Application of Vector Quantization Algorithms to Protein Classification and Secondary Structure Computation. - Juan Julián Merelo Guervós; Miguel A. Andrade; Carlos Ureña; Alberto Prieto; Federico Morán (IWANN, 1991)

A Model for the Development of Neurons Selective to Visual Stimulus Size. - Miguel A. Andrade; Federico Morán (IWANN, 1993)

Proteinotopic feature maps. - Juan Julián Merelo Guervós; Miguel A. Andrade; Alberto Prieto; Federico Morán (Neurocomputing, 1994)

A Neural Network Model for Plasticity in Adult Striate Cortex. - Federico Morán; Miguel A. Andrade (IWANN, 1995)

Structural study of the development of ocularity domains using a neural network model. - Miguel A. Andrade; Federico Morán (Biol. Cybern., 1996)

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)

Development of On-Off and Off-On Receptive Fields Using a Semistochastic Model. - Enrique M. Muro; Pedro Isasi; Miguel A. Andrade; Federico Morán (IWANN, 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)

Receptive Field Map Development by Anti-Hebbian Learning. - Miguel A. Andrade; Federico Morán (Neural Networks, 1997)

Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families. - Miguel A. Andrade; 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)

Position-Specific Annotation of Protein Function Based on Multiple Homologs. - Miguel A. Andrade (ISMB, 1999)

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

A Self-Organizing Model for the Development of Ocular Dominance and Orientation Columns in the Virtual Cortex. - Enrique M. Muro; Miguel A. Andrade; Pedro Isasi; Federico Morán (IWANN (1), 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)

NAIL-Network Analysis Interface for Linking HMMER results. - Luis Sánchez-Pulido; Yan P. Yuan; Miguel A. Andrade; Peer Bork (Bioinform., 2000)

Simulation of plasticity in the adult visual cortex. - Miguel A. Andrade; Enrique M. Muro; Federico Morán (Biol. Cybern., 2001)

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)

Information extraction from full text scientific articles: Where are the keywords? - Parantu K. Shah; Carolina Perez-Iratxeta; Peer Bork; Miguel A. Andrade (BMC Bioinform., 2003)

Update on XplorMed: a web server for exploring scientific literature. - Carolina Perez-Iratxeta; Antonio J. Pérez-Pulido; Peer Bork; Miguel A. Andrade (Nucleic Acids Res., 2003)

Gene annotation from scientific literature using mappings between keyword systems. - Antonio J. Pérez-Pulido; Carolina Perez-Iratxeta; Peer Bork; Guillermo Thode; Miguel A. Andrade (Bioinform., 2004)

Inconsistencies over time in 5% of NetAffx probe-to-gene annotations. - Carolina Perez-Iratxeta; Miguel A. Andrade (BMC Bioinform., 2005)

Ranking the whole MEDLINE database according to a large training set using text indexing. - Brian P. Suomela; Miguel A. Andrade (BMC Bioinform., 2005)

Amplification of the Gene Ontology annotation of Affymetrix probe sets. - Enrique M. Muro; Carolina Perez-Iratxeta; Miguel A. Andrade-Navarro (BMC Bioinform., 2006)

Taxonomic colouring of phylogenetic trees of protein sequences. - Gareth A. Palidwor; Emmanuel G. Reynaud; Miguel A. Andrade-Navarro (BMC Bioinform., 2006)

Evolving research trends in bioinformatics. - Carolina Perez-Iratxeta; Miguel A. Andrade-Navarro; Jonathan D. Wren (Briefings Bioinform., 2007)

BiasViz: visualization of amino acid biased regions in protein alignments. - Matthew R. Huska; Henrik Buschmann; Miguel A. Andrade-Navarro (Bioinform., 2007)

Update of the G2D tool for prioritization of gene candidates to inherited diseases. - Carolina Perez-Iratxeta; Peer Bork; Miguel A. Andrade-Navarro (Nucleic Acids Res., 2007)

A Customized Class of Functions for Modeling and Clustering Gene Expression Profiles in Embryonic Stem Cells. - Shenggang Li; Miguel A. Andrade-Navarro; David Sankoff (BSB, 2008)

Text Mining and Semantic Search with a Predicate Argument Structure Database. - Mircea Trifan; Dan Ionescu; Carolina Perez-Iratxeta; Miguel A. Andrade (BIOCOMP, 2009)

MedlineRanker: flexible ranking of biomedical literature. - Jean-Fred Fontaine; Adriano Barbosa-Silva; Martin H. Schaefer 001; Matthew R. Huska; Enrique M. Muro; Miguel A. Andrade-Navarro (Nucleic Acids Res., 2009)

Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin. - Gareth A. Palidwor; Sergey Shcherbinin; Matthew R. Huska; Tamas Rasko; Ulrich Stelzl; Anup Arumughan; Raphaele Foulle; Pablo Porras; Luis Sánchez-Pulido; Erich E. Wanker; Miguel A. Andrade-Navarro (PLoS Comput. Biol., 2009)

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships. - Adriano Barbosa-Silva; Theodoros G. Soldatos; Ivan L. F. Magalhães; Georgios A. Pavlopoulos; Jean-Fred Fontaine; Miguel A. Andrade-Navarro; Reinhard Schneider 002; José Miguel Ortega (BMC Bioinform., 2010)

PDBpaint, a visualization webservice to tag protein structures with sequence annotations. - David Fournier; Miguel A. Andrade-Navarro (Bioinform., 2011)

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. - Tiago J. S. Lopes; Martin H. Schaefer 001; Jason E. Shoemaker; Yukiko Matsuoka; Jean-Fred Fontaine; Gabriele Neumann; Miguel A. Andrade-Navarro; Yoshihiro Kawaoka; Hiroaki Kitano (Bioinform., 2011)

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. - Adriano Barbosa-Silva; Jean-Fred Fontaine; Elisa R. Donnard; Fernanda Stussi; José Miguel Ortega; Miguel A. Andrade-Navarro (BMC Bioinform., 2011)

Génie: literature-based gene prioritization at multi genomic scale. - Jean-Fred Fontaine; Florian Priller; Adriano Barbosa-Silva; Miguel A. Andrade-Navarro (Nucleic Acids Res., 2011)

Keynote lectures. - Metin Akay; Yuan-Ting Zhang; Konstantina S. Nikita; Miguel A. Andrade; Christos A. Ouzounis (BIBE, 2012)

Peer2ref: a peer-reviewer finding web tool that uses author disambiguation. - Miguel A. Andrade-Navarro; Gareth A. Palidwor; Carolina Perez-Iratxeta (BioData Min., 2012)

Using cited references to improve the retrieval of related biomedical documents. - Francisco M. Ortuño Guzman; Ignacio Rojas; Miguel A. Andrade-Navarro; Jean-Fred Fontaine (BMC Bioinform., 2013)

A novel approach for protein subcellular location prediction using amino acid exposure. - Arvind Mer; Miguel A. Andrade-Navarro (BMC Bioinform., 2013)

SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations. - Joachim von Eichborn; Mathias Dunkel; Björn O. Gohlke; Sarah C. Preissner; Michael F. Hoffmann; Jakob M. J. Bauer; J. Douglas Armstrong; Martin H. Schaefer 001; Miguel A. Andrade-Navarro; Nicolas Le Novère; Michael D. R. Croning; Seth G. N. Grant; et al. (Nucleic Acids Res., 2013)

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions. - Martin H. Schaefer 001; Tiago J. S. Lopes; Nancy Mah; Jason E. Shoemaker; Yukiko Matsuoka; Jean-Fred Fontaine; Caroline Louis-Jeune; Amie J. Eisfeld; Gabriele Neumann; Carol Perez-Iratxeta; Yoshihiro Kawaoka; Hiroaki Kitano; et al. (PLoS Comput. Biol., 2013)

CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data. - Sander Bollen; Mathias Leddin; Miguel A. Andrade-Navarro; Nancy Mah (Bioinform., 2014)

Alkemio: association of chemicals with biomedical topics by text and data mining. - José A. Gijón-Correas; Miguel A. Andrade-Navarro; Jean-Fred Fontaine (Nucleic Acids Res., 2014)

CellFinder: a cell data repository. - Harald Stachelscheid; Stefanie Seltmann; Fritz Lekschas; Jean-Fred Fontaine; Nancy Mah; Mariana L. Neves; Miguel A. Andrade-Navarro; Ulf Leser; Andreas Kurtz 003 (Nucleic Acids Res., 2014)

uORFdb - a comprehensive literature database on eukaryotic uORF biology. - Klaus Wethmar; Adriano Barbosa-Silva; Miguel A. Andrade-Navarro; Achim Leutz (Nucleic Acids Res., 2014)

Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen. - Apichat Suratanee; Martin H. Schaefer 001; Matthew J. Betts; Zita Soons; Heiko A. Mannsperger; Nathalie Harder; Marcus Oswald; Markus Gipp; Ellen Ramminger; Guillermo Marcus Martinez; Reinhard Männer; Karl Rohr; et al. (PLoS Comput. Biol., 2014)

Manifold learning and maximum likelihood estimation for hyperbolic network embedding. - Gregorio Alanis-Lobato; Pablo Mier; Miguel A. Andrade-Navarro (Appl. Netw. Sci., 2016)

Distance Distribution between Complex Network Nodes in Hyperbolic Space. - Gregorio Alanis-Lobato; Miguel A. Andrade-Navarro (Complex Syst., 2016)

FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases. - Pablo Mier; Miguel A. Andrade-Navarro (J. Comput. Biol., 2016)

Disease-Genes Must Guide Data Source Integration in the Gene Prioritization Process. - Marco Frasca 001; Jean-Fred Fontaine; Giorgio Valentini; Marco Mesiti; Marco Notaro; Dario Malchiodi; Miguel A. Andrade-Navarro (CIBB, 2017)

Lost Strings in Genomes: What Sense Do They Make? - Michael G. Sadovsky; Jean-Fred Fontaine; Miguel A. Andrade-Navarro; Yury Yakubailik; Natalia Rudenko (IWBBIO (2), 2017)

dAPE: a web server to detect homorepeats and follow their evolution. - Pablo Mier; Miguel A. Andrade-Navarro (Bioinform., 2017)

HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. - Gregorio Alanis-Lobato; Miguel A. Andrade-Navarro; Martin H. Schaefer 001 (Nucleic Acids Res., 2017)

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures. - Lisanna Paladin; Layla Hirsh; Damiano Piovesan; Miguel A. Andrade-Navarro; Andrey V. Kajava; Silvio C. E. Tosatto (Nucleic Acids Res., 2017)

Geometric characterisation of disease modules. - Franziska Härtner; Miguel A. Andrade-Navarro; Gregorio Alanis-Lobato (Appl. Netw. Sci., 2018)

The latent geometry of the human protein interaction network. - Gregorio Alanis-Lobato; Pablo Mier; Miguel A. Andrade-Navarro (Bioinform., 2018)

Automated selection of homologs to track the evolutionary history of proteins. - Pablo Mier; Antonio J. Pérez-Pulido; Miguel A. Andrade-Navarro (BMC Bioinform., 2018)

Toward completion of the Earth's proteome: an update a decade later. - Pablo Mier; Miguel A. Andrade-Navarro (Briefings Bioinform., 2019)

Traitpedia: a collaborative effort to gather species traits. - Pablo Mier; Miguel A. Andrade-Navarro (Bioinform., 2019)

Towards Identifying Drug Side Effects from Social Media Using Active Learning andCrowd Sourcing. - Sophie Burkhardt; Julia Siekiera; Josua Glodde; Miguel A. Andrade-Navarro; Stefan Kramer 001 (PSB, 2020)

Disentangling the complexity of low complexity proteins. - Pablo Mier; Lisanna Paladin; Stella Tamana; Sophia Petrosian; Borbála Hajdu-Soltész; Annika Urbanek; Aleksandra Gruca; Dariusz Plewczynski; Marcin Grynberg; Pau Bernadó; Zoltán Gáspári; Christos A. Ouzounis; et al. (Briefings Bioinform., 2020)

MIPPIE: the mouse integrated protein-protein interaction reference. - Gregorio Alanis-Lobato; Jannik S. Möllmann; Martin H. Schaefer 001; Miguel A. Andrade-Navarro (Database J. Biol. Databases Curation, 2020)

CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats. - Alejandro Rubio; Pablo Mier; Miguel A. Andrade-Navarro; Andrés Garzón; Juan Jiménez; Antonio J. Pérez-Pulido (Database J. Biol. Databases Curation, 2020)

PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. - Patryk Jarnot; Joanna Ziemska-Legiecka; Laszlo Dobson; Matthew Merski; Pablo Mier; Miguel A. Andrade-Navarro; John M. Hancock; Zsuzsanna Dosztányi; Lisanna Paladin; Marco Necci; Damiano Piovesan; Silvio C. E. Tosatto; et al. (Nucleic Acids Res., 2020)

LipiDisease: associate lipids to diseases using literature mining. - Piyush More; Laura Bindila; Philipp Wild; Miguel A. Andrade-Navarro; Jean-Fred Fontaine (Bioinform., 2021)

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures. - Lisanna Paladin; Martina Bevilacqua; Sara Errigo; Damiano Piovesan; Ivan Micetic; Marco Necci; Alexander Miguel Monzon; Maria Laura Fabre; José Luis López; Juliet F. Nilsson; Javier Ríos; Pablo Lorenzano Menna; et al. (Nucleic Acids Res., 2021)

Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality. - Maximilian Sprang; Miguel A. Andrade-Navarro; Jean-Fred Fontaine (BMC Bioinform., 2022)

The sequence context in poly-alanine regions: structure, function and conservation. - Pablo Mier; Carlos A. Elena-Real; Juan Cortés; Pau Bernadó; Miguel A. Andrade-Navarro (Bioinform., 2022)