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Items: 27

1.

A fecal sequel: Testing the limits of a genetic assay for bat species identification.

Walker FM, Tobin A, Simmons NB, Sobek CJ, Sanchez DE, Chambers CL, Fofanov VY.

PLoS One. 2019 Nov 14;14(11):e0224969. doi: 10.1371/journal.pone.0224969. eCollection 2019.

2.

Selective whole genome amplification and sequencing of Coxiella burnetii directly from environmental samples.

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.

Genomics. 2019 Oct 31. pii: S0888-7543(19)30205-8. doi: 10.1016/j.ygeno.2019.10.022. [Epub ahead of print]

PMID:
31678592
3.

Epidemiology of Incarceration: Characterizing Jail Incarceration for Public Health Research.

Camplain R, Warren M, Baldwin JA, Camplain C, Fofanov VY, Trotter RT 2nd.

Epidemiology. 2019 Jul;30(4):561-568. doi: 10.1097/EDE.0000000000001021.

PMID:
30985527
4.

Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 Role.

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.

mBio. 2019 Jan 22;10(1). pii: e02262-18. doi: 10.1128/mBio.02262-18.

5.

Rapid Next-Generation Sequencing Method for Prediction of Prostate Cancer Risks.

Fofanov VY, Upadhyay K, Pearlman A, Loke J, O V, Shao Y, Freedland S, Ostrer H.

J Mol Diagn. 2019 Jan;21(1):49-57. doi: 10.1016/j.jmoldx.2018.07.007. Epub 2018 Dec 12.

6.

Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest.

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.

PLoS One. 2018 Nov 26;13(11):e0205801. doi: 10.1371/journal.pone.0205801. eCollection 2018.

7.

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.

Trotter RT 2nd, Lininger MR, Camplain R, Fofanov VY, Camplain C, Baldwin JA.

Int J Environ Res Public Health. 2018 Nov 8;15(11). pii: E2500. doi: 10.3390/ijerph15112500.

8.

Health Disparities and Converging Epidemics in Jail Populations: Protocol for a Mixed-Methods Study.

Trotter Ii RT, Camplain R, Eaves ER, Fofanov VY, Dmitrieva NO, Hepp CM, Warren M, Barrios BA, Pagel N, Mayer A, Baldwin JA.

JMIR Res Protoc. 2018 Oct 24;7(10):e10337. doi: 10.2196/10337.

9.

Guano exposed: Impact of aerobic conditions on bat fecal microbiota.

Fofanov VY, Furstenau TN, Sanchez D, Hepp CM, Cocking J, Sobek C, Pagel N, Walker F, Chambers CL.

Ecol Evol. 2018 Apr 27;8(11):5563-5574. doi: 10.1002/ece3.4084. eCollection 2018 Jun.

10.

Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites.

Furstenau TN, Cocking JH, Sahl JW, Fofanov VY.

BMC Bioinformatics. 2018 Jun 11;19(1):222. doi: 10.1186/s12859-018-2225-z.

11.

Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing.

Jaing CJ, McLoughlin KS, Thissen JB, Zemla A, Gardner SN, Vergez LM, Bourguet F, Mabery S, Fofanov VY, Koshinsky H, Jackson PJ.

PLoS One. 2016 Sep 26;11(9):e0163458. doi: 10.1371/journal.pone.0163458. eCollection 2016.

12.

Correction: A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing.

Poojari S, Alabi OJ, Fofanov VY, Naidu RA.

PLoS One. 2016 Jan 15;11(1):e0147510. doi: 10.1371/journal.pone.0147510. eCollection 2016. No abstract available.

13.

Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread.

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.

J Infect Dis. 2015 Jul 15;212(2):302-10. doi: 10.1093/infdis/jiv025. Epub 2015 Jan 18.

14.

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.

Microb Ecol. 2015 Feb;69(2):346-55. doi: 10.1007/s00248-014-0517-z. Epub 2014 Oct 29.

15.

Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing.

Be NA, Thissen JB, Gardner SN, McLoughlin KS, Fofanov VY, Koshinsky H, Ellingson SR, Brettin TS, Jackson PJ, Jaing CJ.

PLoS One. 2013 Sep 9;8(9):e73455. doi: 10.1371/journal.pone.0073455. eCollection 2013.

16.

A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing.

Poojari S, Alabi OJ, Fofanov VY, Naidu RA.

PLoS One. 2013 Jun 5;8(6):e64194. doi: 10.1371/journal.pone.0064194. Print 2013. Erratum in: PLoS One. 2016;11(1):e0147510.

17.

Small RNA populations for two unrelated viruses exhibit different biases in strand polarity and proximity to terminal sequences in the insect host Homalodisca vitripennis.

Nandety RS, Fofanov VY, Koshinsky H, Stenger DC, Falk BW.

Virology. 2013 Jul 20;442(1):12-9. doi: 10.1016/j.virol.2013.04.005. Epub 2013 May 1.

18.

Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig.

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.

Clin Vaccine Immunol. 2012 Aug;19(8):1227-37. doi: 10.1128/CVI.00250-12. Epub 2012 Jun 20.

19.

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction.

Bryant DH, Moll M, Chen BY, Fofanov VY, Kavraki LE.

BMC Bioinformatics. 2010 May 11;11:242. doi: 10.1186/1471-2105-11-242.

20.

PIQA: pipeline for Illumina G1 genome analyzer data quality assessment.

Martínez-Alcántara A, Ballesteros E, Feng C, Rojas M, Koshinsky H, Fofanov VY, Havlak P, Fofanov Y.

Bioinformatics. 2009 Sep 15;25(18):2438-9. doi: 10.1093/bioinformatics/btp429. Epub 2009 Jul 14.

21.

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

Kristensen DM, Ward RM, Lisewski AM, Erdin S, Chen BY, Fofanov VY, Kimmel M, Kavraki LE, Lichtarge O.

BMC Bioinformatics. 2008 Jan 11;9:17. doi: 10.1186/1471-2105-9-17.

22.

Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

Chen BY, Bryant DH, Cruess AE, Bylund JH, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE.

Comput Syst Bioinformatics Conf. 2007;6:343-55.

23.

The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.

Chen BY, Fofanov VY, Bryant DH, Dodson BD, Kristensen DM, Lisewski AM, Kimmel M, Lichtarge O, Kavraki LE.

J Comput Biol. 2007 Jul-Aug;14(6):791-816.

PMID:
17691895
24.

Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction.

Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE.

J Bioinform Comput Biol. 2007 Apr;5(2a):353-82.

PMID:
17589966
25.

Cavity-aware motifs reduce false positives in protein function prediction.

Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE.

Comput Syst Bioinformatics Conf. 2006:311-23.

26.

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity.

Kristensen DM, Chen BY, Fofanov VY, Ward RM, Lisewski AM, Kimmel M, Kavraki LE, Lichtarge O.

Protein Sci. 2006 Jun;15(6):1530-6. Epub 2006 May 2.

27.

Algorithms for structural comparison and statistical analysis of 3D protein motifs.

Chen BY, Fofanov VY, Kristensen DM, Kimmel M, Lichtarge O, Kavraki LE.

Pac Symp Biocomput. 2005:334-45.

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