Paliy Lab
Diggs Laboratory for Life Science Research : Department of Biochemistry and Molecular Biology : Wright State University
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Publications


  • O. Paliy and V. Shankar

    Applications of phylogenetic microarrays to profiling of human microbiomes (2014) [in press] in Microarrays: Current Technology, Innovations and Applications, Caister Academic Press, Norfolk, UK.

Chapter pdf

  • V. Shankar, M.J. Hamilton, A. Khoruts, A. Kilburn, T. Unno, O. Paliy, and M.J. Sadowsky

    Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation (2014) Microbiome, 2:13.

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  • O. Paliy, V. Shankar, and M. Sagova-Mareckova

    Phylogenetic microarrays (2014) in Bioinformatics and Data Analysis in Microbiology, Caister Academic Press, Norfolk, UK.

Chapter pdf

  • O. Paliy, C.J. Piyathilake, A. Kozyrskyj, G. Celep, F. Marotta, R. Rastmanesh

    Excess body weight during pregnancy and offspring obesity: Potential mechanisms (2014) Nutrition, 30: 245-251.

Abstract
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  • O. Paliy

    The golden age of molecular ecology (2013) J Phylogen & Evolution Biol, 1(3): e105.

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  • V. Shankar, R. Agans, B. Holmes, M. Raymer, and O. Paliy

    Do gut microbial communities differ in pediatric IBS and health? (2013) Gut Microbes, 4(4): 347–352.

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  • B. Withman, T.S. Gunasekera, P. Beesetty, R. Agans, and O. Paliy

    Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea (2013) Infect. Immun., 81(1): 80-89.

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  • L. Rigsbee, R. Agans, V. Shankar, H. Kenche, H. Khamis, S. Michail, and O. Paliy

    Quantitative profiling of gut microbiota of children with diarrhea-predominant irritable bowel syndrome (2012) Am. J. Gastroenterol., 107: 1740-51.

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  • O. Paliy and R. Agans

    Application of phylogenetic microarrays to interrogation of human microbiota (2012) FEMS Microbiol. Ecol., 79(1): 2-11.

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  • O. Paliy and B. Foy

    Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays (2011) Bioinformatics, 27(15): 2134-40.

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  • R. Agans, L. Rigsbee, H. Kenche, S. Michail, H. Khamis, and O. Paliy

    Distal gut microbiota of adolescent children is different from that of adults (2011) FEMS Microbiol. Ecol., 77(2): 404-12.

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  • M. Sugawara, G.R. Shah, M.J. Sadowsky, O. Paliy, J. Speck, A.W. Vail, and P. Gyaneshwar

    Expression and functional roles of Bradyrhizobium japonicum genes involved in the utilization of inorganic and organic sulfur compounds in free-living and symbiotic conditions (2011) Mol. Plant Microbe Interact. 24(4), 451-7.

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  • L. Rigsbee, R. Agans, B. Foy, and O. Paliy

    Optimizing the analysis of human intestinal microbiota with phylogenetic microarray (2011) FEMS Microbiol. Ecol., 75, 332-42.

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  • O. Paliy, H. Kenche, F. Abernathy, and S. Michail

    High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray (2009) Appl. Environ. Microbiol. 75(11), 3572-9.

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  • O. Paliy, S.M. Gargac, Y. Cheng, V.N. Uversky, and A.K. Dunker

    Protein disorder is positively correlated with gene expression in E. coli (2008) J. Proteome Research 7(6), 2234-45.

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  • T.S. Gunasekera, L.N. Csonka, and O. Paliy

    Genome-wide transcriptional responses of Escherichia coli K12 to heat and osmotic stresses (2008) J. Bacteriology 190 (10), 3712-20.

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  • J. M. Frazier, N. Kelley-Loughnane, S. Trott, O. Paliy, M. Rodriquez, and L. Viveros

    Cell-Like Entities: On the boundary between non-living and living in "Protocells: Bridging nonliving and living matter" (2008) MIT Press, pp. 615-640.

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  • T.S. Gunasekera and O. Paliy

    Growth of E. coli BL21 in minimal media with different gluconeogenic carbon sources and salt contents (2007) Appl. Microbiol. Biotechnol., 73(5), 1169-72.

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  • O. Paliy, B. Thomas, R.W. Corbin, F. Yang, J. Shabanowitz, M. Platt, C.E. Lyons, K. Root, D. Hunt, and S. Kustu

    A protein profile of Escherichia coli by coupled high pressure liquid chromatography-tandem mass spectrometry: Consideration of examples (2006) Epub at WSU online.

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  • P. Gyaneshwar, O. Paliy, J. McAuliffe, A. Jones, M.I. Jordan and S. Kustu

    Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation (2005) Proc. Natl. Acad. Sci. USA, 102(9), 3453-3458.

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  • P. Gyaneshwar, O. Paliy, J. McAuliffe, D.L. Popham, M.I. Jordan and S. Kustu

    Sulfur and nitrogen limitation in Escherichia coli K12 (2005) J. Bacteriol., 187(3), 2074-1090.

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  • D.P. Zimmer, O. Paliy, B. Thomas, P. Gyaneshwar, and S. Kustu

    Genome Image programs: visualization and interpretation of Escherichia coli microarray experiments (2004) Genetics, 167, 2111-2119.

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  • R.W. Corbin, O. Paliy, F. Yang, J. Shabanowitz, M. Platt, C.E. Lyons, K. Root, J. McAuliffe, M.I. Jordan, S. Kustu, E. Soupene, and D.F. Hunt

    Toward a protein profile of Escherichia coli: comparison to its transcription profile. (2003) Proc. Natl. Acad. Sci. USA, 100(16), 9232-9237.

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  • E. Soupene, W.C. van Heeswijk, J. Plumbridge, V. Stewart, D. Bertenthal, H. Lee, G. Prasad, O. Paliy, P. Charernnoppakul, and S. Kustu

    Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. (2003) J. Bacteriol., 185(18), 5611-5626.

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  • O. Paliy, D. Bloor, D. Brockwell, P. Gilbert, and J. Barber

    Improved methods of cultivation and production of deuteriated proteins from E. coli strains grown on fully deuteriated minimal medium. (2003) J. Appl. Microbiol. 94, 580–586.

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