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Yuriy Fofanov, PhD

Associate Affiliate Member, Research Institute
Houston Methodist


Dr. Fofanov received his first academic appointment in 1989, as a Head of the Lab in the Russian Academy of Science. He joined the faculty in the Department of Computer Science at the University of Houston as an Assistant Professor in 2001. At present, Dr. Fofanov holds two faculty appointments in the College of Natural Sciences; Associate Professor, Department of Computer Science, and Associate Professor, Department of Biology and Biochemistry. He is also a faculty member at the W.M. Keck Center for Computational and Structural Biology.

Dr. Fofoanov has published numerous peer-reviewed papers in the literature, and has been the principal investigator on four research grants funded by the Homeland Security Advanced Research Projects Agency.

Description of Research

Dr. Fofanov’s research centers on population-scale HLA typing, and tools for ultraspecific probe/primer design. His bioinformatics research specifically focuses on gene expression, including investigations into micro-array data normalization approaches, and genomic sequence analysis, which includes studies of the statistical properties of short subsequences in microbial and viral genomes.

Areas Of Expertise

Bioinformatics Computer science Applied statistics
Education & Training

, Kuibyshev (Samara) State University

The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome
Albayrak, L, Khanipov, K, Pimenova, M, Golovko, G, Rojas, M, Pavlidis, I, Chumakov, S, Aguilar, G, Chávez, A, Widger, WR & Fofanov, Y 2016, BMC Genomics, vol 17, no. 1, 1017. DOI:

Small Regulatory RNAs of Rickettsia conorii
Narra, HP, Schroeder, CLC, Sahni, A, Rojas, M, Khanipov, K, Fofanov, Y & Sahni, SK 2016, Scientific Reports, vol 6, 36728. DOI:

Bartonella melophagi in blood of domestic sheep (Ovis aries) and sheep keds (Melophagus ovinus) from the southwestern US: Cultures, genetic characterization, and ecological connections
Kosoy, M, Bai, Y, Enscore, R, Rizzo, MR, Bender, S, Popov, V, Albayrak, L, Fofanov, Y & Chomel, B 2016, Veterinary Microbiology, vol 190, pp. 43-49. DOI:

Identification and characterization of novel small RNAs in Rickettsia prowazekii
Schroeder, CLC, Narra, HP, Sahni, A, Rojas, M, Khanipov, K, Patel, J, Shah, R, Fofanov, Y & Sahni, SK 2016, Frontiers in Microbiology, vol 7, no. JUN, 859. DOI:

Bacterial small RNAs in the Genus Rickettsia
Schroeder, CLC, Narra, HP, Rojas, M, Sahni, A, Patel, J, Khanipov, K, Wood, TG, Fofanov, Y & Sahni, SK 2015, BMC Genomics, vol 16, no. 1, 1075. DOI:

CoCo: An application to store High-Throughput Sequencing data in compact text and binary file formats
Khanipov, K, Golovko, G, Rojas, M, Albayrak, L, Dobretsberger, O, Pimenova, M, Olson, N, Chumakov, S & Fofanov, Y 2015, . in Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015., 7359838, Institute of Electrical and Electronics Engineers Inc. pp. 1117-1122, IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015, Washington, United States, 9-12 November. DOI:

Survey of viral populations within Lake Michigan nearshore waters at four Chicago area beaches
Sible, E, Cooper, A, Malki, K, Bruder, K, Watkins, SC, Fofanov, Y & Putonti, C 2015, Data in Brief, vol 5, pp. 9-12. DOI:

The main challenges that remain in applying high-throughput sequencing to clinical diagnostics
Loeffelholz, M & Fofanov, Y 2015, Expert Review of Molecular Diagnostics, vol 15, no. 11, pp. 1405-1408. DOI:

Secondary analysis of the NCI-60 whole exome sequencing data indicates significant presence of propionibacterium acnes genomic material in leukemia (RPMI-8226) and central nervous system (SF-295, SF-539, and SNB-19) cell lines
Rojas, M, Golovko, G, Khanipov, K, Albayrak, L, Chumakov, S, Pettitt, BM, Strongin, AY & Fofanov, Y 2015, PLoS ONE, vol 10, no. 6, e0127799. DOI:

The presence of nitrate dramatically changed the predominant microbial community in perchlorate degrading cultures under saline conditions
Stepanov, VG, Xiao, Y, Tran, Q, Rojas, M, Willson, RC, Fofanov, Y, Fox, GE & Roberts, DJ 2014, BMC Microbiology, vol 14, no. 1, 225. DOI:

Epigenetic alteration by DNA-demethylating treatment restores apoptotic response to glucocorticoids in dexamethasone-resistant human malignant lymphoid cells
Miller, AL, Geng, C, Golovko, G, Sharma, M, Schwartz, JR, Yan, J, Sowers, L, Widger, WR, Fofanov, Y, Vedeckis, WV & Thompson, EB 2014, Cancer Cell International, vol 14, no. 1, 35. DOI:

Metagenomic Analysis of the Airborne Environment in Urban Spaces
Be, NA, Thissen, JB, Fofanov, VY, Allen, JE, Rojas, M, Golovko, G, Fofanov, Y, Koshinsky, H & Jaing, CJ 2014, Microbial Ecology, vol 69, no. 2, pp. 346-355. DOI:

Where does Neisseria acquire foreign DNA from: An examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus
Putonti, C, Nowicki, B, Shaffer, M, Fofanov, Y & Nowicki, S 2013, BMC Evolutionary Biology, vol 13, no. 1, 184. DOI:

Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum
Saxer, G, Havlak, P, Fox, SA, Quance, MA, Gupta, S, Fofanov, Y, Strassmann, JE & Queller, DC 2012, PLoS ONE, vol 7, no. 10, e46759. DOI:

Generation of PVY Coat Protein siRNAs in Transgenic Potatoes Resistant to PVY
McCue, KF, Ponciano, G, Rockhold, DR, Whitworth, JL, Gray, SM, Fofanov, Y & Belknap, WR 2012, American Journal of Potato Research, vol 89, no. 5, pp. 374-383. DOI:

Slim-Filter: An interactive windows-based application for illumina genome analyzer data assessment and manipulation
Golovko, G, Khanipov, K, Rojas, M, Martinez-Alcántara, A, Howard, JJ, Ballesteros, E, Gupta, S, Widger, W & Fofanov, Y 2012, BMC Bioinformatics, vol 13, no. 1, 166. DOI:

Detection and typing of viruses using broadly sensitive cocktail-PCR and mass spectrometric cataloging: Demonstration with dengue virus
Gijavanekar, C, Drabek, R, Soni, M, Jackson, GW, Strych, U, Fox, GE, Fofanov, Y & Willson, RC 2012, Journal of Molecular Diagnostics, vol 14, no. 4, pp. 402-407. DOI:

Rare target enrichment for ultrasensitive PCR detection using cot-rehybridization and duplex-specific nuclease
Gijavanekar, C, Strych, U, Fofanov, Y, Fox, GE & Willson, RC 2012, Analytical Biochemistry, vol 421, no. 1, pp. 81-85. DOI:

Ehrlichia chaffeensis TRP120 binds a G+C-rich motif in host cell DNA and exhibits eukaryotic transcriptional activator function
Zhu, B, Kuriakose, JA, Luo, T, Ballesteros, E, Gupta, S, Fofanov, Y & McBride, JW 2011, Infection and Immunity, vol 79, no. 11, pp. 4370-4381. DOI:

PCR detection of nearly any dengue virus strain using a highly sensitive primer 'cocktail'
Gijavanekar, C, Añez-Lingerfelt, M, Feng, C, Putonti, C, Fox, GE, Sabo, A, Fofanov, Y & Willson, RC 2011, FEBS Journal, vol 278, no. 10, pp. 1676-1687. DOI: