The Perkins Computational Biology and Bioinformatics Lab

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Matthew A. Scott, Amelia R. Woolums, Cyprianna E. Swiderski, Andy D. Perkins, Bindu Nanduri, David R. Smith, Brandi B. Karisch, William B. Epperson, and John R. Blanton, Jr. Whole blood transcriptomic analysis of beef cattle at arrival identifies potential predictive molecules and mechanisms that indicate animals that naturally resist bovine respiratory disease. PLOS One, submitted.

 

Adam Thrash, Federico G. Hoffmann, and Andy D. Perkins. Toward a More Holistic Approach to Genome Quality Assessment. BMC Bioinformatics, in revision.

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Chathurani Ranathunge, Gregory L. Wheeler, Melody Chimahusky, Andy D. Perkins, Sreepriya Pramod, and Mark E. Welch. Transcribed microsatellites often influence gene expression in natural sunflower populations. Molecular Biology and Evolution, in revision.

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Hossam Abdelhamed, Ozan Ozdemir, Geoffrey Waldbieser, Andy Perkins, Mark L. Lawrence, and Attila Karsi. Effects of florfenicol feeding on diversity and composition of the intestinal microbiota of channel catfish (Ictalurus punctatus). Aquaculture Research, accepted for publication.

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Hasan C. Tekedar, Salih Kumru, Jochen Blom, Andy D. Perkins, Matt J. Griffin, Hossam Abelhamed, Atilla Karsi, and Mark L. Lawrence. Comparative phylogenomics of Aeromonas veronii: identification of a pathotype impacting aquaculture globally. PLOS ONE, accepted for publication.

 

Tamer Aldwairi, Federico Hoffmann, and Andy D. Perkins. Prediction of Novel PiRNA Rat Clusters Based on Mouse piRNA Clusters Using Downstream and Upstream Analysis. Eleventh International Conference on Bioinformatics and Computational Biology, Honolulu, Hawaii, March 2019.

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C. Ranathunge, G. L. Wheeler, M. E. Kennedy, J. Morrison, B. Baldwin, A. D. Perkins, and M. E. Welch. Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence. Molecular Ecology, 27, 1188-1199, 2018.

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T. Aldwairi, B. Elam, F. H. Hoffmann, and A. D. Perkins. RepCalc: A Tool for Calculating Transposable Element Density within the Genome. Tenth International Conference on Bioinformatics and Computational Biology, Las Vegas, Nevada, March 2018.

 

N. A. Kutchy, E. S. B. Menezes, A. Chiappetta, W. Tan, R. W. Wills, A. Kaya, E. Topper, A. A. Moura, A. D. Perkins, and E. Memili. Acetylation and methylation of sperm histone 3 lysine 27 (H3K27ac and H3K27me3) are associated with bull fertility. Andrologia, 50(3): e12915, 2017.

 

N. A. Kutchy, A. Velho, E. S. B. Menezes, M. Jacobsen, G. Thibaudeau, R. W. Willis, A. Moura, A. Kaya, A. Perkins, and E. Memili. Testis specific histone 2B is associated with sperm chromatin dynamics and bull fertility-a pilot study. Reproductive Biology and Endocrinology, 15:59, 2017.

 

Jason H. Moore, Steven F. Jennings, Casey S. Greene, Lawrence E. Hunter, Andy D. Perkins, Clarlynda Williams-Devane, Donald C. Wunsch, Zhongming Zhao, and Xiuzhen Huang. No-Boundary Thinking in Bioinformatics (Workshop). Pacific Symposium for Biocomputing 22:646-648, Big Island, Hawaii, January 2017.

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Juliet D. Tang, Andy Perkins, W. Paul Williams, and Marilyn L. Warburton. Using genome-wide associations to identify metabolic pathways involved in maize aflatoxin accumulation resistance. BMC Genomics, 16(1):673, 2015.

 

Harun Pirim, Burak Eksioglu, and Andy D. Perkins. Clustering high throughput biological data with B-MST, a minimum spanning tree based heuristic. Computers in Biology and Medicine, 62: 94-102, 2015.

 

Marilyn Warburton, Juliet Tang, Gary Windham, Leigh Hawkins, Seth Murray, Wenwei Xu, Deborah Boykin, Andy Perkins, and Paul Williams. Genome-wide association mapping of Aspergillus flavus and aflatoxin accumulation resistance in maize. Crop Science, 55:1-11, 2015.

 

Kamilah E. Grant, Rodrigo V. de Oliveira, Bettye Sue Hennington, Aruna Govindaraju, Andy Perkins, John Stokes, Dennis Rowe, Einko Topper, Abdullah Kaya, Arlindo Moura, and Erodgan Memili. Sperm Superoxide Dismutase is Associated with Bull Fertility. Reproduction, Fertility and Development, 28(9):1405-1413, 2015.

 

Xiuzhen Huang, Steven F. Jennings, Barry Bruce, Alison Buchan, Liming Cai, Pengyin Chen, Carole L. Cramer, Weihua Guan, Uwe KK Hilgert, Homgmei Jiang, Zenglu Li, Gail McClure, Donald F. McMullen, Bindu Nanduri, Andy Perkins, Bhanu Rekepalli, Saeed Salem, Jennifer Specker, Karl Walker, Donald Wunsch, Donghai Xiong, Shuzhong Zhang, Yu Zhang, Zhongming Zhao, and Jason H. Moore. Big Data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm. BioData Mining, 8:7, 2015.

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F. Uzbas, I. D. May, A. M. Parisi, S. K. Thompson, A. Kaya, A. Perkins, and E. Memili. Molecular Physiognomies and Applications of Adipose-Derived Stem Cells. Stem Cell Reviews and Reports, 11(2): 298-308, 2014.

 

Jonathan Wren, Mikhail Dozmorov, Dennis Burian, Andy Perkins, Chaoyang Zhang, Peter Hoyt, Rakesh Kaundal. Proceedings of the 2014 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. BMC Bioinformatics,15(Suppl 11): I1, 2014.

 

Sreepriya Pramod, Andy Perkins, and Mark Welch. Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome. Journal of Genetics, 93(2):431-442, 2014.

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Matthew C. Asters, W. Paul Williams, Andy D. Perkins, J. Erik Mylroie, Gary L. Windham, and Xueyan Shan. Relating significance and relations of differentially expressed genes in response to Aspergillus flavus infection in maize. Scientific Reports, 4:4815, 2014.

 

Xiuzhen Huang, Barry Bruce, Alison Buchan, Clare Bates Congdon, Carole L. Cramer, Steven F. Jennings, Hongmei Jiang, Zenglu Li, Gail McClure, Rick McMullen, Jason H. Moore, Bindu Nanduri, Joan Peckham, Andy Perkins, Shawn W. Polson, Bhanu Rekepalli, Saeed Salem, Jennifer Specker, Donald Wunsch, Donghai Xiong, Shuzhong Zhang, and Zhongming Zhao. No-boundary thinking in bioinformatics research. BioData Mining, 6:19, 2013.

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Juliet D. Tang, Leslie A. Parker, Andy D. Perkins, Tad S. Sonstegard, Steven G. Schroeder, Darrel D. Nicholas, and Susan V. Diehl. Gene expression analysis of copper tolerance and wood decay in the brown rot fungus Fibroporia radiculosa. Applied and Environmental Microbiology, 79(5), 1523-1533, 2013.

 

Tamer Aldwairi, David Chevalier, and Andy D. Perkins. A Computational Investigation of Climatic effects on SNPs within FHA-Domain genes in Eurasian Arabidopsis Ecotypes (short abstract). Proceedings of the International Symposium on Bioinformatics Research and Applications, Charlotte, North Carolina, May 2013. Presented as poster, appearing in online conference proceedings.

 

Sreepriya Pramod, Sebastien Renaut, Andy Perkins, Loren Rieseberg, and Mark Welch. Microsatellites as agents of rapid adaptive change: A RNASeq based comparative study of transcriptomes in nine closely related Helianthus species (short abstract). Proceedings of the International Symposium on Bioinformatics Research and Applications, Charlotte, North Carolina, May 2013. Presented as poster, appearing in online conference proceedings.

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Aruna Govindaraju, Alper Uzun, LaShonda Robertson, Osman Atli, Abdullah Kaya, Einko Topper, Elizabeth A. Crate, James Padbury, Andy Perkins, and Erdogan Memili. Dynamics of microRNAs in bull spermatozoa. Reproductive Biology and Endocrinology, 10(82), 2012.

 

Juliet D. Tang, Andy Perkins, Tad Sonstegard, Shane Burgess, and Susan V. Diehl. Short read sequencing to predict genes of the brown rot fungus Antrodia radiculosa. Applied and Environmental Microbiology, 78(7):2272-2281, 2012.

 

Jeremy J. Jay, John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, and Michael A. Langston. A Systematic Comparison of Genome Scale Clustering Algorithms. BMC Bioinformatics, 13(Suppl 10):S7, 2012.

 

Harun Pirim, Burak Eksioglu, Andy Perkins, and Cetin Yuceer. Clustering of High Throughput Biological Data. Computers and Operations Research, 39(12):3046-3061, 2012.

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Tamer Aldwairi, Lifang Yan, Kanchana Weerasinghe, and Andy D. Perkins. Comparison of miRNA Target Prediction Algorithms Using Computational Methods. Proceedings of the 4th International Conference on Bioinformatics and Computational Biology, Las Vegas, Nevada, March 2012.

 

Harun Pirim, Dilip Gautam, Tanmay Bhowmik, Andy D. Perkins, Burak Eksioglu, and Ahmet Alkan. Performance of an Ensemble Clustering Algorithm on Biological Data Sets. Mathematical and Computational Applications, 16(1):87-96, 2011.

 

Jeremy J. Jay, John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, and Michael A. Langston. A Systematic Comparison of Genome Scale Clustering Algorithms. Proceedings of the International Symposium on Bioinformatics Research and Applications, Changsha, China, May 2011.

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Harun Pirim, Dilip Gautam, Tanmay Bhowmik, Andy Perkins, and Burak Eksioglu. Performance evaluation of a community structure finding algorithm using modularity and C-rand measures. Proceedings of the IEEE International Joint Conference on Neural Networks, Barcelona, Spain, July 2010.

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A. D. Perkins and Michael A. Langston. Threshold Selection in Gene Expression Networks Using Spectral Graph Theory Techniques. BMC Bioinformatics, 10(Suppl 11):S4, 2009.

 

Brandon Malone, Andy D. Perkins, and Susan Bridges. Predicting Gene Function using an Integrated Similarity Graph. BMC Bioinformatics, 10(Suppl 11):S20, 2009.

 

Reza Mobini, Bengt A. Andersson, Jonas Erjefalt, Mirjana Hahn-Zoric, Michael A. Langston, Andy D. Perkins, Lars Olaf Cardell, and Mikael Benson. A module-based analytical strategy to identify novel disease genes shows an inhibitory role for interleukin 7 receptor in allergic inflammation. BMC Systems Biology, 3(19), 2009.

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Gary L. Rogers, Andy D. Perkins, Charles A. Phillips, John D. Eblen, Faisal N. Abu-Khzam, and Michael A. Langston. Using Out-of-Core Techniques to Produce Exact Solutions to the Maximum Clique Problem on Extremely Large Graphs. Proceedings of the ACS/IEEE International Conference on Computer Systems and Applications, Rabat, Morocco, May 2009.

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Fredrik Barrenas, Bengt Andersson, Lars Olaf Cardell, Michael Langston, Reza Mobini, Andy Perkins, Juhani Soini, Arne Stahl, and Mikael Benson. Gender differences in inflammatory proteins and pathways in seasonal allergic rhinitis. Cytokine, 42(3):325-329, 2008.

Michael A. Langston, Andy D. Perkins, Arnold M. Saxton, Jon A. Scharff, and Brynn H. Voy. Innovative computational methods for transcriptomic data analysis: a case study in the use of FPT for practical algorithm design and implementation. The Computer Journal, 51(1):26-38, 2008.

Daniel Gatti, Akira Maki, Elissa Chesler, Oksana Kosyk, Roumyana Kirova, Lu Lu, Kenneth Manly, Yanhua Qu, Robert Williams, Andy Perkins, Michael Langston, David Threadgill, and Ivan Rusyn. Genome-level analysis of genetic regulation of liver gene expression networks. Hepatology, 46(2):548-557, 2007.

Brynn H. Voy, Jon A. Scharff, Andy D. Perkins, Arnold M. Saxton, Bhavesh Borate, Elissa J. Chesler, Lisa K. Branstetter, and Michael A. Langston. Extracting gene networks for low dose radiation using graph theoretical algorithms. PLoS Computational Biology, 2(7):e89, 2006.

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Roumyana Kirova, Michael A. Langston, Xinxia Peng, Andy D. Perkins, and Elissa J. Chesler. A systems genetic analysis of chronic fatigue syndrome: combinatorial data integration from SNPs to dierential diagnosis of disease. Proceedings of the International Conference for the Critical Assessment of Microarray Data Analysis, Durham, North Carolina, June 2006.

Michael A. Langston, Andy D. Perkins, Arnold M. Saxton, Jon A. Scharff, and Brynn H. Voy. Innovative computational methods for transcriptomic data analysis. Proceedings of the ACM Symposium on Applied Computing, Dijon, France, April 2006.

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A. Fadiel, M. A. Langston, X. Peng, A. D. Perkins, H. S. Taylor, O. Tuncalp, D. Vitello, P. Pevsner, and F. Naftolin. Computational analysis of mass spectrometry data using novel combinatorial methods. Proceedings of the ACS/IEEE International Conference on Computer Systems and Applications, Dubai/Sharjah, United Arab Emirates, March 2006.

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