Mariola J. Ferraro, Andy D. Perkins, Mahalingam Ramkumar, and Bindu Nanduri. No Boundary Thinking for Transcriptomics and Proteomics Big Data. No Boundary Thinking in Bioinformatics. Ed. Xiuzhang Huang, Jason H. Moore, and Yu Zhang. Cambridge (England): Cambridge University Press, 2024.
Joan Peckham, Bryan Dewsbury, Bindu Nanduri, Andy Perkins, Don Wunsch, and Yu Zhang. No-Boundary Course Developments. No Boundary Thinking in Bioinformatics. Ed. Xiuzhang Huang, Jason H. Moore, and Yu Zhang. Cambridge (England): Cambridge University Press, 2023.
Journal Articles
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”. In: PLoS Comput Biol 2.7 (2006), e89.
Daniel Gatti, Akira Maki, Elissa J Chesler, Roumyana Kirova, Oksana Kosyk, Lu Lu, Kenneth F Manly, Robert W Williams, Andy Perkins, Michael A Langston, et al. “Genome-level analysis of genetic regulation of liver gene expression networks”. In: Hepatology 46.2 (2007), pp. 548–557.
B Mobini R Andersson, F Barrenas, M Langston, J Soini, A Perkins, and M Benson. “Identification of signalling pathways and transcription factors in allergen-stimulated CD4+ cells: 1054”. In: Allergy: European Journal of Allergy and Clinical Immunology 62 (2007).
Bengt Barrenas Fredrik 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”. In: Cytokine 42.3 (2008), pp. 325– 329.
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”. In: The Computer Journal 51.1 (2008), pp. 26–38.
Brandon M Malone, Andy D Perkins, and Susan M Bridges. “Integrating phenotype and gene expression data for predicting gene function”. In: BMC Bioinformatics 10.Suppl 11 (2009), S20.
Bengt Andersson, Reza Mobini, 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-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation”. In: BMC Systems Biology 3.1 (2009), pp. 1–11.
Andy D Perkins and Michael A Langston. “Threshold selection in gene co-expression networks using spectral graph theory techniques”. In: BMC Bioinformatics 10.Suppl 11 (2009), S4.
Harun Pirim, Dilip Gautam, Tanmay Bhowmik, Andy D Perkins, Burak Eksioglu, and Ahmet Alkan. “Performance of an ensemble clustering algorithm on biological data sets”. In: Mathematical and Computational Applications 16.1 (2011), pp. 87–96.
Aruna Govindaraju, Alper Uzun, LaShonda Robertson, Mehmet O Atli, Abdullah Kaya, Einko Topper, Elizabeth A Crate, James Padbury, Andy Perkins, and Erdogan Memili. “Dynamics of microRNAs in bull spermatozoa”. In: Reproductive Biology and Endocrinology 10.1 (2012), pp. 1–10.
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”. In: 13.S10 (2012), S7.
Harun Pirim, Burak Eksioglu, Andy D Perkins, and Cetin Yuceer. “Clustering of high throughput gene expression data”. In: Computers & Operations Research 39.12 (2012), pp. 3046–3061.
Juliet D Tang, Andy D Perkins, Tad S Sonstegard, Steven G Schroeder, Shane C Burgess, and Susan V Diehl. “Short-read sequencing for genomic analysis of the brown rot fungus Fibroporia radiculosa”. In: Applied and Environmental Microbiology 78.7 (2012), pp. 2272– 2281.
Xiuzhen Huang, Barry Bruce, Alison Buchan, Clare Bates Congdon, Carole L Cramer, Steven F Jennings, Hongmei Jiang, Zenglu Li, Gail McClure, Rick McMullen, et al. “No-boundary thinking in bioinformatics research”. In: BMC BioData Mining 6.1 (2013), pp. 1–6.
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”. In: Applied and Environmental Microbiology 79.5 (2013), pp. 1523–1533.
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”. In: Scientific Reports 4 (2014), p. 4815.
Sreepriya Pramod, Andy D Perkins, and Mark E Welch. “Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome”. In: Journal of Genetics 93.2 (2014), pp. 431–442.
Xiuzhen Huang, Steven F Jennings, Barry Bruce, Alison Buchan, Liming Cai, Pengyin Chen, Carole L Cramer, Weihua Guan, Uwe KK Hilgert, Hongmei Jiang, et al. “Big data-a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm”. In: BMC BioData Mining 8 (2015), 7.
Harun Pirim, Burak Eksioglu, and Andy D Perkins. “Clustering high throughput biological data with B-MST, a minimum spanning tree based heuristic”. In: Computers in Biology and Medicine 62 (2015), pp. 94–102.
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”. In: BMC Genomics 16.1 (2015), p. 673.
F Uzbas, ID May, AM Parisi, SK Thompson, A Kaya, AD Perkins, and E Memili. “Molecular physiognomies and applications of adipose derived stem cells”. In: Stem Cell Reviews and Reports 11.2 (2015), pp. 298–308.
Marilyn L Warburton, Juliet D Tang, Gary L Windham, Leigh K Hawkins, Seth C Murray, Wenwei Xu, Debbie Boykin, Andy Perkins, and W Paul Williams. “Genome-wide association mapping of Aspergillus flavus and aflatoxin accumulation resistance in maize”. In: Crop Science 55.5 (2015), pp. 1857–1867.
Kamilah E Grant, Rodrigo V de Oliveira, Bettye Sue Hennington, Aruna Govindaraju, Andy Perkins, John Stokes, Dennis Rowe, Einko Topper, Abdullah Kaya, Arlindo Moura, et al. “Sperm superoxide dismutase is associated with bull fertility”. In: Reproduction, Fertility and Development 28.9 (2016), pp. 1405–1413.
Naseer A Kutchy, Ana Velho, Erika SB Menezes, Marie Jacobsen, Giselle Thibaudeau, Robert W Wills, Arlindo Moura, Abdullah Kaya, Andy Perkins, and Erdogan Memili. “Testis specific histone 2B is associated with sperm chromatin dynamics and bull fertility-a pilot study”. In: Reproductive Biology and Endocrinology 15.1 (2017), p. 59.
NA Kutchy, ESB Menezes, Austin Chiappetta, Wei Tan, Robert W Wills, Abdullah Kaya, Einko Topper, AA Moura, AD Perkins, and Erdogan Memili. “Acetylation and methylation of sperm histone 3 lysine 27 (H3K27ac and H3K27me3) are associated with bull fertility”. In: Andrologia 50.3 (2018), e12915.
Chathurani Ranathunge, Gregory L Wheeler, Melody E Chimahusky, Meaghan M Kennedy, Jesse I Morrison, Brian S Baldwin, Andy D Perkins, and Mark E Welch. “Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence”. In: Molecular Ecology 27.5 (2018), pp. 1188–1199.
Hossam Abdelhamed, Ozan Ozdemir, Geoffrey Waldbieser, Andy D Perkins, Mark L Lawrence, and Attila Karsi. “Effects of florfenicol feeding on diversity and composition of the intestinal microbiota of channel catfish (Ictalurus punctatus)”. In: Aquaculture Research 50.12 (2019), pp. 3663–3672.
Hasan C Tekedar, Salih Kumru, Jochen Blom, Andy D Perkins, Matt J Griffin, Hossam Abdelhamed, Attila Karsi, and Mark L Lawrence. “Comparative genomics of Aeromonas veronii: Identification of a pathotype impacting aquaculture globally”. In: PloS One 14.8 (2019), e0221018.
Chathurani Ranathunge, Gregory L Wheeler, Melody E Chimahusky, Andy D Perkins, Sreepriya Pramod, and Mark E Welch. “Transcribed microsatellite allele lengths are often correlated with gene expression in natural sunflower populations”. In: Molecular Ecology (2020).
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”. In: PloS one 15.1 (2020), e0227507.
Adam Thrash, Federico Hoffmann, and Andy Perkins. “Toward a more holistic method of genome assembly assessment”. In: BMC Bioinformatics 21.4 (2020), pp. 1–8.
Tamer Aldwairi, David J Chevalier, and Andy D Perkins. “Exploring the Effect of Climate Factors on SNPs within FHA Domain Genes in Eurasian Arabidopsis Ecotypes”. In: Agriculture 11.166 (2021).
Tayo Obafemi-Ajayi, Andy Perkins, Bindu Nanduri, Donald Wunsch, James A Foster, and Joan Peckham. “No-Boundary Thinking: a Viable Solution to Ethical Data-driven AI in Precision Medicine”. In: AI and Ethics (2021).
Chathurani Ranathunge, Sreepriya Pramod, S´ebastien Renaut, Wheeler Gregory, Andy D Perkins, Loren H Rieseberg, and Mark E Welch. “Microsatellites as agents of adaptive change: An RNA-seq based comparative study of transcriptomes from five helianthus species”. In: Symmetry 13.933 (2021).
Matthew A Scott, Amelia R Woolums, Cyprianna E Swiderski, Andy D Perkins, and Bindu Nanduri. “Genes and Mechanisms associated with experimentally induced bovine respiratory disease identified with supervised machine learning methodology on integrated transcriptomic datasets”. In: Scientific Reports 11 (2021), 22916.
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. “Comprehensive atarrival transcriptomic analysis of post-weaned beef cattle uncovers type I interferon and antiviral mechanisms associated with bovine respiratory disease mortality”. In: PLOS One 14.4 (2021), e0250758.
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. “Multipopulational transcriptome analysis of post-weaned beef cattle at arrival further validates candidate biomarkers for predicting clinical bovine respiratory disease”. In: Scientific Reports 11.1 (2021), p. 23877.
Hasan C Tekedar, Salih Kumru, Mark L Lawrence, Jochen Blom, and Geoffrey C Waldbieser. “Edwardsiella genus reveals species based diversity”. In: BMC Genomics (2021).
Matthew A Scott, Amelia R Woolums, Cyprianna E Swiderski, Alexis C Thompson, Andy D Perkins, Bindu Nanduri, Brandi B Karisch, and Dan R Goehl. “Use of nCounter mRNA profiling to identify at-arrival gene expression patterns for predicting bovine respiratory disease in beef cattle”. In: BMC Veterinary Research 18 (2022), 77.
Conference Papers
Ahmed Fadiel, Michael A Langston, Xinxia Peng, Andy D Perkins, Hugh S Taylor, Ozge Tuncalp, D Vitello, Paul H Pevsner, and Frederick Naftolin. “Computational Analysis of Mass Spectrometry Data Using Novel Combinatorial Methods.” In: AICCSA 6 (2006), pp. 8–11.
Doug Beare, K Winpenny, C Haughton, M Langston, HR Skjoldal, and A Perkins. “Building multi-discipline, multivariate databases for use in integrated ecosystem assessments: experiences and recommendations”. In: Proceedings of the International Council for the Exploration of the Seas Annual Science Conference. 2006.
MA Langston, AD Perkins, DJ Beare, RW Gauldie, PJ Kershaw, JB Reid, K Winpenny, and AJ Kenny. “Combinatorial algorithms and high performance implementations for elucidating complex ecosystem relationships from North Sea historical data”. In: Proc. International Council for the Exploration of the Seas Annual Science Conference. 2006.
AJ Kenny, P Kershaw, D Beare, M Devlin, JB Reid, P Licandro, A Gallego, K Winpenny, C Houghton, MA Langston, et al. “Integrated assessment of the North Sea to identify the relationship between human pressures and ecosystem state changes–implications for marine management”. In: Proc. International Council for the Exploration of the Seas Annual Science Conference (2006).
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 differential diagnosis of disease”. In: Proceedings, International Conference for the Critical Assessment of Microarray Data Analysis (CAMDA06). 2006.
Michael A Langston, Andy D Perkins, Arnold M Saxton, Jon A Scharff, and Brynn H Voy. “Innovative computational methods for transcriptomic data analysis”. In: Proceedings of the 2006 ACM Symposium on Applied Computing. 2006, pp. 190–194.
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”. In: 2009 IEEE/ACS International Conference on Computer Systems and Applications. IEEE. 2009, pp. 374–381.
Harun Pirim, Dilip Gautam, Tanmay Bhowmik, Andy D Perkins, and Burak Eksioglu. “Performance evaluation of a community structure finding algorithm using modularity and C-rand measures”. In: The 2010 International Joint Conference on Neural Networks (IJCNN). IEEE. 2010, pp. 1–8.
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”. In: International Symposium on Bioinformatics Research and Applications. Springer, Berlin, Heidelberg. 2011, pp. 416–427.
JD Tang, A Perkins, SV Diehl, et al. “Gene expression analysis of a copper-tolerant brown rot fungus on MCQ-treated wood.” In: 42nd Annual Meeting of the International Research Group on Wood Protection, Queenstown, New Zealand, 8-12 May 2011. IRG Secretariat. 2011.
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”. In: Pacific Sympoium on Biocomputing. 2017, pp. 646–648.
Tamer Aldwairi, Benjamin Elam, Federico Hoffmann, and Andy D Perkins. “RepCalc: a Tool For Calculating Transposable Element Density within the Genome”. In: Proceedings of the Tenth International Conference on Bioinformatics and Computational Biology. 2018.
Tamer Aldwairi, Federico Hoffmann, and Andy D Perkins. “Prediction Of Novel Pirna Rat Clusters Based On Mouse Pirna Clusters Using Downstream and Upstream Analysis”. In: Proceedings of 11th International Conference on Bioinformatics and Computational Biology. Vol. 60. 2019, pp. 190–199.
