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Results: 1 to 20 of 30

1.

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 Apr 3;10(4):303-18. doi: 10.1080/15592294.2015.1020000. Epub 2015 Feb 19.

PMID:
25695131
2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

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.

PMID:
22155054
10.

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.

11.

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.

PMID:
21410643
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.
18.

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.

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.

20.

PIDA:A new algorithm for pattern identification.

Putonti C, Pettitt B, Reid J, Fofanov Y.

Online J Bioinform. 2007 Jan 1;8(1):30-40.

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