNCor for MicroRNA Annotations.
Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, 2016
2015
Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.
PLoS Comput. Biol., 2015
ChiTaRS 2.1 - an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.
Nucleic Acids Res., 2015
J. Cheminformatics, 2015
J. Cheminformatics, 2015
Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces.
Bioinform., 2015
Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals.
Bioinform., 2015
2014
Predicting Protein Relationshipsto Human Pathways througha Relational Learning ApproachBased on Simple Sequence Features.
IEEE ACM Trans. Comput. Biol. Bioinform., 2014
Nucleic Acids Res., 2014
Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis.
Proceedings of the 8th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2014
2013
Nucleic Acids Res., 2013
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.
Nucleic Acids Res., 2013
wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases.
BMC Bioinform., 2013
RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.
Bioinform., 2013
Database J. Biol. Databases Curation, 2013
Proceedings of the Working Notes for CLEF 2013 Conference , 2013
2012
Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region
CoRR, 2012
Bioinform., 2012
JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.
Bioinform., 2012
Bioinform., 2012
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.
Database J. Biol. Databases Curation, 2012
2011
Nucleic Acids Res., 2011
BMC Bioinform., 2011
BMC Bioinform., 2011
On the organization of bioinformatics core services in biology-based research institutes.
Bioinform., 2011
2010
The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions.
BMC Bioinform., 2010
Extending pathways and processes using molecular interaction networks to analyse cancer genome data.
BMC Bioinform., 2010
Proceedings of the Bioinformatics for Personalized Medicine, 2010
Proceedings of the Bioinformatics for Personalized Medicine, 2010
2009
Nucleic Acids Res., 2009
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.
Nucleic Acids Res., 2009
Nucleic Acids Res., 2009
Extraction of human kinase mutations from literature, databases and genotyping studies.
BMC Bioinform., 2009
An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D.
BMC Bioinform., 2009
Briefings Bioinform., 2009
Proceedings of the 2009 IEEE Congress on Services, Part I, 2009
2008
Enhancing the prediction of protein pairings between interacting families using orthology information.
BMC Bioinform., 2008
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008
Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology.
Proceedings of the Linking Literature, Information, and Knowledge for Biology, 2008
Proceedings of the Proceeding of the 2nd International Workshop on Data and Text Mining in Bioinformatics, 2008
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008
Proceedings of the Protein-protein Interactions and Networks: Identification, 2008
2007
<i>firestar</i> - prediction of functionally important residues using structural templates and alignment reliability.
Nucleic Acids Res., 2007
FireDB - a database of functionally important residues from proteins of known structure.
Nucleic Acids Res., 2007
Nucleic Acids Res., 2007
2006
Nucleic Acids Res., 2006
An analysis of the Sargasso Sea resource and the consequences for database composition.
BMC Bioinform., 2006
Semantic Mining in Biomedicine <i>(Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005)</i>.
Bioinform., 2006
2005
Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories.
Trans. Comp. Sys. Biology, 2005
A sentence sliding window approach to extract protein annotations from biomedical articles.
BMC Bioinform., 2005
BMC Bioinform., 2005
A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005
Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps.
Proceedings of the Data Analysis and Visualization in Genomics and Proteomics, 2005
2004
SIGIR Forum, 2004
SPOC: A widely distributed domain associated with cancer, apoptosis and transcription.
BMC Bioinform., 2004
YAdumper: extracting and translating large information volumes from relational databases to structured flat files.
Bioinform., 2004
Bioinformatic Analyses of the Dio Family of Proteins.
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004
XML Databases, are Ready for Bioinformatics?
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004
The Biodegradation Network, a New Scenario for Computational Systems Biology Research.
Proceedings of the Computational Methods in Systems Biology, International Conference, 2004
Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications, 2004
2003
Bioinform., 2003
2002
IEEE Intell. Syst., 2002
Bioinform., 2002
2001
A hierarchical unsupervised growing neural network for clustering gene expression patterns.
Bioinform., 2001
Bioinform., 2001
1999
Bioinform., 1999
Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions.
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999
1998
Computational space reduction and parallelization of a new clustering approach for large groups of sequences.
Bioinform., 1998
EUCLID: automatic classification of proteins in functional classes by their database annotations.
Bioinform., 1998
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Bioinform., 1998
1997
A graphical interface for correlated mutations and other protein structure prediction methods.
Comput. Appl. Biosci., 1997
Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function.
Comput. Appl. Biosci., 1997
Classification of protein families and detection of the determinant residues with an improved self-organizing map.
Biol. Cybern., 1997
Automatic Annotation for Biological Sequences by Etraction of Keywords from MEDLINE Abstracts: Development of a Prototype System.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997
Comparative Analysis of Different Methods for the Detection of Specificity Regions in Protein Families.
Proceedings of the Biocomputing and emergent computation: Proceedings of BCEC97, 1997
1995
The Functional Composition of Living Machines as a Design Principle for Artificial Organisms.
Proceedings of the Advances in Artificial Life, 1995
1994
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994