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Results: 1 to 20 of 27

1.

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.

PMID:
24795534
[PubMed]
Free PMC Article
2.

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.

PMID:
24007216
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
23056439
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
22800377
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22579629
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
21859854
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
[PubMed - indexed for MEDLINE]
9.

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.

PMID:
21084522
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
20926707
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
20142485
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
19602525
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
19232123
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Exhaustive computational identification of pathogen sequences far-distant from background genomes: Identification and experimental verification of human-blind dengue PCR primers.

Añez M, Putonti C, Fox GE, Fofanov Y, Willson RC.

J Biotechnol. 2008 Feb 1;133(3):267-76. Epub 2007 Sep 16.

PMID:
17996971
[PubMed - indexed for MEDLINE]
15.

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.

PMID:
17881407
[PubMed - indexed for MEDLINE]
Free Article
16.

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.

PMID:
17343762
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
19834570
[PubMed]
Free PMC Article
18.

Using Mutual Information to Discover Temporal Patterns in Gene Expression Data.

Chumakov S, Ballesteros E, Rodriguez Sanchez JE, Chavez A, Zhang M, Pettit BM, Fofanov Y.

Med Phys Mex Symp Med Phys. 2006 Sep 8;854(1):25-30.

PMID:
20428481
[PubMed]
Free PMC Article
19.

A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences.

Putonti C, Luo Y, Katili C, Chumakov S, Fox GE, Graur D, Fofanov Y.

Mol Biol Evol. 2006 Oct;23(10):1863-8. Epub 2006 Jul 7.

PMID:
16829541
[PubMed - indexed for MEDLINE]
Free Article
20.

Human-blind probes and primers for dengue virus identification.

Putonti C, Chumakov S, Mitra R, Fox GE, Willson RC, Fofanov Y.

FEBS J. 2006 Jan;273(2):398-408.

PMID:
16403026
[PubMed - indexed for MEDLINE]

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