GeneQuiz: A Workbench for Sequence Analysis. - Michael Scharf; Reinhard Schneider 002; Georg Casari; Peer Bork; Alfonso Valencia; Christos A. Ouzounis; Chris Sander (ISMB, 1994)

The Functional Composition of Living Machines as a Design Principle for Artificial Organisms. - Christos A. Ouzounis; Alfonso Valencia; Javier Tamames; Peer Bork; Chris Sander (ECAL, 1995)

Comparative Analysis of Different Methods for the Detection of Specificity Regions in Protein Families. - Florencio Pazos; Luis Sánchez-Pulido; Juan Antonio Garcia-Ranca; Miguel A. Andrade; Silvia Atrian; Alfonso Valencia (BCEC, 1997)

Automatic Annotation for Biological Sequences by Etraction of Keywords from MEDLINE Abstracts: Development of a Prototype System. - Miguel A. Andrade; Alfonso Valencia (ISMB, 1997)

Classification of protein families and detection of the determinant residues with an improved self-organizing map. - Miguel A. Andrade; Georg Casari; Chris Sander; Alfonso Valencia (Biol. Cybern., 1997)

Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. - Miguel A. Andrade; Georg Casari; Antoine de Daruvar; Chris Sander; Reinhard Schneider 002; Javier Tamames; Alfonso Valencia; Christos A. Ouzounis (Comput. Appl. Biosci., 1997)

A graphical interface for correlated mutations and other protein structure prediction methods. - Florencio Pazos; O. Olmea; Alfonso Valencia (Comput. Appl. Biosci., 1997)

Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. - Miguel A. Andrade; Alfonso Valencia (Bioinform., 1998)

EUCLID: automatic classification of proteins in functional classes by their database annotations. - Javier Tamames; Christos A. Ouzounis; Georg Casari; Chris Sander; Alfonso Valencia (Bioinform., 1998)

Computational space reduction and parallelization of a new clustering approach for large groups of sequences. - Oswaldo Trelles; Miguel A. Andrade; Alfonso Valencia; Emilio L. Zapata; José María Carazo (Bioinform., 1998)

Automatic Extraction of Biological Information from Scientific Text: Protein-Protein Interactions. - Christian Blaschke; Miguel A. Andrade; Christos A. Ouzounis; Alfonso Valencia (ISMB, 1999)

Automated genome sequence analysis and annotation. - Miguel A. Andrade; Nigel P. Brown; Christophe Leroy; S. Hörsch; Antoine de Daruvar; C. Reich; Angelo Franchini; Javier Tamames; Alfonso Valencia; Christos A. Ouzounis; Chris Sander (Bioinform., 1999)

A platform for integrating threading results with protein family analyses. - Florencio Pazos; Burkhard Rost; Alfonso Valencia (Bioinform., 1999)

EVA: continuous automatic evaluation of protein structure prediction servers. - Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; András Fiser; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Bioinform., 2001)

A hierarchical unsupervised growing neural network for clustering gene expression patterns. - Javier Herrero; Alfonso Valencia; Joaquín Dopazo (Bioinform., 2001)

Challenges for Intelligent Systems in Biology. - Russ B. Altman; Alfonso Valencia; Satoru Miyano; Shoba Ranganathan (IEEE Intell. Syst., 2001)

Information extraction in molecular biology. - Christian Blaschke; Lynette Hirschman; Alfonso Valencia (Briefings Bioinform., 2002)

Clustering of proximal sequence space for the identification of protein families. - Federico Abascal; Alfonso Valencia (Bioinform., 2002)

Bioinformatics in structural genomics - Editorial. - Burkhard Rost; Barry Honig; Alfonso Valencia (Bioinform., 2002)

Bioinformatics: Biology by other means. - Alfonso Valencia (Bioinform., 2002)

The Frame-Based Module of the SUISEKI Information Extraction System. - Christian Blaschke; Alfonso Valencia (IEEE Intell. Syst., 2002)

Evaluation of annotation strategies using an entire genome sequence. - Ioannis Iliopoulos; Sophia Tsoka; Miguel A. Andrade; Anton J. Enright; Mark Carroll; Patrick Poullet; Vasilis J. Promponas; Theodore Liakopoulos; Giorgos Palaios; Claude Pasquier; Stavros J. Hamodrakas; Javier Tamames; et al. (Bioinform., 2003)

Early bioinformatics: the birth of a discipline - a personal view. - Christos A. Ouzounis; Alfonso Valencia (Bioinform., 2003)

Meta, Metan and Cyber Servers. - Alfonso Valencia (Bioinform., 2003)

EVA: evaluation of protein structure prediction servers. - Ingrid Y. Y. Koh; Volker A. Eyrich; Marc A. Martí-Renom; Dariusz Przybylski; Mallur S. Madhusudhan; Narayanan Eswar; Osvaldo Graña; Florencio Pazos; Alfonso Valencia; Andrej Sali; Burkhard Rost (Nucleic Acids Res., 2003)

Assessing the Correlation between Contextual Patterns and Biological Entity Tagging. - Martin Krallinger; Maria Padron; Christian Blaschke; Alfonso Valencia (NLPBA/BioNLP, 2004)

The Biodegradation Network, a New Scenario for Computational Systems Biology Research. - Florencio Pazos; David Guijas; Manuel J. Gómez; Almudena Trigo; Victor de Lorenzo; Alfonso Valencia (CMSB, 2004)

XML Databases, are Ready for Bioinformatics? - José María Fernández 001; Alfonso Valencia (Spanish Bioinformatics Conference, 2004)

Bioinformatic Analyses of the Dio Family of Proteins. - Ana María Rojas; Luis Sánchez-Pulido; Agnes Fütterer; Karel H. M. van Wely; Carlos Martínez-A; Alfonso Valencia (Spanish Bioinformatics Conference, 2004)

New Leadership for Bioinformatics. - Alex Bateman; Alfonso Valencia (Bioinform., 2004)

YAdumper: extracting and translating large information volumes from relational databases to structured flat files. - José María Fernández 001; Alfonso Valencia (Bioinform., 2004)

SQUARE-determining reliable regions in sequence alignments. - Michael L. Tress; Osvaldo Graña; Alfonso Valencia (Bioinform., 2004)

SPOC: A widely distributed domain associated with cancer, apoptosis and transcription. - Luis Sánchez-Pulido; Ana María Rojas; Karel H. M. van Wely; Carlos Martínez-A; Alfonso Valencia (BMC Bioinform., 2004)

IntAct: an open source molecular interaction database. - Henning Hermjakob; Luisa Montecchi-Palazzi; Chris Lewington; Sugath Mudali; Samuel Kerrien; Sandra E. Orchard; Martin Vingron; Bernd Roechert; Peter Roepstorff; Alfonso Valencia; Hanah Margalit; John Armstrong; et al. (Nucleic Acids Res., 2004)

SIGIR 2003 workshop on text analysis and search for bioinformatics. - Eric W. Brown 001; William R. Hersh; Alfonso Valencia (SIGIR Forum, 2004)

Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps. - Martin Krallinger; Alfonso Valencia (Data Analysis and Visualization in Genomics and Proteomics, 2005)

ECCB/JBI 2005. - Roderic Guigó; Federico Morán; Alfonso Valencia; Josep F. Abril (ECCB/JBI, 2005)

Implementing the iHOP concept for navigation of biomedical literature. - Robert Hoffmann; Alfonso Valencia (ECCB/JBI, 2005)

A framework for computational and experimental methods: Identifying dimerization residues in CCR chemokine receptors. - David de Juan; Mario Mellado; José Miguel Rodríguez-Frade; Patricia Hernanz-Falcón; Antonio Serrano; Antonio del Sol; Alfonso Valencia; Carlos Martínez-A; Ana María Rojas (ECCB/JBI, 2005)

An update from the Bioinformatics Editors. - Alex Bateman; Alfonso Valencia (Bioinform., 2005)

Do you do text? - Christian Blaschke; Alexander S. Yeh; Evelyn Camon; Marc E. Colosimo; Rolf Apweiler; Lynette Hirschman; Alfonso Valencia (Bioinform., 2005)

Increasing the Impact of Bioinformatics. - Alfonso Valencia; Alex Bateman (Bioinform., 2005)

Evaluation of BioCreAtIvE assessment of task 2. - Christian Blaschke; Eduardo Andrés León; Martin Krallinger; Alfonso Valencia (BMC Bioinform., 2005)

Overview of BioCreAtIvE: critical assessment of information extraction for biology. - Lynette Hirschman; Alexander S. Yeh; Christian Blaschke; Alfonso Valencia (BMC Bioinform., 2005)

A sentence sliding window approach to extract protein annotations from biomedical articles. - Martin Krallinger; Maria Padron; Alfonso Valencia (BMC Bioinform., 2005)

EVAcon: a protein contact prediction evaluation service. - Osvaldo Graña; Volker A. Eyrich; Florencio Pazos; Burkhard Rost; Alfonso Valencia (Nucleic Acids Res., 2005)

HCAD, closing the gap between breakpoints and genes. - Robert Hoffmann; Joaquín Dopazo; Juan C. Cigudosa; Alfonso Valencia (Nucleic Acids Res., 2005)

MetaRouter: bioinformatics for bioremediation. - Florencio Pazos; David Guijas; Alfonso Valencia; Victor de Lorenzo (Nucleic Acids Res., 2005)

Accessible Protein Interaction Data for Network Modeling. Structure of the Information and Available Repositories. - Manuel J. Gómez; Ramón Alonso-Allende; Florencio Pazos; Osvaldo Graña; David de Juan; Alfonso Valencia (Trans. Comp. Sys. Biology, 2005)

Structural genomics meets computational biology. - Alex Bateman; Alfonso Valencia (Bioinform., 2006)

Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005). - Udo Hahn; Alfonso Valencia (Bioinform., 2006)

Bioinformatics in the human interactome project. - Trey Ideker; Alfonso Valencia (Bioinform., 2006)

Synthetic Biology: challenges ahead. - Victor de Lorenzo; Luis Serrano; Alfonso Valencia (Bioinform., 2006)

Phylogeny-independent detection of functional residues. - Florencio Pazos; Antonio Rausell; Alfonso Valencia (Bioinform., 2006)

Software patents in Bioinformatics. - Alfonso Valencia; Alex Bateman (Bioinform., 2006)

An analysis of the Sargasso Sea resource and the consequences for database composition. - Michael L. Tress; Domenico Cozzetto; Anna Tramontano; Alfonso Valencia (BMC Bioinform., 2006)

TreeDet: a web server to explore sequence space. - Angel Carro; Michael L. Tress; David de Juan; Florencio Pazos; Pedro Lopez-Romero; Antonio del Sol; Alfonso Valencia; Ana María Rojas (Nucleic Acids Res., 2006)

TSEMA: interactive prediction of protein pairings between interacting families. - José M. G. Izarzugaza; David de Juan; Carles Pons; Juan A. G. Ranea; Alfonso Valencia; Florencio Pazos (Nucleic Acids Res., 2006)

Editorial. - Alfonso Valencia; Alex Bateman (Bioinform., 2007)

CARGO: a web portal to integrate customized biological information. - Ildefonso Cases; David G. Pisano; Eduardo Andrés León; Angel Carro; José María Fernández 001; Gonzalo Gómez-López; José Manuel Rodriguez; Jaime F. Vera; Alfonso Valencia; Ana María Rojas (Nucleic Acids Res., 2007)

iHOP web services. - José María Fernández 001; Robert Hoffmann; Alfonso Valencia (Nucleic Acids Res., 2007)

FireDB - a database of functionally important residues from proteins of known structure. - Gonzalo López; Alfonso Valencia; Michael L. Tress (Nucleic Acids Res., 2007)

firestar - prediction of functionally important residues using structural templates and alignment reliability. - Gonzalo López; Alfonso Valencia; Michael L. Tress (Nucleic Acids Res., 2007)

Computational Methods to Predict Protein Interaction Partners. - Alfonso Valencia; Florencio Pazos (Protein-protein Interactions and Networks, 2008)

Protein Interactions Extracted from Genomes and Papers. - Alfonso Valencia (APBC, 2008)

iProLINK: A Framework for Linking Text Mining with Ontology and Systems Biology. - Zhang-Zhi Hu; K. Bretonnel Cohen; Lynette Hirschman; Alfonso Valencia; Hongfang Liu; Michelle G. Giglio; Cathy H. Wu (BIBM, 2008)

Text mining in genomics and systems biology. - Alfonso Valencia (DTMBIO, 2008)

Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology. - Christian Blaschke; Lynette Hirschman; Hagit Shatkay; Alfonso Valencia (BioLINK@ISMB/ECCB, 2008)

Editorial. - Alfonso Valencia; Ildefonso Cases (ISMB, 2008)

Determination and validation of principal gene products. - Michael L. Tress; Jan-Jaap Wesselink; Adam Frankish; Gonzalo López; Nick Goldman; Ari Löytynoja; Tim Massingham; Fabio Pardi; Simon Whelan; Jennifer L. Harrow; Alfonso Valencia (Bioinform., 2008)

Enhancing the prediction of protein pairings between interacting families using orthology information. - José M. G. Izarzugaza; David de Juan; Carles Pons; Florencio Pazos; Alfonso Valencia (BMC Bioinform., 2008)

Defining functional distances over Gene Ontology. - Angela del Pozo; Florencio Pazos; Alfonso Valencia (BMC Bioinform., 2008)

SOA-Based Integration of Text Mining Services. - Johannes Starlinger; Florian Leitner; Alfonso Valencia; Ulf Leser (SERVICES I, 2009)

Progress and challenges in predicting protein-protein interaction sites. - Iakes Ezkurdia; Lisa Bartoli; Piero Fariselli; Rita Casadio; Alfonso Valencia; Michael L. Tress (Briefings Bioinform., 2009)

Automated Alphabet Reduction for Protein Datasets. - Jaume Bacardit; Michael Stout; Jonathan D. Hirst; Alfonso Valencia; Robert Elliott Smith; Natalio Krasnogor (BMC Bioinform., 2009)

An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. - José M. G. Izarzugaza; Anja Baresic; Lisa E. M. McMillan; Corin Yeats; Andrew B. Clegg; Christine A. Orengo; Andrew C. R. Martin; Alfonso Valencia (BMC Bioinform., 2009)

Extraction of human kinase mutations from literature, databases and genotyping studies. - Martin Krallinger; José M. G. Izarzugaza; Carlos Rodríguez Penagos; Alfonso Valencia (BMC Bioinform., 2009)

Bionemo: molecular information on biodegradation metabolism. - Guillermo Carbajosa; Almudena Trigo; Alfonso Valencia; Ildefonso Cases (Nucleic Acids Res., 2009)

PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction. - Martin Krallinger; Carlos Rodríguez Penagos; Ashish V. Tendulkar; Alfonso Valencia (Nucleic Acids Res., 2009)

EcID. A database for the inference of functional interactions in E. coli. - Eduardo Andrés León; Iakes Ezkurdia; Beatriz García Jiménez; Alfonso Valencia; David de Juan (Nucleic Acids Res., 2009)

iHOP Web Services Family. - José María Fernández 001; Robert Hoffmann; Alfonso Valencia (JBI, 2010)

Bioinformatic Software Developments in Spain. - José María Fernández 001; Alfonso Valencia (JBI, 2010)

TopoGSA: network topological gene set analysis. - Enrico Glaab; Anaïs Baudot; Natalio Krasnogor; Alfonso Valencia (Bioinform., 2010)

Extending pathways and processes using molecular interaction networks to analyse cancer genome data. - Enrico Glaab; Anaïs Baudot; Natalio Krasnogor; Alfonso Valencia (BMC Bioinform., 2010)

The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions. - Martin Krallinger; Ashish V. Tendulkar; Florian Leitner; Andrew Chatr-aryamontri; Alfonso Valencia (BMC Bioinform., 2010)

An Overview of BioCreative II.5. - Florian Leitner; Scott A. Mardis; Martin Krallinger; Gianni Cesareni; Lynette Hirschman; Alfonso Valencia (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

On the organization of bioinformatics core services in biology-based research institutes. - Olli-P. Kallioniemi; Lodewyk F. A. Wessels; Alfonso Valencia (Bioinform., 2011)

Overview of the BioCreative III Workshop. - Cecilia N. Arighi; Zhiyong Lu; Martin Krallinger; Kevin Bretonnel Cohen; W. John Wilbur; Alfonso Valencia; Lynette Hirschman; Cathy H. Wu (BMC Bioinform., 2011)

Selection of organisms for the co-evolution-based study of protein interactions. - Dorota Herman; David Ochoa; David de Juan; Daniel Lopez; Alfonso Valencia; Florencio Pazos (BMC Bioinform., 2011)

Characterization of pathogenic germline mutations in human Protein Kinases. - José M. G. Izarzugaza; Lisa E. M. Hopcroft; Anja Baresic; Christine A. Orengo; Andrew C. R. Martin; Alfonso Valencia (BMC Bioinform., 2011)

firestar - advances in the prediction of functionally important residues. - Gonzalo López; Paolo Maietta; José Manuel Rodriguez; Alfonso Valencia; Michael L. Tress (Nucleic Acids Res., 2011)

Machine Reading of Biomedical Texts about Alzheimer's Disease. - Roser Morante; Martin Krallinger; Alfonso Valencia; Walter Daelemans (CLEF (Online Working Notes/Labs/Workshop), 2012)

Text mining for the biocuration workflow. - Lynette Hirschman; Gully A. P. C. Burns; Martin Krallinger; Cecilia N. Arighi; K. Bretonnel Cohen; Alfonso Valencia; Cathy H. Wu; Andrew Chatr-aryamontri; Karen G. Dowell; Eva Huala; Anália Lourenço; Robert S. Nash; et al. (Database J. Biol. Databases Curation, 2012)

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. - Martin Krallinger; Florian Leitner; Miguel Vazquez; David Salgado; Christophe Marcelle; Mike Tyers; Alfonso Valencia; Andrew Chatr-aryamontri (Database J. Biol. Databases Curation, 2012)

BioCreative-2012 Virtual Issue. - Cathy H. Wu; Cecilia N. Arighi; Kevin Bretonnel Cohen; Lynette Hirschman; Martin Krallinger; Zhiyong Lu; Carolyn J. Mattingly; Alfonso Valencia; Thomas C. Wiegers; W. John Wilbur (Database J. Biol. Databases Curation, 2012)

Novel domain combinations in proteins encoded by chimeric transcripts. - Milana Frenkel-Morgenstern; Alfonso Valencia (Bioinform., 2012)

EnrichNet: network-based gene set enrichment analysis. - Enrico Glaab; Anaïs Baudot; Natalio Krasnogor; Reinhard Schneider 002; Alfonso Valencia (Bioinform., 2012)

Mirroring co-evolving trees in the light of their topologies. - Iman Hajirasouliha; Alexander Schönhuth; David de Juan; Alfonso Valencia; Süleyman Cenk Sahinalp (Bioinform., 2012)

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. - Thilo Muth; Juan A. García-Martín; Antonio Rausell; David de Juan; Alfonso Valencia; Florencio Pazos (Bioinform., 2012)

Bioimage informatics: a new category in Bioinformatics. - Hanchuan Peng; Alex Bateman; Alfonso Valencia; Jonathan D. Wren (Bioinform., 2012)

MyMiner: a web application for computer-assisted biocuration and text annotation. - David Salgado; Martin Krallinger; Marc Depaule; Elodie Drula; Ashish V. Tendulkar; Florian Leitner; Alfonso Valencia; Christophe Marcelle (Bioinform., 2012)

Accurate Demarcation of Protein Domain Linkers based on Structural Analysis of Linker Probable Region - Vivekanand Samant; Arvind Hulgeri; Alfonso Valencia; Ashish V. Tendulkar (CoRR, 2012)

Chapter 14: Cancer Genome Analysis. - Miguel Vazquez; Victor de la Torre; Alfonso Valencia (PLoS Comput. Biol., 2012)

BioC: a minimalist approach to interoperability for biomedical text processing. - Donald C. Comeau; Rezarta Islamaj Dogan; Paolo Ciccarese; Kevin Bretonnel Cohen; Martin Krallinger; Florian Leitner; Zhiyong Lu; Yifan Peng 002; Fabio Rinaldi 001; Manabu Torii; Alfonso Valencia; Karin Verspoor; et al. (Database J. Biol. Databases Curation, 2013)

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. - Miriam Rubio-Camarillo; Gonzalo Gómez-López; José María Fernández 001; Alfonso Valencia; David G. Pisano (Bioinform., 2013)

wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases. - José M. G. Izarzugaza; Miguel Vazquez; Angela del Pozo; Alfonso Valencia (BMC Bioinform., 2013)

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. - Milana Frenkel-Morgenstern; Alessandro Gorohovski; Vincent Lacroix; Mark F. Rogers; Kristina Ibáñez; Cesar Boullosa; Eduardo Andrés León; Asa Ben-Hur; Alfonso Valencia (Nucleic Acids Res., 2013)

APPRIS: annotation of principal and alternative splice isoforms. - José Manuel Rodriguez; Paolo Maietta; Iakes Ezkurdia; Alessandro Pietrelli; Jan-Jaap Wesselink; Gonzalo López; Alfonso Valencia; Michael L. Tress (Nucleic Acids Res., 2013)

Retrieval and Discovery of Cell Cycle Literature and Proteins by Means of Machine Learning, Text Mining and Network Analysis. - Martin Krallinger; Florian Leitner; Alfonso Valencia (PACBB, 2014)

BioCreative-IV virtual issue. - Cecilia N. Arighi; Cathy H. Wu; Kevin Bretonnel Cohen; Lynette Hirschman; Martin Krallinger; Alfonso Valencia; Zhiyong Lu; W. John Wilbur; Thomas C. Wiegers (Database J. Biol. Databases Curation, 2014)

CheNER: chemical named entity recognizer. - Anabel Usie; Rui Alves; Francesc Solsona; Miguel Vazquez; Alfonso Valencia (Bioinform., 2014)

FireDB: a compendium of biological and pharmacologically relevant ligands. - Paolo Maietta; Gonzalo López; Angel Carro; Benjamin J. Pingilley; Leticia G. Leon; Alfonso Valencia; Michael L. Tress (Nucleic Acids Res., 2014)

Predicting Protein Relationshipsto Human Pathways througha Relational Learning ApproachBased on Simple Sequence Features. - Beatriz García Jiménez; Tirso Pons; Araceli Sanchis; Alfonso Valencia (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals. - Federico Abascal; Michael L. Tress; Alfonso Valencia (Bioinform., 2015)

FUN-L: gene prioritization for RNAi screens. - Jonathan G. Lees; Jean-Karim Hériché; Ian Morilla; José María Fernández 001; Priit Adler; Martin Krallinger; Jaak Vilo; Alfonso Valencia; Jan Ellenberg; Juan A. G. Ranea; Christine A. Orengo (Bioinform., 2015)

Detection of significant protein coevolution. - David Ochoa; David de Juan; Alfonso Valencia; Florencio Pazos (Bioinform., 2015)

Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces. - Miguel Vazquez; Alfonso Valencia; Tirso Pons (Bioinform., 2015)

Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013. - Karin Verspoor; Hagit Shatkay; Lynette Hirschman; Christian Blaschke; Alfonso Valencia (Bioinform., 2015)

CHEMDNER: The drugs and chemical names extraction challenge. - Martin Krallinger; Florian Leitner; Obdulia Rabal; Miguel Vazquez; Julen Oyarzabal; Alfonso Valencia (J. Cheminformatics, 2015)

The CHEMDNER corpus of chemicals and drugs and its annotation principles. - Martin Krallinger; Obdulia Rabal; Florian Leitner; Miguel Vazquez; David Salgado; Zhiyong Lu; Robert Leaman; Yanan Lu; Donghong Ji; Daniel M. Lowe; Roger A. Sayle; Riza Theresa Batista-Navarro; et al. (J. Cheminformatics, 2015)

ChiTaRS 2.1 - an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. - Milana Frenkel-Morgenstern; Alessandro Gorohovski; Dunja Vucenovic; Lorena Maestre; Alfonso Valencia (Nucleic Acids Res., 2015)

APPRIS WebServer and WebServices. - José Manuel Rodriguez; Angel Carro; Alfonso Valencia; Michael L. Tress (Nucleic Acids Res., 2015)

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level. - Federico Abascal; Iakes Ezkurdia; Juan Rodriguez-Rivas; José Manuel Rodriguez; Angela del Pozo; Jesús Vázquez; Alfonso Valencia; Michael L. Tress (PLoS Comput. Biol., 2015)

Annotation Process, Guidelines and Text Corpus of Small Non-Coding RNA Molecules: the MiNCor for MicroRNA Annotations. - Jose Camilla Sammartino; Martin Krallinger; Alfonso Valencia (SMBM, 2016)

The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge. - Martín Pérez-Pérez; Gael Pérez Rodríguez; Obdulia Rabal; Miguel Vazquez; Julen Oyarzabal; Florentino Fdez-Riverola; Alfonso Valencia; Martin Krallinger; Anália Lourenço (Database J. Biol. Databases Curation, 2016)

A computational approach inspired by simulated annealing to study the stability of protein interaction networks in cancer and neurological disorders. - Kristina Ibáñez; María Guijarro; Gonzalo Pajares; Alfonso Valencia (Data Min. Knowl. Discov., 2016)

ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing. - Bonnie Berger; Terry Gaasterland; Thomas Lengauer; Christine A. Orengo; Bruno Gaëta; Scott Markel; Alfonso Valencia (PLoS Comput. Biol., 2016)

The Biomedical Abbreviation Recognition and Resolution (BARR) Track: Benchmarking, Evaluation and Importance of Abbreviation Recognition Systems Applied to Spanish Biomedical Abstracts. - Ander Intxaurrondo; Martín Pérez-Pérez; Gael Pérez Rodríguez; Jose Antonio López-Martín; Jesus Santamaría; Santiago de la Peña; Marta Villegas; Saber Ahmad Akhondi; Alfonso Valencia; Anália Lourenço; Martin Krallinger (IberEval@SEPLN, 2017)

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing. - Bonnie Berger; Terry Gaasterland; Thomas Lengauer; Christine A. Orengo; Bruno Gaëta; Scott Markel; Alfonso Valencia (Bioinform., 2017)

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets. - Åsmund Flobak; Miguel Vazquez; Astrid Lægreid; Alfonso Valencia (Bioinform., 2017)

LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. - Andrés Cañada; Salvador Capella-Gutiérrez; Obdulia Rabal; Julen Oyarzabal; Alfonso Valencia; Martin Krallinger (Nucleic Acids Res., 2017)

Algorithmic complexity in Computational Biology. - Davide Cirillo; Alfonso Valencia (CoRR, 2018)

APPRIS 2017: principal isoforms for multiple gene sets. - José Manuel Rodriguez; Juan Rodriguez-Rivas; Tomás Di Domenico; Jesús Vázquez; Alfonso Valencia; Michael L. Tress (Nucleic Acids Res., 2018)

Precision medicine needs pioneering clinical bioinformaticians. - Gonzalo Gómez-López; Joaquín Dopazo; Juan C. Cigudosa; Alfonso Valencia; Fátima Al-Shahrour (Briefings Bioinform., 2019)

BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications. - Adrián Bazaga; Alfonso Valencia; María-José Rementeria (Bioinform., 2019)

vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer. - Javier Perales-Patón; Tomás Di Domenico; Coral Fustero Torre; Elena Piñeiro-Yáñez; Carlos Carretero-Puche; Héctor Tejero; Alfonso Valencia; Gonzalo Gómez-López; Fátima Al-Shahrour (Bioinform., 2019)

Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention. - Jonathan D. Wren; Alfonso Valencia; Janet Kelso (Bioinform., 2019)

Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm. - Martín Pérez-Pérez; Gael Pérez Rodríguez; Aitor Blanco-Míguez; Florentino Fdez-Riverola; Alfonso Valencia; Martin Krallinger; Anália Lourenço (J. Cheminformatics, 2019)

Patient Dossier: Healthcare queries over distributed resources. - Miguel Vazquez; Alfonso Valencia (PLoS Comput. Biol., 2019)

Interactive Extreme: Scale Analytics Towards Battling Cancer. - Nikos Giatrakos; Nikos Katzouris; Antonios Deligiannakis; Alexander Artikis; Minos N. Garofalakis; George Paliouras; Holger Arndt 003; Raffaele Grasso; Ralf Klinkenberg; Miguel Ponce de Leon; Gian Gaetano Tartaglia; Alfonso Valencia; et al. (IEEE Technol. Soc. Mag., 2019)

GOPHER, an HPC Framework for Large Scale Graph Exploration and Inference. - Marc Josep-Fabregó; Xavier Teruel; Victor Gimenez-Abalos; Davide Cirillo; Dario Garcia-Gasulla; Sergio Álvarez-Napagao; Marta Garcia-Gasulla; Eduard Ayguadé; Alfonso Valencia (ISC Workshops, 2020)

TiFoSi: an efficient tool for mechanobiology simulations of epithelia. - Oriol Canela-Xandri; Samira Anbari; Javier Buceta; Alfonso Valencia (Bioinform., 2020)

ECCB2020: the 19th European Conference on Computational Biology. - Salvador Capella-Gutiérrez; Eva Alloza; Edurne Gallastegui; Ioannis Kavakiotis; Jen Harrow; Alberto Langtry; Alfonso Valencia (Bioinform., 2020)

On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. - Miguel Ponce de Leon; Iñigo Apaolaza; Alfonso Valencia; Francisco J. Planes (Bioinform., 2020)

Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning (DCTL). - Sen Li; Qi Yang; Hao Jiang 028; Jesús A. Cortés-Vecino; Yang Zhang 057; Alfonso Valencia (Bioinform., 2020)

Chromatin network markers of leukemia. - Noël Malod-Dognin; Vera Pancaldi; Alfonso Valencia; Natasa Przulj (Bioinform., 2020)

Towards FAIR principles for research software. - Anna-Lena Lamprecht; Leyla J. García; Mateusz Kuzak; Carlos Martinez-Ortiz; Ricardo Arcila; Eva Martin Del Pico; Victoria Dominguez Del Angel; Stephanie van de Sandt; Jon C. Ison; Paula Andrea Martínez; Peter McQuilton; Alfonso Valencia; et al. (Data Sci., 2020)

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. - David Salgado; Irina M. Armean; Michael Baudis; Sergi Beltran; Salvador Capella-Gutiérrez; Denise Carvalho-Silva; Victoria Dominguez Del Angel; Joaquín Dopazo; Laura I. Furlong; Bo Gao; Leyla Jael García Castro; Dietlind Gerloff; et al. (F1000Research, 2020)

PDBe-KB: a community-driven resource for structural and functional annotations. - Mihaly Varadi; John M. Berrisford; Mandar S. Deshpande; Sreenath Nair; Aleksandras Gutmanas; David R. Armstrong; Lukás Pravda; Bissan Al-Lazikani; Stephen Anyango; Geoffrey J. Barton; Karel Berka; Tom L. Blundell; et al. (Nucleic Acids Res., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare. - Davide Cirillo; Silvina Catuara-Solarz; Czuee Morey; Emre Guney; Laia Subirats; Simona Mellino; Annalisa Gigante; Alfonso Valencia; María-José Rementeria; Antonella Santuccione Chadha; Nikolaos Mavridis (npj Digit. Medicine, 2020)

BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems. - Gaurav Saxena; Miguel Ponce de Leon; Arnau Montagud; David Vicente Dorca; Alfonso Valencia (CMSB, 2021)

Simulating SARS-CoV-2 epidemics by region-specific variables and modeling contact tracing app containment. - Alberto Ferrari; Enrico Santus; Davide Cirillo; Miguel Ponce de Leon; Nicola Marino; Maria Teresa Ferretti; Antonella Santuccione Chadha; Nikolaos Mavridis; Alfonso Valencia (npj Digit. Medicine, 2021)

Pretrained Biomedical Language Models for Clinical NLP in Spanish. - Casimiro Pio Carrino; Joan Llop; Marc Pàmies; Asier Gutiérrez-Fandiño; Jordi Armengol-Estapé; Joaquín Silveira-Ocampo; Alfonso Valencia; Aitor Gonzalez-Agirre; Marta Villegas (BioNLP@ACL, 2022)

ECCB2022: the 21st European Conference on Computational Biology. - Salvador Capella-Gutiérrez; Eva Alloza; Laura Rubinat-Ripoll; Ana Conesa; Alfonso Valencia (Bioinform., 2022)

Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools. - Carlos A. Garcia-Prieto; Francisco Martínez-Jiménez; Alfonso Valencia; Eduard Porta-Pardo (Bioinform., 2022)

Parallel model exploration for tumor treatment simulations. - Charilaos Akasiadis; Miguel Ponce de Leon; Arnau Montagud; Evangelos Michelioudakis; Alexia Atsidakou; Elias Alevizos; Alexander Artikis; Alfonso Valencia; Georgios Paliouras (Comput. Intell., 2022)

The structural coverage of the human proteome before and after AlphaFold. - Eduard Porta-Pardo; Victoria Ruiz-Serra; Samuel Valentini; Alfonso Valencia (PLoS Comput. Biol., 2022)

Lessons Learned from a Performance Analysis and Optimization of a Multiscale Cellular Simulation. - Marc Clascà; Marta Garcia-Gasulla; Arnau Montagud; José Carbonell-Caballero; Alfonso Valencia (PASC, 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. - Antonio Miranda-Escalada; Farrokh Mehryary; Jouni Luoma; Darryl Estrada-Zavala; Luis Gascó; Sampo Pyysalo; Alfonso Valencia; Martin Krallinger (Database J. Biol. Databases Curation, 2023)

PretoxTM: a text mining system for extracting treatment-related findings from preclinical toxicology reports. - Javier Corvi; Nicolás Díaz-Roussel; José M. Fernández; Francesco Ronzano; Emilio Centeno; Pablo Accuosto; Celine Ibrahim; Shoji Asakura; Frank Bringezu; Mirjam Fröhlicher; Annika Kreuchwig; Yoko Nogami; et al. (J. Cheminformatics, 2025)