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Lab Publications
- Refereed Publications in Archival Journals
- Reed C, Fofanov V, Putonti C, Slezak T, Fofanov Y.
Computational modeling of the effect of the background size on the quality of pathogen identification.
Bioinformatics (in press).
- Putonti C, Pettitt BM, Reid JG, Fofanov Y.
(2007) PIDA: A new algorithm for pattern identification.
Online Journal of Bioinformatics, 8(1): 30-40.
- Tucker DL, Ott CM, Huff S, Fofanov Y, Pierson DL, Willson RC, Fox GE.
(2007) Characterization of Escherichia coli MG1655 grown in a low-shear modeled microgravity environment.
BMC Microbiol. 2007 Mar 7;7:15. PMID: 17343762
- Putonti, C., Luo, Y., Katili, C., Chumakov, S., Fox, G.E., Graur, D., Fofanov, Y.
(2006) 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: 1863-1868.
- Zhu D, Y. Fofanov, R. C. Willson and G. E. Fox.
(2006) A Parallel Computing Algorithm for 16S rRNA Probe Design.
Journal of parallel and distributed Computing 66 (12): 1546-1551
- Putonti C, Chumakov S, Mitra R, Fox GE, Willson RC, Fofanov Y.
(2006) Human-blind probes and primers for Dengue virus identification: Exhaustive analysis of subsequences present in the human and 83 Dengue genome sequences.
FEBS 273: 398-408.
- Chumakov S, Belapurkar C, Putonti C, Li T-B, Pettitt BM, Fox GE, Willson RC, Fofanov Y.
(2005) Theoretical Basis for Universal Identification Systems for Bacteria and Viruses.
Journal of Biological Physics and Chemistry 5(4): 121-128.
- Tucker DL, Karouia F, Wang J, Luo Y, Li, TB, Willson RC, Fofanov Y, Fox GE.
(2005) The Effect of an Artificial RNA Marker on Gene Expression in Escherichia coli. Applied Environmental Microbiology 71(7): 4156-4159.
- Thompson EB, Webb MS, Miller AL, Fofanov Y, Johnson BH.
(2004) Identification of genes leading to glucocorticoid-induced leukemic cell death. Lipids 39(8): 821-5.
- Fofanov Y, Belapurkar C, Luo Y, Katili C, Wang J, Belosludtsev Y, Powdrill T, Fofanov V, Li T-B, Chumakov S, Pettitt BM.
(2004) How independent are the appearances of n-mers in different genomes?
Bioinformatics 20(15): 2421-8.
- Medh RD, Webb MS, Miller AL, Johnson BH, Fofanov Y, Li T, Wood TG, Luxon BA, Thompson EB.
(2003) Gene expression profile of human lymphoid CEM cells sensitive and resistant to glucocorticoid-evoked apoptosis.
Genomics 81: 543-55.
- Webb MS, Miller AL, Johnson BH, Fofanov Y, LI T-B, Wood TG, Thompson EB.
(2003) Gene networks in glucocorticoid-evoked apoptosis of leukemic cells.
The Journal of Steroid Biochemistry and Molecular Biology 85: 183-193.
- Fofanov Y, Pettitt BM.
(2002) Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: Local Invariants approach.
Journal of Biomedical Informatics 35: 343-351.
- Refereed Conference Publications
- Putonti, C., Fofanov, V., Fofanov, Y.
Computational Methods for Estimating the Size and Identifying the Members of Microbial Communities. In: Du, D.-Z. (ed.)
Proceedings of the IASTED International Conference on Computational and Systems Biology (Dallas, Texas), 2006: 540-033.
- Zhang, M., Putonti, C., Fofanov, Y.
A New Set of Algorithms for Designing Ultra-specific Probes for High-throughput Allele Detection. In: Du, D.-Z. (ed.)
Proceedings of the IASTED International Conference on Computational and Systems Biology (Dallas, Texas), 2006: 540-038.
- Putonti, C., Zhang, M., Johnsson, L., Fofanov, Y.
Two Challenges in Genomics That Can Benefit from Petascale Platforms.
In: Lecture Notes in Computer Science - Proceedings of the International Euro-Par Workshops (Dresden, Germany), 2006. [IN PRESS]
- Putonti, C., Chumakov, S., Luo, Y., Graur, D., Fox, G.E., Fofanov, Y.
Regions of Unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli.
In: Mercado-Uribe, H., García-Torales, G., Flores-Núñez, J., Castillo-Corona, E. (eds.) Proceedings of the IX Mexican Symposium on Medical Physics (Guadalajara, Jalisco, Mexico), 2006: 126-128
- Zhang, M., Putonti, C., Chumakov, S., Gupta, A., Fox, G.E., Graur, D., Fofanov, Y.
Statistical properties of short subsequences in microbial genomes and their link to pathogen identification and evolution.
In: Mercado-Uribe, H., García-Torales, G., Flores-Núñez, J., Castillo-Corona, E. (eds.) Proceedings of the IX Mexican Symposium on Medical Physics (Guadalajara, Jalisco, Mexico), 2006: 13-18.
- Zhu D, Y. Fofanov, R. C. Willson and G. E. Fox,
ProkProbePicker (PPP): a Fast Program to Extract 16S rRNA-Targeted Probes for Prokaryotes
Proceedings of The 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '05) (2005), pp. 41-47
- Zhu D, Fofanov Y, Willson RC, Fox GE. (2005)
ProkProbePicker (PPP):a Fast Program to Extract 16S rRNA-Targeted Probes for Prokaryotes.
In: Proceedings of the 2005 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (Las Vegas, NV): 41-47.
- Putonti C, Fofanov Y.
(2004) Analysis of Promoter Regions for Essential Genes of Bacillus subtilis using PIDA.
In: Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (Las Vegas, NV): 276-82.
- Chumakov S, Putonti C, Pettitt BM, Fox G, Willson RC, Fofanov Y.
(2004) Using Statistical Properties of Short Subsequences in Microbial Identification.
In: Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (Las Vegas, NV): 363-7.
- Refereed Conference Abstracts
- Fofanov, Y., Feng, C., Quance, M., Fofanova, T., Putonti, C.
Designing assays for the detection of unknown infectious organisms.
Wellcome Trust Microbial Genomes 2007 (Hinxton, UK), 2007: 16.
- Putonti, C., Graur, D., Fofanov, Y.
Visualizing compositional similarities and dissimilarities in complete genomic sequences.
Wellcome Trust Microbial Genomes 2007 (Hinxton, UK), 2007: 40.
- Putonti, C., Añez, M., Kourentzi, K., Fox, G.E., Willson, R.C., Fofanov, Y.
Ultraspecific assays for the detection of pathogens in human samples.
ASM Biodefense and Emerging Diseases Research Meeting. (Washington, D.C.), Feb. 27- Mar. 2, 2007: 50.
- Putonti, C., Feng, C., Quance, M., Fofanova, T., Fofanov, Y.
Computational challenges in designing assays for the detection of infectious agents.
24th Annual Houston Conference on Biomedical Engineering Research (Houston, TX), February 8-9, 2006: 256.
- Dasu, S., Putonti, C., Fofanov, Y.
A new computational approach for estimation of the genomic diversity of environmental samples.
24th Annual Houston Conference on Biomedical Engineering Research (Houston, TX), February 8-9, 2006: 255.
- Putonti, C., Fofanov, V., Fofanov, Y.
Improving Nucleic Acid-Based Pathogen Detection Assays Through the Estimation of the Total Genomic Diversity of Complex Backgrounds.
Texas Branch Meeting of the American Society for Microbiology Fall Meeting (Galveston, TX), 2006: 34.
- Putonti, C., Añez, M., Fox, G.E., Willson, R.C., Fofanov, Y.
Ultraspecific PCR Assays for Dengue Detection.
Texas Branch Meeting of the American Society for Microbiology Fall Meeting (Galveston, TX), 2006: 34.
- Putonti, C., Willson, R.C., Fox, G.E., Fofanov, Y.
Ultraspecific Assay Design for the Detection of West Nile virus in Human Samples. Advances in Microarray Technology (Amsterdam, Netherlands),
2006. Invited speaker.
- Zhang, M., Putonti, C., Fofanov, Y.
The Design of Ultra-specific Probes for High-throughput HLA Typing.
62nd Southwest Regional Meeting of the American Chemical Society (Houston, TX), 2006: 94.
- Añez, M., Putonti, C., Fox, G.E., Fofanov, Y., Willson, R.C.
Ultraspecific PCR Assays for Dengue Virus Detection.
62nd Southwest Regional Meeting of the American Chemical Society (Houston, TX), 2006: 66.
- Putonti, C., DeVille, T., Fox, G.E., Willson, R.C., Fofanov, Y.
The Host-Blind Database: A Portal to Ultraspecific Signatures for Assay Design.
Chemical and Biological Countermeasure Technologies for Homeland Security (Boulder, CO), 2006.
- Putonti, C., Travisano, M., Willson, R.C., Fofanov, Y.
Improving Nucleic Acid-Based Assay Design through the Estimation of the Total Genomic Diversity of Complex Backgrounds.
Chemical and Biological Countermeasure Technologies for Homeland Security (Boulder, CO), 2006.
- Zhang M, Putonti C, Gupta A, Beres SB, Musser J, Fofanov Y.
(2006) Using statistical properties to identify evolutionary significant regions and genomic rearrangements in twelve group A Streptococcus strains.
DNA Structure, Genomic Rearrangements, and Human Disease (Houston, TX): 78.
- Putonti C, Mitra R, Fox GE, Chumakov S, Willson RC, Fofanov Y.
(2005) Dengue and Yellow Fever Identification Using Ultraspecific Probes "Blind" to Hosts and Aedes aegypti DNA.
The XIII International Congress of Virology (San Francisco, CA): 88. Symposia Speaker.
- Hart-Van Tassell A, Urvil P, Putonti C, Nowicki B, Zhang M, Fofanov Y, Nowicki S.
(2005) Evolution of the Neisserial Genomic Sequences: Insertions vs. Deletions.
The XI International Congress of Bacteriology and Applied Microbiology (San Francisco, CA): 46.
- Zhang M, Putonti C, Luo Y, Chumakov S, Fox GE, Fofanov Y.
(2005) The S-plot: A Novel Approach to Sequence Comparisons in Genomic-Scale.
The XI International Congress of Bacteriology and Applied Microbiology (San Francisco, CA): 64.
- Putonti C, Mitra R, Fox GE, Chumakov S, Willson RC, Fofanov Y.
(2005) Flavivirus Detection Using Ultraspecific Human-blind Probes.
European Conference on Mathematical and Theoretical Biology (Dresden, Germany): 460. Contributing Speaker.
- Putonti C, Mitra R, Fox GE, Chumakov S, Willson RC, Fofanov Y.
(2005) Pathogen Detection Using Ultraspecific Probes “Blind” to Vector DNA.
Bioinformatics and Disease SIG (Detroit, MI): 13.
- Putonti C, Yi L, Zhang M, Chumakov S, Fox GE, Fofanov Y.
(2005) Genome Visualization and Analysis with S-plot.
Annual Meeting of the International Society for Computational Biology (Detroit, MI): 172. Software Demonstration.
- Putonti C, Hart-van Tassell A, Urvil P, Zhang M, Chumakov S, Nowicki B, Nowicki S, Fofanov Y.
(2005) Identification of Genomic Islands: a key to the evolution of Neisseria.
Annual Meeting of the International Society for Computational Biology (Detroit, MI): 117.
- Putonti C, Luo Y, Graur D, Fox GE, Fofanov Y.
(2005) Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli.
International Conference on Microbial Genomes (Halifax, Nova Scotia, Canada): 59-60.
- Nowicki S, Chumakov S, Hart-Van Tassell A, Nowicki B, Putonti C, Urvil P, Zhang M, Fofanov, Y.
(2004) Evolution of Neisseria species virulence: what else can be deleted?
Polish Conference in Genetics (Gdansk, Poland): 210-211.
- Nowicki B, Nowicki S, Fofanov Y, Hart-Van Tassell A, Urvil P, Goluszko P.
(2004) Molecular mechanism of bacterial virulence from global genome analysis to structure-function and prevention of chronic infection.
Polish Conference in Genetics (Gdansk, Poland): 205.
- Chumakov S, Putonti C, Zhang M, Luo Y, Fox GE, Fofanov Y.
(2004) The S-plot: a novel approach to genome visualization and analysis.
In: Proceedings of TIGR’s 16th International Genome Sequencing and Analysis Conference (Washington, D.C.): 36.
- Putonti C, Fox GE, Willson RC, Fofanov Y.
(2004) Flavivirus identification using ultraspecific probes “blind” to host and background DNA.
In: Proceedings of TIGR’s 16th International Genome Sequencing and Analysis Conference (Washington, D.C.):47.
- Putonti C, Fox GE, Chumakov S, Willson RC, Fofanov Y.
(2004) Pathogen identification using ultraspecific probes.
In: Electronic proceedings of IBC’s 11th Annual International Congress Chips to Hits® (Boston, MA): PA-46.
- Putonti, C, Fox GE, Willson RC, Pettitt BM, Fofanov Y.
(2004) DNA microbial and viral identification using ultraspecific probes "blind" to host and background DNA.
In: The National Library of Medicine Informatics Training Conference (Indianapolis, IN): 73.
- Webb MS, Miller AL, Johnson BH, Medh RD, Fofanov Y, Li T-B, Wood TG, Luxon BA, and Thompson EB.
(2003) Basal and early gene expression profiles of human lymphoid CEM clones sensitive and resistant to glucocorticoid-evoked apoptosis.
In: The 85th Annual Meeting of the Endocrine Society (Philadelphia, PA): 311.
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