Pharmacology and Toxicology - Research

Yuriy Fofanov, Ph.D.

Professor

  • group web page

  • Research Interests

    Our laboratory specializes in the research areas of Bioinformatics, Applied Statistics, Mathematical Modeling and Information Theory. We are particularly interested in environmental metagenomics and the analysis of human DNA. Our focus includes the development of new methodologies for the analysis and interpretation of next generation DNA sequencing (NGS) data and to create new computational tools for the rapid analysis of NGS data. Such computational tools under development are for the detection of:
    1. Unknown and known pathogens in complex backgrounds such as environmental (soil, water or air)and clinical samples. 2. Changes in the host genome caused by environmental changes or by diseased states all of which can alter the copy number or methylation patterns. 3. Changes in the metagenome of environmental samples due to man-made or natural disasters including the loss of microbial diversity or the appearance of specific bacterial populations. 4. Microbial metagenomes involved in industrial applications such as biofilm analysis and bio corrosion.

    Selected Publications

    Saxer G, Havlak P, Fox SA, Quance MA, Gupta S, Fofanov Y, Strassmann JE, Queller DC. Whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba Dictyostelium discoideum. PLoS One. 2012;7(10):e46759. doi: 10.1371/journal.pone.0046759. Epub 2012 Oct 8.

    Golovko G, Khanipov K, Rojas M, Martinez-Alcántara A, Howard JJ, Ballesteros E, Gupta S, Widger W, Fofanov Y. Slim-filter: an interactive Windows-based application for illumina genome analyzer data assessment and manipulation. BMC Bioinformatics. 2012 Jul 16;13:166. doi: 10.1186/1471-2105-13-166.

    Gijavanekar C, Drabek R, Soni M, Jackson GW, Strych U, Fox GE, Fofanov Y, Willson RC. Detection and typing of viruses using broadly sensitive cocktail-PCR and mass spectrometric cataloging: demonstration with dengue virus. J Mol Diagn. 2012 Jul;14(4):402-7. doi: 10.1016/j.jmoldx.2012.02.006. Epub 2012 May 9.

    Gijavanekar C, Strych U, Fofanov Y, Fox GE, Willson RC. Rare target enrichment for ultrasensitive PCR detection using cot-rehybridization and duplex-specific nuclease. Anal Biochem. 2012 Feb 1;421(1):81-5. doi: 10.1016/j.ab.2011.11.010. Epub 2011 Nov 18.

    Zhu B, Kuriakose JA, Luo T, Ballesteros E, Gupta S, Fofanov Y, McBride JW. Ehrlichia chaffeensis TRP120 binds a G+C-rich motif in host cell DNA and exhibits eukaryotic transcriptional activator function. Infect Immun. 2011 Nov;79(11):4370-81. doi: 10.1128/IAI.05422-11. Epub 2011 Aug 22.

    Gijavanekar C, Añez-Lingerfelt M, Feng C, Putonti C, Fox GE, Sabo A, Fofanov Y, Willson RC. PCR detection of nearly any dengue virus strain using a highly sensitive primer 'cocktail'. FEBS J. 2011 May;278(10):1676-87. doi: 10.1111/j.1742-4658.2011.08091.x. Epub 2011 Apr 18.

    Medina RA, Rojas M, Tuin A, Huff S, Ferres M, Martinez-Valdebenito C, Godoy P, García-Sastre A, Fofanov Y, SantaLucia J Jr. 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. J Clin Microbiol. 2011 Jan;49(1):335-44. doi: 10.1128/JCM.01142-10. Epub 2010 Nov 17.

    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. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics.Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4371-6. doi: 10.1073/pnas.0911295107. Epub 2010 Feb 8.

    Feng C, Putonti C, Zhang M, Eggers R, Mitra R, Hogan M, Jayaraman K, Fofanov Y. Ultraspecific probes for high throughput HLA typing. BMC Genomics. 2009 Feb 20;10:85. doi: 10.1186/1471-2164-10-85.

    Añez M, Putonti C, Fox GE, Fofanov Y, Willson RC. Exhaustive computational identification of pathogen sequences far-distant from background genomes: Identification and experimental verification of human-blind dengue PCR primers. J Biotechnol. 2008 Feb 1;133(3):267-76. Epub 2007 Sep 16.

    Reed C, Fofanov V, Putonti C, Chumakov S, Slezak T, Fofanov Y. Effect of the mutation rate and background size on the quality of pathogen identification. bioinformatics. 2007 Oct 15;23(20):2665-71. Epub 2007 Sep 19.

    Tucker DL, Ott CM, Huff S, Fofanov Y, Pierson DL, Willson RC, Fox GE. Characterization of Escherichia coli MG1655 grown in a low-shear modeled microgravity environment. BMC Microbiol. 2007 Mar 7;7:15.

    Chumakov S, Ballesteros E, Rodriguez Sanchez JE, Chavez A, Zhang M, Pettit BM, Fofanov Y. Using Mutual Information to Discover Temporal Patterns in Gene Expression Data. Med Phys Mex Symp Med Phys. 2006 Sep 8;854(1):25-30.

    Putonti C, Luo Y, Katili C, Chumakov S, Fox GE, Graur D, Fofanov Y. A computational tool for the genomic identification of regions of unusual compositional properties and its utilization in the detection of horizontally transferred sequences. Mol Biol Evol. 2006 Oct/23(10):1863-8. Epub 2006 Jul 7.

    Putonti C. Chumakov S, Mitra R, Fox GE, Willson RC, Fofanov Y. Human-blind probes and primers for dengue virus identification. FEBS J. 2006 Jan;273(2):398-408.

    Tucker DL, Karouia F, Wang J, Luo Y, Li TB, Willson RC, Fofanov Y, Fox GE. Effect of an artificial RNA marker on gene expression in Escherichia coli. Appl Environ Microbiol. 2005 Jul;71(7):4156-9.

    Fofanov Y, Luo Y, Katili C, Wang J, Belosludtsev Y, Powdrill T, Belapurkar C, Fofanov V, Li TB, Chumakov S, Pettitt BM. How independent are the appearances of n-mers in different genomes? Bioinformatics. 2004 Oct 12;20(15):2421-8. Epub 2004 Apr 15.

    Fofanov Y, Pettitt BM. Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: Local invariants approach.J Biomed Inform. 2002 Oct-Dec;35(5-6):343-51.

    Webb MS, Miller AL, Johnson BH, Fofanov Y, Li T, Wood TG, Thompson EB. Gene networks in glucocorticoid-evoked apoptosis of leukemic cells. J Steroid Biochem Mol Biol. 2003 Jun;85(2-5):183-93.

    Medh RD, Webb MS, Miller AL, Johnson BH, Fofanov Y, Li T, Wood TG, Luxon BA, Thompson EB. Gene expression profile of human lymphoid CEM cells sensitive and resistant to glucocorticoid-evoked apoptosis. Genomics. 2003 Jun;81(6):543-55.