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


  • A. Delgado-Osorio, B. Navajas-Porras, S. Pérez-Burillo, D. Hinojosa-Nogueira, Á. Toledano-Marín, S. Pastoriza de la Cueva, O. Paliy, and J.Á. Rufián-Henares

    Cultivar and Harvest Time of Almonds Affect Their Antioxidant and Nutritional Profile through Gut Microbiota Modifications (2024) Antioxidants, 13(1): 84.

Abstract
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  • L.M. Ketelboeter, A. Gordon, S.U. Welmillage, V. S. Sreevidya, O. Paliy and P. Gyaneshwar

    Transcriptomic and physiological responses of Rhizobium sp. IRBG74 to Sesbania cannabina and Rice (Oryza sativa L) rhizosphere (2023) Plant Soil, 483(1-2): 515-532.

Abstract
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  • S. Rajakaruna, S. Pérez-Burillo, D.L. Kramer, J.Á. Rufián-Henares, and O. Paliy

    Dietary Melanoidins from Biscuits and Bread Crust Alter the Structure and Short-Chain Fatty Acid Production of Human Gut Microbiota (2022) Microorganisms, 10(7): 1268.

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  • S. Perez-Burillo, S. Rajakaruna, and O. Paliy

    Growth of Bifidobacterium species is inhibited by free fatty acids and bile salts but not by glycerides (2022) AIMS Microbiol., 8(1): 53–60.

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  • O. Paliy and S. Rajakaruna

    Development of Microbiota - Is the Process Continuing Through Adolescence? (2022) in: Glibetic, M. (Ed.), Comprehensive Gut Microbiota, vol. 2. Elsevier, pp. 59–68.

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  • S. Pérez-Burillo, S. Rajakaruna, O. Paliy, S. Pastoriza, J.Á. Rufián-Henares

    Bioactivity of food melanoidins is mediated by gut microbiota (2020) Food Chem. 316: 126309.

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  • M.P. Craig, S. Rajakaruna, O. Paliy, M. Sajjad, S. Madhavan, N. Reddy, J. Zhang, M. Bottomley, S. Agrawal, M.P. Kadakia

    Differential MicroRNA Signatures in the Pathogenesis of Barrett’s Esophagus (2020) Clin. Transl. Gastroenterol. 11(1): e00125.

Abstract
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  • R.T. Agans, A. Gordon, S. Hussain, O. Paliy.

    Titanium dioxide nanoparticles elicit lower direct inhibitory effect on human gut microbiota than silver nanoparticles (2019) Toxicol. Sci., 172(2): 411-416.

          This article was chosen for Tox Spotlight section.

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  • S. Rajakaruna, D.A. Freedman, A.R. Sehgal, X. Bui, and O. Paliy

    Diet quality and body mass indices show opposite associations with distal gut microbiota in a low-income cohort (2019) J. Food Sci. Technol., 4(7): 846-851.

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  • S. Pérez-Burillo, T. Mehta, S. Pastoriza, D.L. Kramer, O. Paliy, J.Á. Rufián-Henares

    Potential probiotic salami with dietary fiber modulates antioxidant capacity, short chain fatty acid production and gut microbiota community structure (2019) Food Sci. Technol. 105: 355-362.

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  • S. Pérez-Burillo, T. Mehta, A. Esteban-Muñoz, S. Pastoriza, O. Paliy, J.Á. Rufián-Henares

    Effect of in vitro digestion-fermentation on green and roasted coffee bioactivity: The role of the gut microbiota (2019) Food Chem. 279: 252-259.

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  • R. Agans, A. Gordon, D.L. Kramer, S. Pérez-Burillo, J.A. Rufián-Henares, and O. Paliy

    Dietary fatty acids sustain the growth of the human gut microbiota (2018) Appl. Environ. Microbiol. 84(21): e01525-18.

    This article was highlighted in AEM and Wright State BSoM press-releases.

Abstract
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AEM spotlight
AEM press-release
BSoM press-release

  • E. Labib, M. Blaut, L. Hussein, M. Gouda, D.L. Kramer, O. Paliy, B. Ganesh, P. Schumann, R. Pukall, A. Woting, M.T. Fouad

    Molecular diversity of gut microbiota and short chain fatty acids in egyptian adults following dietary intervention with fermented sobya (2018) J. Food Microbiol. Saf. Hyg. 3 (2): 1000139.

Abstract
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  • E. Kim, M. Lambert, G. Fallata, J. Rowe, T. Martin, A. Satoskar, N. Reo, O. Paliy, E. Cormet-Boyaka, and P.N. Boyaka

    Intestinal epithelial cells regulate gut CCL11 responses and severity of allergy (2018) Front. Immunol. 9: 1692.

Abstract
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  • S. Sakaram, M. Craig, N. Hill, A. Aljagthmi, C. Garrido, O. Paliy, M. Bottomley, M.L. Raymer, and M. Kadakia

    Identification of novel ΔNp63α-regulated miRNAs using an optimized small RNA-Seq analysis pipeline (2018) Sci. Rep. 8: 10069.

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  • M.C. Jugan, A.J. Rudinsky, A. Gordon, D.L. Kramer, J.B. Daniels, O. Paliy, P. Boyaka, and C. Gilor

    Effects of oral Akkermansia muciniphila supplementation in healthy dogs following antimicrobial administration (2018) Am. J. Vet. Res. 79(8): 884-892.

Abstract
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  • V. Shankar, R. Agans, and O. Paliy

    Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities (2017) Sci. Rep. 7(1): 6481.

Abstract
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Supplementary material

  • V. Shankar, M. Gouda, J. Moncivaiz, A. Gordon, N.V. Reo, L. Hussein, and O. Paliy

    Differences in gut metabolites and microbial composition and functions between Egyptian and US teenagers are consistent with consumed diets (2017) mSystems 2(1): e00169-16.

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  • O. Paliy and V. Shankar

    Application of multivariate statistical techniques in microbial ecology (2016) Mol. Ecol. 25(5): 1032-57.

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  • V. Shankar, N.V. Reo, and O. Paliy

    Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome (2015) Microbiome 3: 73.

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  • V. Shankar, D. Homer, L. Rigsbee, H.J. Khamis, S. Michail, M. Raymer, N.V. Reo, and O. Paliy

    The networks of human gut microbe-metabolite associations are different between health and irritable bowel syndrome (2015) ISME J., 9(8): 1899-903.

Abstract
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Supplementary material

  • S. Michail, M. Lin, M.R. Frey, R. Fanter, O. Paliy, B. Hilbush, and N.V. Reo

    Altered gut microbial energy and metabolism in children with non-alcoholic fatty liver disease (2015) FEMS Microbiol. Ecol., 91(2): 1-9.

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  • O. Paliy and V. Shankar

    Applications of phylogenetic microarrays to profiling of human microbiomes (2014) 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.

Abstract
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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.

Abstract
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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.

Abstract
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Supplementary material

  • 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.

Abstract
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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.

Abstract
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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.

Abstract
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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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Supplementary material

  • 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.

Abstract
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Supplementary material

  • 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.

Abstract
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Supplementary material


  • 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.

Abstract
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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.

Abstract
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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.

Abstract
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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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Supplementary material

  • 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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Wright State University
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