How independent are the appearances of n-mers in different genomes? - Yuriy Fofanov; Yi Luo; Charles Katili; Jim Wang; Yuri Belosludtsev; Thomas Powdrill; Chetan Belapurkar; Viacheslav Fofanov; Tong-Bin Li; Sergei Chumakov; B. Montgomery Pettitt (Bioinform., 2004)

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)

Statistical Properties of Short n-mers Located in the One Mismatch Area of Microbial Genomes. - Aaron Skewes; Michael Quance; Catherine Putonti; Viacheslav Fofanov; Yuriy Fofanov (BIOCOMP, 2007)

Effect of the mutation rate and background size on the quality of pathogen identification. - Chris Reed 003; Viacheslav Fofanov; Catherine Putonti; Sergei Chumakov; Tom Slezak; Yuriy Fofanov (Bioinform., 2007)

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)

PIQA: pipeline for Illumina G1 genome analyzer data quality assessment. - Antonio Martínez-Alcántara; Efren Ballesteros; Chen Feng; Mark Rojas; H. Koshinsky; Viacheslav Fofanov; Paul Havlak; Yuriy Fofanov (Bioinform., 2009)

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. - Drew H. Bryant; Mark Moll; Brian Y. Chen; Viacheslav Fofanov; Lydia E. Kavraki (BMC Bioinform., 2010)

Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites. - Tara N. Furstenau; Jill H. Cocking; Jason W. Sahl; Viacheslav Fofanov (BMC Bioinform., 2018)