Selected Publications
Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 Role
J.R. Bowers, M.Valentine, V. Harrison, V.Y. Fofanov, J. Gillece, J. Delisle, B. Patton, J. Schupp, K.Sheridan, D. Lemmer, S. Ostdiek, H.K. Bains, J. Heim, T. Sylvester, S. Prasai, M. Kretschmer, N. Fowle, K. Komatsu, S. Brady, S. Robinson, K. Fitzpatrick, G.A. Ostovar, E. Alsop, E. Hutchins, K. Jensen, P. Keim, D.M. Engelthaler.
mBio. 2019 Jan 10.1128/mBio.02262-18.
Rapid Next-Generation Sequencing Method for Prediction of Prostate Cancer Risks
V.Y. Fofanov, K. Upadhyay, A. Pearlman, J. Loke, O. Vivian, Y. Shao, S. Freedland, H. Ostrer.
J Mol Diagn. 2019 Jan 10.1016/j.jmoldx.2018.07.007.
Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites
T.N. Furstenau, J.H. Cocking, J.W. Sahl, V.Y. Fofanov.
BMC bioinformatics. 2018 Dec 10.1186/s12859-018-2225-z.
Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest
C.M. Hepp, J.H. Cocking, M. Valentine, S.J. Young, D. Damian, K.E. Samuels-Crow, K. Sheridan, V.Y. Fofanov, T.N. Furstenau, J.D. Busch, D.E. Erickson, R.C. Lancione, K. Smith, J. Will, J. Townsend, P.S. Keim, D.M. Engelthaler.
PloS one. 2018 Dec 26;13(11):e0205801.
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
R. Trotter, M. Lininger, R. Camplain, V. Fofanov, C. Camplain, J. Baldwin.
PloS one. 2018 Nov 10.3390/ijerph15112500.
Health Disparities and Converging Epidemics in Jail Populations: Protocol for a Mixed-Methods Study
R.T. Trotter II, R. Camplain, E.R. Eaves, V.Y. Fofanov, N.O. Dmitrieva, C.M. Hepp, M. Warren, B.A. Barrios, N. Pagel, A. Mayer, J.A. Baldwin.
JMIR research protocols. 2018 Oct 10.2196/10337.
Guano exposed: Impact of aerobic conditions on bat fecal microbiota
V.Y. Fofanov, T.N. Furstenau, D. Sanchez, C.M. Hepp, J. Cocking, C. Sobek, N. Pagel, F. Walker, C.L. Chambers.
Ecol Evol. 2018 Jun 10.1002/ece3.4084.
A Bacillus anthracis genome sequence from the Sverdlovsk 1979 autopsy specimens
J.W. Sahl, T. Pearson, R. Okinaka, J.M. Schupp, J.D. Gillece, H. Heaton, D. Birdsell, C. Hepp, V. Fofanov, R. Noseda, A. Fasanella, A. Hoffmaster, D.M. Wagner, P. Keim.
MBio. 2016 Sep 10.1128/mBio.01501-16.
Identification of genome-wide mutations in ciprofloxacin-resistant F. tularensis LVS using whole genome tiling arrays and next generation sequencing
A.B. Nicholas, J.B. Thissen, V.Y. Fofanov, J.E. Allen, M. Rojas, G. Golovko, Y. Fofanov, H. Koshinsky, C.J. Jaing.
Microb Ecol. 2015 Feb 10.1007/s00248-014-0517-z.
Genomic Epidemiology of Multidrug-Resistant Mycobacterium tuberculosis During Transcontinental Spread
M. Coscolla, P.M. Barry, J.E. Oeltmann, H. Koshinsky, T. Shaw, M. Cilnis, J. Posey, J. Rose, T. Weber, V.Y. Fofanov, S. Gagneux, M. Kato-Maeda, J.Z. Metcalfe.
J Infect Dis. 2015 Jan 10.1093/infdis/jiv025.
Use of Next Generation Sequencing (NGS) Platforms for CE Sequencing on Thousands of Samples
M. Shin, P. Dier, J. Kyle, R. O'Callahan, M. Helmrick, H. Phan, D.L. Hirchberg, V.Y. Fofanov, J. Curry, H. Koshinsky.
JBT. 2014 May PMC4162214.
Metagenomic analysis of the airborne environment in urban spaces.
N.A. Be, J.B. Thissen, V.Y. Fofanov, J.E. Allen, M. Rojas, G. Golovko, Y. Fofanov, H. Koshinsky, and C. Jaing.
Microb Ecol. 2014 (in print).
Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing.
N.A. Be, J.B. Thissen, S.N. Gardner, K.S. McLoughlin, V.Y. Fofanov, H. Koshinsky, S.R. Ellingson, T.S. Brettin, P.J. Jackson, and C. Jaing.
PLOS One. 2013 Sep 9;8(9):e73455.
A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing.
S. Poojari, O.J. Alabi, V.Y. Fofanov, R.A. Naidu.
PLOS One. 2013 Jun 5;8(6):e64194
Small RNA populations for two unrelated viruses exhibit different biases in strand polarity and proximity to terminal sequences in the insect host Homalodisca vitripennis.
R.S. Nandety, V.Y. Fofanov, H. Koshinsky, D.C. Stenger, B.W. Falk.
Virology. 2013 442(1):12-9
Application of next generation sequencing technologies to the identification of highly degraded unknown soldiers' remains.
O. Loreill, H. Koshinsky, V.Y. Fofanov, J.A. Irwin.
Forensic Science International: Genetics Supplement Series. 3:e540-e541.