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Viacheslav Fofanov

TitleAssociate Professor
Faculty RankAssociate Professor
InstitutionNorthern Arizona University
DepartmentInformatics, Computing & Cyber Systems
AddressPO Box 5693
Flagstaff AZ 86011
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Pearson T, Furstenau T, Wood C, Rigas V, Sahl J, Maltinsky S, Currie BJ, Mayo M, Hall C, Keim P, Fofanov V. Population sequencing for diversity and transmission analyses. bioRxiv. 2024 Jun 20. PMID: 38948873.
      Citations:    
    2. Stone NE, Hamond C, Clegg J, McDonough RF, Bourgeois RM, Ballard R, Thornton NB, Nuttall M, Hertzel H, Anderson T, Whealy RN, Timm S, Roberts AK, Barrag?n V, Phipatanakul W, Leibler JH, Benson H, Specht A, White R, LeCount K, Furstenau TN, Galloway RL, Hill NJ, Madison JD, Fofanov VY, Pearson T, Sahl JW, Busch JD, Weiner Z, Nally JE, Wagner DM, Rosenbaum MH. Host population structure and rare dispersal events drive leptospirosis transmission patterns among Rattus norvegicus in Boston, Massachusetts, US. bioRxiv. 2024 Jun 14. PMID: 38915728.
      Citations:    
    3. Williamson CHD, Vazquez AJ, Nunnally AE, Kyger K, Fofanov VY, Furstenau TN, Hornstra HM, Terriquez J, Keim P, Sahl JW. ColiSeq: a multiplex amplicon assay that provides strain level resolution of Escherichia coli directly from clinical specimens. Microbiol Spectr. 2024 Jun 04; 12(6):e0413923. PMID: 38651881.
      Citations:    Fields:    Translation:HumansCells
    4. Erickson DE, Simmons KM, Barrand ZA, Ridenour CL, Hawkinson PB, Lemke L, Sellner SP, Brock BN, Rivas AN, Sheridan K, Lemmer D, Yaglom HD, Porter WT, Belanger M, Torrey RM, Stills AJR, McCormack K, Black M, Holmes W, Rostain D, Mikus J, Sotelo K, Haq E, Neupane R, Weiss J, Johnson J, Collins C, Avalle S, White C, Howard BJ, Maltinsky SA, Whealy RN, Gordon NB, Sahl JW, Pearson T, Fofanov VY, Furstenau T, Driebe EM, Caporaso JG, Barber J, Terriquez J, Engelthaler DM, Hepp CM. Pan-Enterovirus Characterization Reveals Cryptic Circulation of Clinically Relevant Subtypes in Arizona Wastewater. medRxiv. 2024 Mar 20. PMID: 38562876.
      Citations:    
    5. Russakoff B, Wood C, Lininger MR, Barger SD, Trotter RT, Maltinsky S, Mbegbu M, Coyne B, Panisello Yag?e D, Kyman S, Tucker-Morgan K, Ceniceros K, Padilla C, Hurtado K, Menard A, Villa F, Wayment HA, Hepp C, Furstenau T, Fofanov V, Liu CM, Pearson TR. A Quantitative Assessment of Staphylococcus aureus Community Carriage in Yuma, Arizona. J Infect Dis. 2023 04 26; 227(9):1031-1041. PMID: 36322556.
      Citations: 3     Fields:    Translation:HumansCells
    6. Highlander SK, Wood JM, Gillece JD, Folkerts M, Fofanov V, Furstenau T, Singh NK, Guan L, Seuylemezian A, Benardini JN, Engelthaler DM, Venkateswaran K, Keim PS. Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition. PLoS One. 2023; 18(3):e0282428. PMID: 36947490.
      Citations:    Fields:    Translation:HumansCells
    7. Furstenau TN, Schneider T, Shaffer I, Vazquez AJ, Sahl J, Fofanov V. MTSv: rapid alignment-based taxonomic classification and high-confidence metagenomic analysis. PeerJ. 2022; 10:e14292. PMID: 36389404.
      Citations: 1     Fields:    
    8. Ridenour CL, Cocking J, Poidmore S, Erickson D, Brock B, Valentine M, Roe CC, Young SJ, Henke JA, Hung KY, Wittie J, Stefanakos E, Sumner C, Ruedas M, Raman V, Seaton N, Bendik W, Hornstra O'Neill HM, Sheridan K, Centner H, Lemmer D, Fofanov V, Smith K, Will J, Townsend J, Foster JT, Keim PS, Engelthaler DM, Hepp CM. St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event. Front Genet. 2021; 12:667895. PMID: 34168675.
      Citations:    
    9. Chuckran PF, Fofanov V, Hungate BA, Morrissey EM, Schwartz E, Walkup J, Dijkstra P. Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community. mSystems. 2021 May 11; 6(3). PMID: 33975966.
      Citations: 5     Fields:    
    10. Furstenau TN, Cocking JH, Hepp CM, Fofanov VY. Sample pooling methods for efficient pathogen screening: Practical implications. PLoS One. 2020; 15(11):e0236849. PMID: 33175841.
      Citations: 8     Fields:    Translation:HumansCellsPHPublic Health
    11. Chuckran PF, Huntemann M, Clum A, Foster B, Foster B, Roux S, Palaniappan K, Varghese N, Mukherjee S, Reddy TBK, Daum C, Copeland A, Ivanova NN, Kyrpides NC, Del Rio TG, Eloe-Fadrosh EA, Morrissey EM, Schwartz E, Fofanov V, Hungate B, Dijkstra P. Metagenomes and Metatranscriptomes of a Glucose-Amended Agricultural Soil. Microbiol Resour Announc. 2020 Oct 29; 9(44). PMID: 33122409.
      Citations:    
    12. Walker FM, Tobin A, Simmons NB, Sobek CJ, Sanchez DE, Chambers CL, Fofanov VY. A fecal sequel: Testing the limits of a genetic assay for bat species identification. PLoS One. 2019; 14(11):e0224969. PMID: 31725795.
      Citations: 6     Fields:    Translation:Animals
    13. Cocking JH, Deberg M, Schupp J, Sahl J, Wiggins K, Porty A, Hornstra HM, Hepp C, Jardine C, Furstenau TN, Schulte-Hostedde A, Fofanov VY, Pearson T. Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples. Genomics. 2020 03; 112(2):1872-1878. PMID: 31678592.
      Citations: 4     Fields:    Translation:AnimalsCells
    14. Camplain R, Warren M, Baldwin JA, Camplain C, Fofanov VY, Trotter RT. Epidemiology of Incarceration: Characterizing Jail Incarceration for Public Health Research. Epidemiology. 2019 07; 30(4):561-568. PMID: 30985527.
      Citations: 17     Fields:    Translation:HumansPHPublic Health
    15. Bowers JR, Valentine M, Harrison V, Fofanov VY, Gillece J, Delisle J, Patton B, Schupp J, Sheridan K, Lemmer D, Ostdiek S, Bains HK, Heim J, Sylvester T, Prasai S, Kretschmer M, Fowle N, Komatsu K, Brady S, Robinson S, Fitzpatrick K, Ostovar GA, Alsop E, Hutchins E, Jensen K, Keim P, Engelthaler DM. Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 Role. mBio. 2019 01 22; 10(1). PMID: 30670612.
      Citations: 8     Fields:    Translation:HumansCells
    16. Trotter RT, Fofanov VY, Camplain R, Arazan CL, Camplain C, Eaves ER, Hanabury M, Hepp CM, Kohlbeck BS, Lininger MR, Peoples M, Dmitrieva NO, Baldwin JA. Health disparities in jail populations: Mixed methods and multi-disciplinary community engagement for justice and health impacts. Pract Anthropol. 2019; 41(4):2-16. PMID: 33110290.
      Citations:    
    17. Fofanov VY, Upadhyay K, Pearlman A, Loke J, O V, Shao Y, Freedland S, Ostrer H. Rapid Next-Generation Sequencing Method for Prediction of Prostate Cancer Risks. J Mol Diagn. 2019 01; 21(1):49-57. PMID: 30553750.
      Citations: 1     Fields:    Translation:Humans
    18. Hepp CM, Cocking JH, Valentine M, Young SJ, Damian D, Samuels-Crow KE, Sheridan K, Fofanov VY, Furstenau TN, Busch JD, Erickson DE, Lancione RC, Smith K, Will J, Townsend J, Keim PS, Engelthaler DM. Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest. PLoS One. 2018; 13(11):e0205801. PMID: 30475820.
      Citations: 8     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    19. Trotter RT, Lininger MR, Camplain R, Fofanov VY, Camplain C, Baldwin JA. A Survey of Health Disparities, Social Determinants of Health, and Converging Morbidities in a County Jail: A Cultural-Ecological Assessment of Health Conditions in Jail Populations. Int J Environ Res Public Health. 2018 11 08; 15(11). PMID: 30413098.
      Citations: 12     Fields:    Translation:Humans
    20. Trotter Ii RT, Camplain R, Eaves ER, Fofanov VY, Dmitrieva NO, Hepp CM, Warren M, Barrios BA, Pagel N, Mayer A, Baldwin JA. Health Disparities and Converging Epidemics in Jail Populations: Protocol for a Mixed-Methods Study. JMIR Res Protoc. 2018 Oct 24; 7(10):e10337. PMID: 30355562.
      Citations:    
    21. Furstenau TN, Cocking JH, Sahl JW, Fofanov VY. Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites. BMC Bioinformatics. 2018 06 11; 19(1):222. PMID: 29890941.
      Citations: 1     Fields:    Translation:HumansCells
    22. Fofanov VY, Furstenau TN, Sanchez D, Hepp CM, Cocking J, Sobek C, Pagel N, Walker F, Chambers CL. Guano exposed: Impact of aerobic conditions on bat fecal microbiota. Ecol Evol. 2018 Jun; 8(11):5563-5574. PMID: 29938074.
      Citations:    
    23. Sahl JW, Pearson T, Okinaka R, Schupp JM, Gillece JD, Heaton H, Birdsell D, Hepp C, Fofanov V, Noseda R, Fasanella A, Hoffmaster A, Wagner DM, Keim P. A Bacillus anthracis Genome Sequence from the Sverdlovsk 1979 Autopsy Specimens. mBio. 2016 Sep 27; 7(5). PMID: 27677796.
      Citations: 36     Fields:    
    24. Jaing CJ, McLoughlin KS, Thissen JB, Zemla A, Gardner SN, Vergez LM, Bourguet F, Mabery S, Fofanov VY, Koshinsky H, Jackson PJ. Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing. PLoS One. 2016; 11(9):e0163458. PMID: 27668749.
      Citations: 10     Fields:    
    25. Poojari S, Alabi OJ, Fofanov VY, Naidu RA. Correction: A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing. PLoS One. 2016; 11(1):e0147510. PMID: 26771745.
      Citations: 2     Fields:    
    26. Coscolla M, Barry PM, Oeltmann JE, Koshinsky H, Shaw T, Cilnis M, Posey J, Rose J, Weber T, Fofanov VY, Gagneux S, Kato-Maeda M, Metcalfe JZ. Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread. J Infect Dis. 2015 Jul 15; 212(2):302-10. PMID: 25601940.
      Citations: 16     Fields:    Translation:HumansCellsPHPublic Health
    27. Be NA, Thissen JB, Fofanov VY, Allen JE, Rojas M, Golovko G, Fofanov Y, Koshinsky H, Jaing CJ. Metagenomic analysis of the airborne environment in urban spaces. Microb Ecol. 2015 Feb; 69(2):346-55. PMID: 25351142.
      Citations: 32     Fields:    Translation:AnimalsCellsPHPublic Health
    28. Be NA, Thissen JB, Gardner SN, McLoughlin KS, Fofanov VY, Koshinsky H, Ellingson SR, Brettin TS, Jackson PJ, Jaing CJ. Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing. PLoS One. 2013; 8(9):e73455. PMID: 24039948.
      Citations: 14     Fields:    Translation:CellsPHPublic Health
    29. Poojari S, Alabi OJ, Fofanov VY, Naidu RA. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing. PLoS One. 2013; 8(6):e64194. PMID: 23755117.
      Citations: 22     Fields:    Translation:AnimalsCellsPHPublic Health
    30. Nandety RS, Fofanov VY, Koshinsky H, Stenger DC, Falk BW. Small RNA populations for two unrelated viruses exhibit different biases in strand polarity and proximity to terminal sequences in the insect host Homalodisca vitripennis. Virology. 2013 Jul 20; 442(1):12-9. PMID: 23642540.
      Citations: 17     Fields:    Translation:AnimalsCells
    31. Kato-Maeda M, Shanley CA, Ackart D, Jarlsberg LG, Shang S, Obregon-Henao A, Harton M, Basaraba RJ, Henao-Tamayo M, Barrozo JC, Rose J, Kawamura LM, Coscolla M, Fofanov VY, Koshinsky H, Gagneux S, Hopewell PC, Ordway DJ, Orme IM. Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig. Clin Vaccine Immunol. 2012 Aug; 19(8):1227-37. PMID: 22718126.
      Citations: 51     Fields:    Translation:HumansAnimalsCells
    32. Mukherjee M, Ge G, Zhang N, Huang E, Nakamura LV, Minor M, Fofanov V, Rao PH, Herron A, Pati D. Separase loss of function cooperates with the loss of p53 in the initiation and progression of T- and B-cell lymphoma, leukemia and aneuploidy in mice. PLoS One. 2011; 6(7):e22167. PMID: 21799785.
      Citations: 18     Fields:    Translation:HumansAnimals
    33. Bryant DH, Moll M, Chen BY, Fofanov VY, Kavraki LE. Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. BMC Bioinformatics. 2010 May 11; 11:242. PMID: 20459833.
      Citations: 8     Fields:    Translation:Cells
    34. Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BMC Bioinformatics. 2008 Jan 11; 9:17. PMID: 18190718.
      Citations: 40     Fields:    Translation:Cells
    35. Reed C, Fofanov V, Putonti C, Chumakov S, Slezak T, Fofanov Y. Effect of the mutation rate and background size on the quality of pathogen identification. Bioinformatics. 2007 Oct 15; 23(20):2665-71. PMID: 17881407.
      Citations: 3     Fields:    
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