CoGenT++: an extensive and extensible data environment for computational genomics. - Leon Goldovsky; Paul J. Janssen; Dag G. Ahrén; Benjamin Audit; Ildefonso Cases; Nikos Darzentas; Anton J. Enright; Núria López-Bigas; José M. Peregrín-Alvarez; Mike Smith 001; Sophia Tsoka; Victor Kunin; et al. (Bioinform., 2005)

PartiGeneDB - collating partial genomes. - José M. Peregrín-Alvarez; Andrew Yam; Gaya Sivakumar; John Parkinson (Nucleic Acids Res., 2005)

Bacteriome.org - an integrated protein interaction database for E. coli. - Chong Su; José M. Peregrín-Alvarez; Gareth Butland; Sadhna Phanse; Vincent Fong; Andrew Emili; John Parkinson (Nucleic Acids Res., 2008)

The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti. - Ignacio Rodriguez-Llorente; Miguel A. Caviedes; Mohammed Dary; Antonio J. Palomares; Francisco M. Cánovas; José M. Peregrín-Alvarez (BMC Syst. Biol., 2009)

The Modular Organization of Protein Interactions in Escherichia coli. - José M. Peregrín-Alvarez; Xuejian Xiong; Chong Su; John Parkinson (PLoS Comput. Biol., 2009)