Detection of protein catalytic residues at high precision using local network properties. - Patrick Slama; Ioannis Filippis; Michael Lappe (BMC Bioinform., 2008)

Defining an Essence of Structure Determining Residue Contacts in Proteins. - Rajagopal Sathyapriya; Jose M. Duarte; Henning Stehr; Ioannis Filippis; Michael Lappe (PLoS Comput. Biol., 2009)

Optimal contact definition for reconstruction of Contact Maps. - Jose M. Duarte; Rajagopal Sathyapriya; Henning Stehr; Ioannis Filippis; Michael Lappe (BMC Bioinform., 2010)

Graphlet based network analysis of protein structures. - Ioannis Filippis (2012)

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. - Tony E. Lewis; Ian Sillitoe; Antonina Andreeva; Tom L. Blundell; Daniel W. A. Buchan; Cyrus Chothia; Alison L. Cuff; Jose M. Dana; Ioannis Filippis; Julian Gough; Sarah Hunter; David T. Jones; et al. (Nucleic Acids Res., 2013)

Genome3D: exploiting structure to help users understand their sequences. - Tony E. Lewis; Ian Sillitoe; Antonina Andreeva; Tom L. Blundell; Daniel W. A. Buchan; Cyrus Chothia; Domenico Cozzetto; Jose M. Dana; Ioannis Filippis; Julian Gough; David T. Jones; Lawrence A. Kelley; et al. (Nucleic Acids Res., 2015)