Alfonso Valencia

According to our database1, Alfonso Valencia
  • authored at least 133 papers between 1994 and 2018.
  • has a "Dijkstra number"2 of four.



In proceedings 
PhD thesis 




APPRIS 2017: principal isoforms for multiple gene sets.
Nucleic Acids Research, 2018

LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes.
Nucleic Acids Research, 2017

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.
Bioinformatics, 2017

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.
Bioinformatics, 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

ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing.
PLoS Computational Biology, 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, 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

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.
PLoS Computational Biology, 2015

APPRIS WebServer and WebServices.
Nucleic Acids Research, 2015

ChiTaRS 2.1 - an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.
Nucleic Acids Research, 2015

The CHEMDNER corpus of chemicals and drugs and its annotation principles.
J. Cheminformatics, 2015

CHEMDNER: The drugs and chemical names extraction challenge.
J. Cheminformatics, 2015

Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013.
Bioinformatics, 2015

Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces.
Bioinformatics, 2015

Detection of significant protein coevolution.
Bioinformatics, 2015

FUN-L: gene prioritization for RNAi screens.
Bioinformatics, 2015

Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals.
Bioinformatics, 2015

Predicting Protein Relationshipsto Human Pathways througha Relational Learning ApproachBased on Simple Sequence Features.
IEEE/ACM Trans. Comput. Biology Bioinform., 2014

FireDB: a compendium of biological and pharmacologically relevant ligands.
Nucleic Acids Research, 2014

CheNER: chemical named entity recognizer.
Bioinformatics, 2014

BioCreative-IV virtual issue.
Database, 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

APPRIS: annotation of principal and alternative splice isoforms.
Nucleic Acids Research, 2013

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.
Nucleic Acids Research, 2013

wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases.
BMC Bioinformatics, 2013

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.
Bioinformatics, 2013

BioC: a minimalist approach to interoperability for biomedical text processing.
Database, 2013

Machine Reading of Biomedical Texts about Alzheimer's Disease.
Proceedings of the Working Notes for CLEF 2013 Conference , 2013

Chapter 14: Cancer Genome Analysis.
PLoS Computational Biology, 2012

Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region
CoRR, 2012

MyMiner: a web application for computer-assisted biocuration and text annotation.
Bioinformatics, 2012

Bioimage informatics: a new category in Bioinformatics.
Bioinformatics, 2012

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures.
Bioinformatics, 2012

Mirroring co-evolving trees in the light of their topologies.
Bioinformatics, 2012

EnrichNet: network-based gene set enrichment analysis.
Bioinformatics, 2012

Novel domain combinations in proteins encoded by chimeric transcripts.
Bioinformatics, 2012

BioCreative-2012 Virtual Issue.
Database, 2012

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.
Database, 2012

Text mining for the biocuration workflow.
Database, 2012

wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases.
Proceedings of the Workshop on Annotation, 2012

Machine Reading of Biomedical Texts about Alzheimer's Disease.
Proceedings of the CLEF 2012 Evaluation Labs and Workshop, 2012

firestar - advances in the prediction of functionally important residues.
Nucleic Acids Research, 2011

Mirroring co-evolving trees in the light of their topologies
CoRR, 2011

Characterization of pathogenic germline mutations in human Protein Kinases.
BMC Bioinformatics, 2011

Selection of organisms for the co-evolution-based study of protein interactions.
BMC Bioinformatics, 2011

Overview of the BioCreative III Workshop.
BMC Bioinformatics, 2011

On the organization of bioinformatics core services in biology-based research institutes.
Bioinformatics, 2011

An Overview of BioCreative II.5.
IEEE/ACM Trans. Comput. Biology Bioinform., 2010

The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions.
BMC Bioinformatics, 2010

Extending pathways and processes using molecular interaction networks to analyse cancer genome data.
BMC Bioinformatics, 2010

TopoGSA: network topological gene set analysis.
Bioinformatics, 2010

Bioinformatic Software Developments in Spain.
Proceedings of the Bioinformatics for Personalized Medicine, 2010

iHOP Web Services Family.
Proceedings of the Bioinformatics for Personalized Medicine, 2010

EcID. A database for the inference of functional interactions in E. coli.
Nucleic Acids Research, 2009

PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction.
Nucleic Acids Research, 2009

Bionemo: molecular information on biodegradation metabolism.
Nucleic Acids Research, 2009

Extraction of human kinase mutations from literature, databases and genotyping studies.
BMC Bioinformatics, 2009

An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D.
BMC Bioinformatics, 2009

Automated Alphabet Reduction for Protein Datasets.
BMC Bioinformatics, 2009

Progress and challenges in predicting protein-protein interaction sites.
Briefings in Bioinformatics, 2009

SOA-Based Integration of Text Mining Services.
Proceedings of the 2009 IEEE Congress on Services, Part I, 2009

Defining functional distances over Gene Ontology.
BMC Bioinformatics, 2008

Enhancing the prediction of protein pairings between interacting families using orthology information.
BMC Bioinformatics, 2008

Determination and validation of principal gene products.
Bioinformatics, 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

Text mining in genomics and systems biology.
Proceedings of the Proceeding of the 2nd International Workshop on Data and Text Mining in Bioinformatics, 2008

iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology.
Proceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine, 2008

Protein Interactions Extracted from Genomes and Papers.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

firestar - prediction of functionally important residues using structural templates and alignment reliability.
Nucleic Acids Research, 2007

FireDB - a database of functionally important residues from proteins of known structure.
Nucleic Acids Research, 2007

iHOP web services.
Nucleic Acids Research, 2007

CARGO: a web portal to integrate customized biological information.
Nucleic Acids Research, 2007

Bioinformatics, 2007

TSEMA: interactive prediction of protein pairings between interacting families.
Nucleic Acids Research, 2006

TreeDet: a web server to explore sequence space.
Nucleic Acids Research, 2006

An analysis of the Sargasso Sea resource and the consequences for database composition.
BMC Bioinformatics, 2006

Software patents in Bioinformatics.
Bioinformatics, 2006

Phylogeny-independent detection of functional residues.
Bioinformatics, 2006

Synthetic Biology: challenges ahead.
Bioinformatics, 2006

Bioinformatics in the human interactome project.
Bioinformatics, 2006

Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005).
Bioinformatics, 2006

Structural genomics meets computational biology.
Bioinformatics, 2006

Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories.
Trans. Computational Systems Biology, 2005

MetaRouter: bioinformatics for bioremediation.
Nucleic Acids Research, 2005

HCAD, closing the gap between breakpoints and genes.
Nucleic Acids Research, 2005

EVAcon: a protein contact prediction evaluation service.
Nucleic Acids Research, 2005

A sentence sliding window approach to extract protein annotations from biomedical articles.
BMC Bioinformatics, 2005

Overview of BioCreAtIvE: critical assessment of information extraction for biology.
BMC Bioinformatics, 2005

Evaluation of BioCreAtIvE assessment of task 2.
BMC Bioinformatics, 2005

Increasing the Impact of Bioinformatics.
Bioinformatics, 2005

Do you do text?
Bioinformatics, 2005

An update from the Bioinformatics Editors.
Bioinformatics, 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

Implementing the iHOP concept for navigation of biomedical literature.
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

ECCB/JBI 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

SIGIR 2003 workshop on text analysis and search for bioinformatics.
SIGIR Forum, 2004

IntAct: an open source molecular interaction database.
Nucleic Acids Research, 2004

SPOC: A widely distributed domain associated with cancer, apoptosis and transcription.
BMC Bioinformatics, 2004

SQUARE-determining reliable regions in sequence alignments.
Bioinformatics, 2004

YAdumper: extracting and translating large information volumes from relational databases to structured flat files.
Bioinformatics, 2004

New Leadership for Bioinformatics.
Bioinformatics, 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

Assessing the Correlation between Contextual Patterns and Biological Entity Tagging.
Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications, 2004

EVA: evaluation of protein structure prediction servers.
Nucleic Acids Research, 2003

Meta, Metan and Cyber Servers.
Bioinformatics, 2003

Early bioinformatics: the birth of a discipline - a personal view.
Bioinformatics, 2003

Evaluation of annotation strategies using an entire genome sequence.
Bioinformatics, 2003

The Frame-Based Module of the SUISEKI Information Extraction System.
IEEE Intelligent Systems, 2002

Bioinformatics: Biology by other means.
Bioinformatics, 2002

Bioinformatics in structural genomics - Editorial.
Bioinformatics, 2002

Clustering of proximal sequence space for the identification of protein families.
Bioinformatics, 2002

Information extraction in molecular biology.
Briefings in Bioinformatics, 2002

Challenges for Intelligent Systems in Biology.
IEEE Intelligent Systems, 2001

A hierarchical unsupervised growing neural network for clustering gene expression patterns.
Bioinformatics, 2001

EVA: continuous automatic evaluation of protein structure prediction servers.
Bioinformatics, 2001

A platform for integrating threading results with protein family analyses.
Bioinformatics, 1999

Automated genome sequence analysis and annotation.
Bioinformatics, 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

Computational space reduction and parallelization of a new clustering approach for large groups of sequences.
Bioinformatics, 1998

EUCLID: automatic classification of proteins in functional classes by their database annotations.
Bioinformatics, 1998

Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Bioinformatics, 1998

A graphical interface for correlated mutations and other protein structure prediction methods.
Computer Applications in the Biosciences, 1997

Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function.
Computer Applications in the Biosciences, 1997

Classification of protein families and detection of the determinant residues with an improved self-organizing map.
Biological Cybernetics, 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

The Functional Composition of Living Machines as a Design Principle for Artificial Organisms.
Proceedings of the Advances in Artificial Life, 1995

GeneQuiz: A Workbench for Sequence Analysis.
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994