Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: Local Invariants approach. - Yuriy Fofanov; B. Montgomery Pettitt (J. Biomed. Informatics, 2002)

Using Statistical Properties of Short Subsequences in Microbial Identification. - Sergei Chumakov; Catherine Putonti; B. Montgomery Pettitt; George E. Fox; Richard C. Willson; Yuriy Fofanov (METMBS, 2004)

Analysis of Promoter Regions for Essential Genes of Bacillus subtilis for Using PIDA. - Catherine Putonti; Yuriy Fofanov (METMBS, 2004)

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)

ProkProbePicker (PPP): a Fast Program to Extract 16S rRNA-Targeted Probes for Prokaryotes. - Dianhui Zhu; Yuriy Fofanov; Richard C. Willson; George E. Fox (METMBS, 2005)

Two Challenges in Genomics That Can Benefit from Petascale Platforms. - Catherine Putonti; Meizhuo Zhang; S. Lennart Johnsson; Yuriy Fofanov (Euro-Par Workshops, 2006)

A parallel computing algorithm for 16S rRNA probe design. - Dianhui Zhu; Yuriy Fofanov; Richard C. Willson; George E. Fox (J. Parallel Distributed Comput., 2006)

Developing Assays for the Detection of Influenza in Human Samples. - Chen Feng; Catherine Putonti; Michael Quance; Stephen Huff; Andrey Belokrylov; S. Lennart Johnsson; Krishna Jayaraman; Michael Hogan; Yuriy Fofanov (BIOCOMP, 2007)

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)

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)

Co-Evolution of the Influenza Virus and Its Hosts. - Stephen Huff; Mark Rojas; Paul Havlak; Yuriy Fofanov (BIOCOMP, 2010)

Slim-Filter: an interactive windows-based application for illumina genome analyzer data assessment and manipulation. - Georgiy Golovko; Kamil Khanipov; Mark Rojas; Antonio Martínez-Alcántara; Jesse J. Howard; Efren Ballesteros; Sharu Gupta; William Widger; Yuriy Fofanov (BMC Bioinform., 2012)

CoCo: An application to store High-Throughput Sequencing data in compact text and binary file formats. - Kamil Khanipov; Georgiy Golovko; Mark Rojas; Levent Albayrak; Otto Dobretsberger; Maria Pimenova; Nels Olson; Sergei Chumakov; Yuriy Fofanov (BIBM, 2015)

Exploration of Natural Alignment Scoring Rules and Clustering Thresholds for Bacterial Core/Pan Genome Analysis. - Levent L. Albayrak; Kamil Khanipov; Mark Rojas; George Golovko; Maria Pimenova; Michael Kosoy; Yuriy Fofanov (BIBE, 2017)

Novel Computational Approach for Identification of Highly Mutated Integrated HIV Genomes. - Kamil Khanipov; Levent Albayrak; George Golovko; Maria Pimenova; Ioannis T. Pavlidis; Yuriy Fofanov; Khanipov K. (BIBE, 2017)

Detection of multi-dimensional co-exclusion patterns in microbial communities. - Levent Albayrak; Kamil Khanipov; George Golovko; Yuriy Fofanov (Bioinform., 2018)

Broom: application for non-redundant storage of high throughput sequencing data. - Levent Albayrak; Kamil Khanipov; George Golovko; Yuriy Fofanov (Bioinform., 2019)

Identification of multivariable Boolean patterns in microbiome and microbial gene composition data. - George Golovko; Kamil Khanipov; Victor Reyes; Irina Pinchuk; Yuriy Fofanov (Biosyst., 2023)