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)

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)

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)

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)

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)

Text Detective: a rule-based system for gene annotation in biomedical texts. - Javier Tamames (BMC Bioinform., 2005)

Metagenomics reveals our incomplete knowledge of global diversity. - Miguel Pignatelli; Gabriel Aparício; Ignacio Blanquer; Vicente Hernández; Andrés Moya; Javier Tamames (Bioinform., 2008)

EnvMine: A text-mining system for the automatic extraction of contextual information. - Javier Tamames; Victor de Lorenzo (BMC Bioinform., 2010)

The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. - Rafael Silva-Rocha; Hidde de Jong; Javier Tamames; Víctor de Lorenzo (BMC Syst. Biol., 2011)

Expert system for clustering prokaryotic species by their metabolic features. - Clara Higuera; Gonzalo Pajares; Javier Tamames; Federico Morán (Expert Syst. Appl., 2013)

High Performance Genomic Sequencing: A Filtered Approach. - Germán Retamosa; Luis de Pedro; Iván González 004; Javier Tamames (PACBB, 2014)

SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o. - Fernando Puente-Sánchez; Natalia García-García; Javier Tamames (BMC Bioinform., 2020)

M&Ms: a versatile software for building microbial mock communities. - Natalia García-García; Javier Tamames; Fernando Puente-Sánchez (Bioinform., 2022)