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Janibacter species with evidence of genomic polymorphism isolated from resected heart valve in a patient with aortic stenosis.

Malania L, Bai Y, Khanipov K, Tsereteli M, Metreveli M, Tsereteli D, Sidamonidze K, Imnadze P, Fofanov Y, Kosoy M.

Infect Dis Rep. 2019 Sep 18;11(2):8132. doi: 10.4081/idr.2019.8132. eCollection 2019 Sep 18.


Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts.

Warmbrod KL, Patterson EI, Kautz TF, Stanton A, Rockx-Brouwer D, Kalveram BK, Khanipov K, Thangamani S, Fofanov Y, Forrester NL.

PLoS Pathog. 2019 Apr 4;15(4):e1007610. doi: 10.1371/journal.ppat.1007610. eCollection 2019 Apr.


16S rRNA gene profiling and genome reconstruction reveal community metabolic interactions and prebiotic potential of medicinal herbs used in neurodegenerative disease and as nootropics.

Peterson CT, Sharma V, Iablokov SN, Albayrak L, Khanipov K, Uchitel S, Chopra D, Mills PJ, Fofanov Y, Rodionov DA, Peterson SN.

PLoS One. 2019 Mar 19;14(3):e0213869. doi: 10.1371/journal.pone.0213869. eCollection 2019.


Global Transcriptomic Profiling of Pulmonary Gene Expression in an Experimental Murine Model of Rickettsia conorii Infection.

Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK.

Genes (Basel). 2019 Mar 8;10(3). pii: E204. doi: 10.3390/genes10030204.


Interleukin-33 Promotes REG3γ Expression in Intestinal Epithelial Cells and Regulates Gut Microbiota.

Xiao Y, Huang X, Zhao Y, Chen F, Sun M, Yang W, Chen L, Yao S, Peniche A, Dann SM, Sun J, Golovko G, Fofanov Y, Miao Y, Liu Z, Chen D, Cong Y.

Cell Mol Gastroenterol Hepatol. 2019;8(1):21-36. doi: 10.1016/j.jcmgh.2019.02.006. Epub 2019 Mar 1.


Enhancer Associated Long Non-coding RNA Transcription and Gene Regulation in Experimental Models of Rickettsial Infection.

Chowdhury IH, Narra HP, Sahni A, Khanipov K, Fofanov Y, Sahni SK.

Front Immunol. 2019 Jan 9;9:3014. doi: 10.3389/fimmu.2018.03014. eCollection 2018.


Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa.

Jeffries CL, Lawrence GG, Golovko G, Kristan M, Orsborne J, Spence K, Hurn E, Bandibabone J, Tantely LM, Raharimalala FN, Keita K, Camara D, Barry Y, Wat'senga F, Manzambi EZ, Afrane YA, Mohammed AR, Abeku TA, Hedge S, Khanipov K, Pimenova M, Fofanov Y, Boyer S, Irish SR, Hughes GL, Walker T.

Version 2. Wellcome Open Res. 2018 Nov 27 [revised 2018 Jan 1];3:113. doi: 10.12688/wellcomeopenres.14765.2. eCollection 2018.


Microbiome Interaction Networks and Community Structure From Laboratory-Reared and Field-Collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus Mosquito Vectors.

Hegde S, Khanipov K, Albayrak L, Golovko G, Pimenova M, Saldaña MA, Rojas MM, Hornett EA, Motl GC, Fredregill CL, Dennett JA, Debboun M, Fofanov Y, Hughes GL.

Front Microbiol. 2018 Sep 10;9:2160. doi: 10.3389/fmicb.2018.02160. eCollection 2018.


S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences.

Kalesinskas L, Cudone E, Fofanov Y, Putonti C.

Evol Bioinform Online. 2018 Sep 17;14:1176934318797354. doi: 10.1177/1176934318797354. eCollection 2018.


Microbiota dysbiosis and its pathophysiological significance in bowel obstruction.

Hegde S, Lin YM, Golovko G, Khanipov K, Cong Y, Savidge T, Fofanov Y, Shi XZ.

Sci Rep. 2018 Sep 3;8(1):13044. doi: 10.1038/s41598-018-31033-0.


Broom: application for non-redundant storage of high throughput sequencing data.

Albayrak L, Khanipov K, Golovko G, Fofanov Y.

Bioinformatics. 2019 Jan 1;35(1):143-145. doi: 10.1093/bioinformatics/bty580.


Detection of multi-dimensional co-exclusion patterns in microbial communities.

Albayrak L, Khanipov K, Golovko G, Fofanov Y.

Bioinformatics. 2018 Nov 1;34(21):3695-3701. doi: 10.1093/bioinformatics/bty414.


Sequential gene regulatory events leading to glucocorticoid-evoked apoptosis of CEM human leukemic cells:interactions of MAPK, MYC and glucocorticoid pathways.

Webb MS, Miller AL, Howard TL, Johnson BH, Chumakov S, Fofanov Y, Nguyen-Vu T, Lin CY, Thompson EB.

Mol Cell Endocrinol. 2018 Aug 15;471:118-130. doi: 10.1016/j.mce.2018.03.004. Epub 2018 Mar 26. Review.


Low-fidelity Venezuelan equine encephalitis virus polymerase mutants to improve live-attenuated vaccine safety and efficacy.

Kautz TF, Guerbois M, Khanipov K, Patterson EI, Langsjoen RM, Yun R, Warmbrod KL, Fofanov Y, Weaver SC, Forrester NL.

Virus Evol. 2018 Mar 6;4(1):vey004. doi: 10.1093/ve/vey004. eCollection 2018 Jan.


Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity.

Patterson EI, Khanipov K, Rojas MM, Kautz TF, Rockx-Brouwer D, Golovko G, Albayrak L, Fofanov Y, Forrester NL.

Virus Evol. 2018 Feb 15;4(1):vey001. doi: 10.1093/ve/vey001. eCollection 2018 Jan.


GPR43 mediates microbiota metabolite SCFA regulation of antimicrobial peptide expression in intestinal epithelial cells via activation of mTOR and STAT3.

Zhao Y, Chen F, Wu W, Sun M, Bilotta AJ, Yao S, Xiao Y, Huang X, Eaves-Pyles TD, Golovko G, Fofanov Y, D'Souza W, Zhao Q, Liu Z, Cong Y.

Mucosal Immunol. 2018 May;11(3):752-762. doi: 10.1038/mi.2017.118. Epub 2018 Feb 7.


Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa).

Robeson MS 2nd, Khanipov K, Golovko G, Wisely SM, White MD, Bodenchuck M, Smyser TJ, Fofanov Y, Fierer N, Piaggio AJ.

Ecol Evol. 2017 Nov 26;8(1):185-196. doi: 10.1002/ece3.3638. eCollection 2018 Jan.


Expression Profiling of Long Noncoding RNA Splice Variants in Human Microvascular Endothelial Cells: Lipopolysaccharide Effects In Vitro.

Chowdhury IH, Narra HP, Sahni A, Khanipov K, Schroeder CLC, Patel J, Fofanov Y, Sahni SK.

Mediators Inflamm. 2017;2017:3427461. doi: 10.1155/2017/3427461. Epub 2017 Sep 25.


Draft Genome Sequence of Zobellella denitrificans ZD1 (JCM 13380), a Salt-Tolerant Denitrifying Bacterium Capable of Producing Poly(3-Hydroxybutyrate).

Wu YW, Shao Y, Khanipov K, Golovko G, Pimenova M, Fofanov Y, Chu KH.

Genome Announc. 2017 Sep 7;5(36). pii: e00948-17. doi: 10.1128/genomeA.00948-17.


Genotyping of Bartonella bacteria and their animal hosts: current status and perspectives.

Kosoy M, McKee C, Albayrak L, Fofanov Y.

Parasitology. 2018 Apr;145(5):543-562. doi: 10.1017/S0031182017001263. Epub 2017 Aug 2. Review.


Transcriptional profiling of Rickettsia prowazekii coding and non-coding transcripts during in vitro host-pathogen and vector-pathogen interactions.

Schroeder CLC, Narra HP, Sahni A, Khanipov K, Patel J, Fofanov Y, Sahni SK.

Ticks Tick Borne Dis. 2017 Oct;8(6):827-836. doi: 10.1016/j.ttbdis.2017.06.008. Epub 2017 Jun 29.


Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media.

Chonmaitree T, Jennings K, Golovko G, Khanipov K, Pimenova M, Patel JA, McCormick DP, Loeffelholz MJ, Fofanov Y.

PLoS One. 2017 Jul 14;12(7):e0180630. doi: 10.1371/journal.pone.0180630. eCollection 2017.


How does inflammation drive mutagenesis in colorectal cancer?

Hsu CW, Sowers ML, Hsu W, Eyzaguirre E, Qiu S, Chao C, Mouton CP, Fofanov Y, Singh P, Sowers LC.

Trends Cancer Res. 2017;12:111-132.


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.

BMC Genomics. 2016 Dec 12;17(1):1017.


Small Regulatory RNAs of Rickettsia conorii.

Narra HP, Schroeder CL, Sahni A, Rojas M, Khanipov K, Fofanov Y, Sahni SK.

Sci Rep. 2016 Nov 11;6:36728. doi: 10.1038/srep36728.


Identification and Characterization of Novel Small RNAs in Rickettsia prowazekii.

Schroeder CL, Narra HP, Sahni A, Rojas M, Khanipov K, Patel J, Shah R, Fofanov Y, Sahni SK.

Front Microbiol. 2016 Jun 8;7:859. doi: 10.3389/fmicb.2016.00859. eCollection 2016.


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.

Vet Microbiol. 2016 Jul 15;190:43-49. doi: 10.1016/j.vetmic.2016.05.009. Epub 2016 May 18.


Bacterial small RNAs in the Genus Rickettsia.

Schroeder CL, Narra HP, Rojas M, Sahni A, Patel J, Khanipov K, Wood TG, Fofanov Y, Sahni SK.

BMC Genomics. 2015 Dec 18;16:1075. doi: 10.1186/s12864-015-2293-7.


The main challenges that remain in applying high-throughput sequencing to clinical diagnostics.

Loeffelholz M, Fofanov Y.

Expert Rev Mol Diagn. 2015;15(11):1405-8. doi: 10.1586/14737159.2015.1088385. Epub 2015 Sep 22.


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.

Data Brief. 2015 Aug 13;5:9-12. doi: 10.1016/j.dib.2015.08.001. eCollection 2015 Dec.


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.

PLoS One. 2015 Jun 3;10(6):e0127799. doi: 10.1371/journal.pone.0127799. eCollection 2015.


Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells.

Chernov AV, Reyes L, Xu Z, Gonzalez B, Golovko G, Peterson S, Perucho M, Fofanov Y, Strongin AY.

Epigenetics. 2015;10(4):303-18. doi: 10.1080/15592294.2015.1020000. Epub 2015 Feb 19.


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.


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.

BMC Microbiol. 2014 Sep 7;14:225. doi: 10.1186/s12866-014-0225-3.


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.

Cancer Cell Int. 2014 Apr 23;14:35. doi: 10.1186/1475-2867-14-35. eCollection 2014.


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.

BMC Evol Biol. 2013 Sep 4;13:184. doi: 10.1186/1471-2148-13-184.


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.

PLoS One. 2012;7(10):e46759. doi: 10.1371/journal.pone.0046759. Epub 2012 Oct 8.


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.

BMC Bioinformatics. 2012 Jul 16;13:166. doi: 10.1186/1471-2105-13-166.


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.

J Mol Diagn. 2012 Jul;14(4):402-7. doi: 10.1016/j.jmoldx.2012.02.006. Epub 2012 May 9.


Rare target enrichment for ultrasensitive PCR detection using cot-rehybridization and duplex-specific nuclease.

Gijavanekar C, Strych U, Fofanov Y, Fox GE, Willson RC.

Anal Biochem. 2012 Feb 1;421(1):81-5. doi: 10.1016/j.ab.2011.11.010. Epub 2011 Nov 18.


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.

Infect Immun. 2011 Nov;79(11):4370-81. doi: 10.1128/IAI.05422-11. Epub 2011 Aug 22.


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.

FEBS J. 2011 May;278(10):1676-87. doi: 10.1111/j.1742-4658.2011.08091.x. Epub 2011 Apr 18.


Development and characterization of a highly specific and sensitive SYBR green reverse transcriptase PCR assay for detection of the 2009 pandemic H1N1 influenza virus on the basis of sequence signatures.

Medina RA, Rojas M, Tuin A, Huff S, Ferres M, Martinez-Valdebenito C, Godoy P, García-Sastre A, Fofanov Y, SantaLucia J Jr.

J Clin Microbiol. 2011 Jan;49(1):335-44. doi: 10.1128/JCM.01142-10. Epub 2010 Nov 17.


Improved detection of Bartonella DNA in mammalian hosts and arthropod vectors by real-time PCR using the NADH dehydrogenase gamma subunit (nuoG).

Colborn JM, Kosoy MY, Motin VL, Telepnev MV, Valbuena G, Myint KS, Fofanov Y, Putonti C, Feng C, Peruski L.

J Clin Microbiol. 2010 Dec;48(12):4630-3. doi: 10.1128/JCM.00470-10. Epub 2010 Oct 6.


Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics.

Beres SB, Carroll RK, Shea PR, Sitkiewicz I, Martinez-Gutierrez JC, Low DE, McGeer A, Willey BM, Green K, Tyrrell GJ, Goldman TD, Feldgarden M, Birren BW, Fofanov Y, Boos J, Wheaton WD, Honisch C, Musser JM.

Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4371-6. doi: 10.1073/pnas.0911295107. Epub 2010 Feb 8.


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.


Ultraspecific probes for high throughput HLA typing.

Feng C, Putonti C, Zhang M, Eggers R, Mitra R, Hogan M, Jayaraman K, Fofanov Y.

BMC Genomics. 2009 Feb 20;10:85. doi: 10.1186/1471-2164-10-85.


Effect of the mutation rate and background size on the quality of pathogen identification.

Reed C, Fofanov V, Putonti C, Chumakov S, Slezak T, Fofanov Y.

Bioinformatics. 2007 Oct 15;23(20):2665-71. Epub 2007 Sep 19.


Characterization of Escherichia coli MG1655 grown in a low-shear modeled microgravity environment.

Tucker DL, Ott CM, Huff S, Fofanov Y, Pierson DL, Willson RC, Fox GE.

BMC Microbiol. 2007 Mar 7;7:15.

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