Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs. - Brian Y. Chen; Viacheslav Fofanov; David M. Kristensen; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (Pacific Symposium on Biocomputing, 2005)

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (RECOMB, 2006)

ET viewer: an application for predicting and visualizing functional sites in protein structures. - Daniel H. Morgan; David M. Kristensen; David Mittelman; Olivier Lichtarge (Bioinform., 2006)

Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction. - Brian Y. Chen; Drew H. Bryant; Viacheslav Fofanov; David M. Kristensen; Amanda E. Cruess; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Bioinform. Comput. Biol., 2007)

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Comput. Biol., 2007)

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. - David M. Kristensen; R. Matthew Ward; Andreas Martin Lisewski; Serkan Erdin; Brian Y. Chen; Viacheslav Fofanov; Marek Kimmel; Lydia E. Kavraki; Olivier Lichtarge (BMC Bioinform., 2008)

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates. - R. Matthew Ward; Eric Venner; Bryce Daines; Stephen Murray; Serkan Erdin; David M. Kristensen; Olivier Lichtarge (Bioinform., 2009)

A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches. - David M. Kristensen; Lavanya Kannan; Michael K. Coleman; Yuri I. Wolf; Alexander Sorokin; Eugene V. Koonin; Arcady R. Mushegian (Bioinform., 2010)

Computational methods for Gene Orthology inference. - David M. Kristensen; Yuri I. Wolf; Arcady R. Mushegian; Eugene V. Koonin (Briefings Bioinform., 2011)

A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea. - David M. Kristensen; Usman Saeed; Dmitrij Frishman; Eugene V. Koonin (BMC Bioinform., 2015)

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation. - Ana Laura Grazziotin; Eugene V. Koonin; David M. Kristensen (Nucleic Acids Res., 2017)

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation. - David M. Kristensen; Yuri I. Wolf; Eugene V. Koonin (Nucleic Acids Res., 2017)

Microbial genome analysis: the COG approach. - Michael Y. Galperin; David M. Kristensen; Kira S. Makarova; Yuri I. Wolf; Eugene V. Koonin (Briefings Bioinform., 2019)