Puigbo P, Wolf YI, Koonin EV. (2010) The tree and net components of prokaryote evolution. Genome Biology and Evolution

Koonin EV, Wolf YI, Puigbo P. (2009) The Phylogenetic Forest and the Quest for the Elusive Tree of Life. Cold Spring Harb Symp Quant Biol.

Puigbo P, Wolf YI, Koonin EV. (2009) Search for a Tree of Life in the thicket of the phylogenetic forest. J Biol, 8:59

Das RD, Puigbo P, Hensley SE, Hurt DE, Bennink JR, Yewdell JW. (2010) Glycosylation Focuses Sequence Variation in the Influenza A Virus H1 Hemagglutinin Globular Domain. PLoS Pathog 6:e1001211

Puigbo P, Pasamontes A, Garcia-Vallve S. (2008) Gaining and losing the thermophilic adaptation in prokaryotes. Trends Genet., 24:10-4.

Puigbo P, Garcia-Vallve S, McInerney JO. (2007) TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics, 23:1556-8.

Puigbo P, Guzman E, Romeu A, Garcia-Vallve S. (2007) OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res., 35:W126-31.

Puigbo P, Bravo IG and Garcia-Vallve S. (2008) E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics, 9:65.

Puigbo P, Romeu A, Garcia-Vallve S. (2008) HEG-DB: a database of predicted highly expressed genes in prokaryotic complete. Nucleic Acids Res., 36:D524-7.

Puigbo P, Bravo IG and Garcia-Vallve S. (2008) CAIcal: a combined set of tools to assess codon usage adaptation. Biology Direct, 3:38.