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Research Results

Publications

(REU students denoted by *)

  • Adam Thrash, Juliet D. Tang, *Mason DeOrnellis, Daniel G. Peterson, Marilyn L. Warburton. PAST: The Pathway Association Studies Tool to Infer Biological Meaning from GWAS Datasets. BMC Bioinformatics. 2020; 9(1):58.
  • Chathurani Ranathunge, Gregory L. Wheeler, Melody E. Chimahusky, *Meaghan M. Kennedy, Jesse I. Morrison, Brian S. Baldwin, Andy D. Perkins, Mark E. Welch. Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence. Molecular Ecology. 2018; 27(5):1188-99.
  • Naseer A. Kutchy, Ana Velho, Erika S. B. Menezes, *Marie Jacobsen, Giselle Thibaudeau, Robert W. Wills, Arlindo Moura, Abdullah Kaya, Andy Perkins, Erdogan Memili. Testis specific histone 2B is associated with sperm chromatin dynamics and bull fertility-a pilot study. Reproductive Biology and Endocrinology. 2017; 15(1):59.
  • Emeline B. Campanini, Michael W. Vandewege, Nisha E. Pillai, Boon-Hui Tay, *Justin L. Jones, Byrappa Venkatesh, Federico G. Hoffmann. Early Evolution of Vertebrate Mybs: An Integrative Perspective Combining Synteny, Phylogenetic, and Gene Expression Analyses. Genome Biology and Evolution. 2015; 7(11):3009-21.
  • F. Uzbas, *I. D. May, *A. M. Parisi, *S. K. Thompson, A. Kaya, A. D. Perkins, et al. Molecular Physiognomies and Applications of Adipose-Derived Stem Cells. Stem Cell Reviews and Reports. 2015; 11(2):298-308.
  • *Alexis M. Parisi, *Shannon K. Thompson, Abdullah Kaya, Erdogan Memili. Molecular, cellular and physiological determinants of bull fertility. Turkish Journal of Veterinary Animal Science. 2014; 38:637-42.
  • Aruna Govindaraju, Alper Uzun, LaShonda Robertson, Osman Atli, Abdullah Kaya, Einko Topper, *Elizabeth Crate, James Padbury, Andy Perkins, and Erdogan Memili. Dynamics of microRNAs in bull spermatozoa. Reproductive Biology and Endocrinology. 2012; 10
  • Erdogan Memili, Sule Dogan, Nelida Rodriguez-Osorio, Xiaojun Wang, Rodrigo V. de Olivera, Melissa C. Mason, Aruna Govindaraju, Kamilah E. Grant, Lauren E. Belser, *Elizabeth Crate, Arlindo Moura, and Abdullah Kaya. Makings of the best spermatozoa: Molecular determinants of high fertility. In: Male Fertility. Edited by Bashamboo A, McElreavey KD; 2012.

Poster Presentations

(REU students denoted by *)

  • *M. Moore, X. Zhang, F. Cunningham, L. Li, K. Hanson-Door, A. D. Perkins, Q. He, L. A. Hanson, X. Wan. Identifying potential agents causing fish disease outbreaks in Mississippi Delta using metagenomics. MidSouth Computational Biology and Bioinformatics Society, Starkville, Mississippi, 2018.
  • *A. M. Chiappetta. N. A. Kutchy, E. Menezes, A. Moura, A. Kaya, A. Perkins, and E. Memili. Methylation and Acetylation of Sperm Histone 3 Regular Chromatin Dynamics and Male Fertility. American Society for Cell Biology, San Francisco, California, December 2016.
  • *Rachel D. Steele, Mark A. Arick II, Andy Perkins, Bindu Nanduri, Daniel G. Peterson, Doug Rhoads, and William S. Sander. A Mitochondrial Genome of the Timber Rattlesnake (Crotalus Horridus) and a Reptilian Mitochondrial Phylogeny. MidSouth Computational Biology and Bioinformatics Society, Memphis, Tennessee, March 2016.
  • *J. S. McNair, A. Velho, A. Lawrence, G. Thibaudeau, A. Moura, A. Kaya, A. Perkins, and E. Memili. Spatiotemporal Cellular Dynamics and Bioinformatics of Sperm Izumo. American Society for Cell Biology, San Francisco, California, December 2015.
  • *M. C. Jacobsen, N. A. Kutchy, A. Velho, G. Lawrence, G. Thibaudeau, A. Moura, A. Kaya, E. Memili, and A. Perkins. Visualizing Sperm TH2B: A combined immunocytochemistry and bioinformatics approach to illuminate a key player in the regulation of chromatin states and mammalian fertility. American Society for Cell Biology, San Francisco, California, December 2015.
  • *Jonathan Rice, Kortni Dees, Adam Thrash, and Andy D. Perkins. Investigating genome similarity through cross mapping percentage. Association for Computing Machinery Conference on Bioinformatics, Computational Biology, and Health Informatics, Atlanta, Georgia, September 2015.
  • L. A. Bright, M. Arick II, S. Kumar, *S. Mack, A. Perkins, C. Hunter, A. Eddy, A. Claude, N. Mujahid, M. Brashier, B. Nanduri, S. C. Burgess, and C. E. Swiderski. Modeling the equine recurrent airway obstruction lunch transcriptome highlights molecular signatures of airway hyperresponsiveness and neutrophilic inflammation. MidSouth Computational Biology and Bioinformatics Society, Little Rock, Arkansas, March 2015.
  • L. A. Bright, M. Arick II, S. Kumar, *S. Mack, A. Perkins, C. Hunter, A. Eddy, A. Claude, N. Mujahid, M. Brashier, B. Nanduri, S. C. Burgess, and C. E. Swiderski. The recurrent airway obstruction restricted lunch transcriptome identifies molecular signatures of airway hyperresponsiveness and neutrophilic inflammation. International Plant and Genome XXVII, San Diego, California, January 2015.
  • *S. Kwok, R. Oliveiro, A. Moura, A. Kaya, A. Perkins, R. Wills, and E. Memili. Functional Epigenomics and Evolutionary Diversification of Mammalian Pre-implanation Blastocysts and Male Fertility. American Society for Cell Biology, New Orleans, Louisiana, December 2014.
  • *Alvaro Arrospide Fletcher, Andy Perkins, Joseph S. Reddy, Mahalingam Ramkumar, and Bindu Nanduri. Impact of Sequence Conservation on RNA-Seq Alignment in Co-infection Studies. Annual Biomedical Research Conference for Minority Students, San Antonio, Texas, November 2014.
  • *Rahunandan Avula, Andy D. Perkins, and Federico G. Hoffmann. Examining Copy Number Variation in Mouse piRNA Clusters. Great Lakes Bioinformatics Conference, Pittsburgh, Pennsylvania, May 2013.
  • Tamer Aldwairi, Dilip Gautam, *Michael Johnson, Bindu Nanduri, Mahalingam Ramkumar, and Andy Perkins. Statistical Methods for Ambiguous Sequence Mappings. MidSouth Computational Biology and Bioinformatics Society, Columbia, Missouri, April 2013.
  • *Elizabeth A. Crate, *Raghunandan Avula, Hollie O’Neal, Andy Perkins, and Erdogan Memili. Expression Dynamics and Evolution of Sperm PIWIL1, PIWIL2, and AGO2, American Society for Cell Biology, San Francisco, California, December 2012.
  • Dilip Gautam, Trey Gaines, *Michael Johnson, Arunkanth Ankala, Tad Sonstegard, Steven Schroeder, Jeff Wilkinson, and Andy D. Perkins. An Integration Pipeline for Improved High-throughput Sequence Mapping of Metatranscriptomic and Ambiguous Sequences. MidSouth Computational Biology and Bioinformatics Society, Oxford, Mississippi, February 2012.
  • *Michael Johnson, Dilip Gautam, Arunkanth Ankala, Tad Sonstegard, Steven Schroeder, Jeff Wilkinson, Mahalingam Ramkumar, and Andy Perkins. A Statistical Approach for Ambiguous Sequence Mappings. MidSouth Computational Biology and Bioinformatics Society, College Station, Texas, April 2011.
  • *Katherine McGinley, Candace Williams, Renuka Shivaji, Andy Kouba, Scott Willard, and Ashli Brown. Using Genomic Techniques to Identify Bacteria in Panda Fecal. 25th Annual Meeting of the Southern Section of the Association of Analytical Communities, Atlanta, GA, April 2011.
  • Carole Nail, Philippe Chouvarine, Janet Weber, *Yachi Spencer, Swati Kumari, Shane Burgess, Carl Schmidt, Parker Antin, Fiona McCarthy. “Manual biocuration to support standardized chicken gene nomenclature at CGNC.” The 6th International Chick Meeting Roslin Institute, Sept. 17-20, 2011.
  • Rajhkeem Beck, Andy Perkins, *Glen Luker, Dilip Gautam, Arunkanth Ankala, Tad Sonstegard, Steven Schroeder, and Jeff Wilkinson. Investigating Functional Annotation of Genes Involved in Aspergillus avus infection in maize. Annual Biomedical Research Conference for Minority Students, Charlotte, North Carolina, November 2010.