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Items: 1 to 20 of 38


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;190:43-9. 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.

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