google-plus
utulsa.edu

Brett McKinney PhD

Associate Professor of Computer Science and William K. Warren, Jr., Associate Professor of Bioinformatics College of Engineering & Natural Sciences
Computer Science
Rayzor Hall 2145 918-631-3444
brett-mckinney@utulsa.edu
faculty-photo

Biography

Brett McKinney has a joint appointment in the Department of Mathematics and Tandy School of Computer Science. He is a native Tulsan who did his undergraduate work summa cum laude at The University of Tulsa in mathematics and physics. He did his graduate work at the University of Oklahoma, obtaining a Ph.D. in theoretical physics, followed by a postdoctoral fellowship in biomathematics and computational biology at the Vanderbilt University Medical Center. He was an assistant professor in the Department of Genetics at the University of Alabama Birmingham School of Medicine before joining TU in 2009.



Ph.D., University of Oklahoma
M.S., University of Oklahoma
B.S., The University of Tulsa


Bioinformatics
Statistical Genetics
Mathematical Biology
Mathematical Physics

Scientific Computing
Machine Learning
Bioinformatics
Network Theory


The following may be selected publications rather than a comprehensive list.

Journal Articles


Oberg, A.L. et al. “Lessons Learned in the Analysis of High-Dimensional Data in Vaccinomics.” Vaccine S0264-410X.15 (2015): 00574–5. Print.

Lareau, C. et al. “Differential Co-Expression Network Centrality and Machine Learning Feature Selection for Identifying Susceptibility Hubs in Networks with Scale-Free Structure.” BioData mining 8 (2015): 5. Print.

Briney, J. et al. “Tissue-Specific Expressed Antibody Variable Gene Repertoires.” PLoS ONE (2014): n. pag. Print.

Davis, N. et al. “Encore: Genetic Association Interaction Network Centrality Pipeline and Application to SLE Exome Data.” Genetic Epidemiology (2013): n. pag. Print.

McKinney, Brett et al. “ReliefSeq: A Gene-Wise Adaptive-k Nearest-Neighbor Feature Selection Tool for Finding Gene-Gene Interactions and Main Effects in MRNA-Seq Gene Expression Data.” PLoS ONE 8.12 (2013): e81527. Print.

Poland, G. et al. “Vaccinomics, Adversomics, and the Immune Response Network Theory: Individualized Vaccinology in the 21st Century.” Seminars in Immunology (2013): n. pag. Print.

Louie, R.J. et al. “A Yeast Phenomic Model for the Gene Interaction Network Modulating CFTR-DeltaF508 Protein Biogenesis.” Genome Med. 4.12 (2012): 103. Print.

Savitz, Jonathan et al. “Inflammation and Neurological Disease-Related Genes Are Differentially Expressed in Depressed Patients with Mood Disorders and Correlate with Morphometric and Functional Imaging Abnormalities.” Brain Behav. Immun. S0889-1591.12 (2012): 00469–2. Print.

Pajewski, N.M. et al. “A Genome-Wide Association Study of Host Genetic Determinants of the Antibody Response to Anthrax Vaccine Adsorbed.” Vaccine 30.32 (2012): 4778–84. Print.

Briney, B.S. et al. “High-Throughput Antibody Sequencing Reveals Genetic Evidence of Global Regulation of the Naïve and Memory Repertoires That Extends across Individuals.” Genes and Immunity (Nature Publishing) (2012): n. pag. Print.

Crooke, P. et al. “Mathematical Modeling of Patient Care.” Computational and Mathematical Methods in Medicine (2012): 2. Print.

Pandey, A. et al. “Epistasis Network Centrality Analysis Yields Pathway Replication across Two GWAS Cohorts for Bipolar Disorder.” Translational Psychiatry 2 (2012): e154. Print.

McKinney, Brett, and N. Pajewski. “Six Degrees of Epistasis: Statistical Network Models of GWAS.” Frontiers in Statistical Genetics and Methodology 2.109 (2012): n. pag. Print.

Pajewski, N. et al. “The Role of HLA DR-DQ Haplotypes in Variable Antibody Response to Anthrax Vaccine Adsorbed.” Genes and Immunity (Nature Publishing) (2011): n. pag. Print.

Davis, N., Ahwan Pandey, and Brett McKinney. “Real-World Comparison of CPU and GPU Implementations of SNPrank: a Network Analysis Tool for Genome-Wide Association Studies.” Bioinformatics 27.2 (2011): 284–285. Print.

Rock, M. et al. “Identification of Potential Human Respiratory Syncytial Virus and Metapneumovirus T Cell Epitopes Using Computational Prediction and MHC Binding Assays.” Journal of Immunological Methods (2011): n. pag. Print.

Guo, J. et al. “Recursive Expectation-Maximization Clustering (REMc): A Method for Identifying Buffering Mechanisms Composed of Phenomic Modules.” Chaos: An Interdisciplinary Journal of Nonlinear Science 5.2 (2010): 026103. Print.

Davis, N. et al. “Surfing a Genetic Association Interaction Network to Identify Modulators of Antibody Response to Smallpox Vaccine.” Genes and Immunity (Nature Publishing) (2010): n. pag. Print.

McKinney, Brett. “New Informatics Approaches for Identifying Biologic Relationships in Time Series Data.” Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology 1 (2009): 60–68. Print.

McKinney, Brett et al. “Capturing the Spectrum of Interaction Effects in Genetic Association Studies by Simulated Evaporative Cooling Network Analysis.” PLoS Genetics 5.3 (2009): e1000432. Print.

Wright, Peter et al. “The Dengue Virus Type 4 Vaccine Candidate rDEN430-4995 Is Highly Attenuated, Safe, and Immunogenic in Healthy Adult Volunteers.” Am. J. Trop. Med. Hyg. (2009): n. pag. Print.

Reif, D. et al. “Integrated Analysis of Genetic and Proteomic Data Identifies Biomarkers Associated with Adverse Events Following Smallpox Vaccination.” Genes and Immunity 10 (2009): 112–119. Print.

Faley, S. et al. “Microfluidic Platform for Real-Time Signaling Analysis of Multiple Single T Cells in Parallel.” Lab Chip 8 (2008): 1700–1712. Print.

Reif, D.M. et al. “Genetic Basis for Adverse Events Following Smallpox Vaccination.” Journal of Infectious Diseases 198 (2008): 16–22. Print.

Bibollet-Ruche, F. et al. “Antibody-Mediated Activation of Chimpanzee T Cells via the TCR/CD3 Pathway Is a Function of the Anti-CD3 Antibody Isotype.” Journal of Virology 82 (2008): 10271–10278. Print.

McKinney, Brett, and D. Tian. “Grammatical Immune System Evolution for Reverse EngineeringNonlinear Dynamic Bayesian Models.” Cancer Informatics 6 (2008): 433–447. Print.

Kallewaard, N. et al. “Functional Maturation of the Human Antibody Response to Rotavirus.” The Journal of Immunology 180 (2008): 3980–3989. Print.

Bush, W.S. et al. “Alternative Contingency Table Measures Improve the Power and Detection of Multifactor Dimensionality Reduction.” BMC Bioinformatics 9 (2008): 238. Print.

Xie, J. et al. “A Computational Model of Quantitative Chromatin Immunoprecipitation (ChIP) Analysis.” Cancer Informatics 4 (2008): 137–145. Print.

McKinney, Brett et al. “Evaporative Cooling Feature Selection for Genotypic Data Involving Interactions.” Bioinformatics 23 (2007): 2113–2120. Print.

McKinney, Brett et al. “Using the Natural Evolution of a Rotavirus-Specific Human Monoclonal Antibody to Predict the Complex Topography of a Viral Antigenic Site.” Immunome Research 3.8 (2007): n. pag. Print.

Reif, D. et al. “Feature Selection Using a Random Forest Classifier for the Integrated Analysis of Multiple Data Types.” Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (2006): 171–178. Print.

McKinney, Brett et al. “Machine Learning for Detecting Gene-Gene Interactions.” Applied Bioinformatics 5.2 (2006): 77–88. Print.

McKinney, Brett et al. “Hybrid Grammar-Based Approach to Nonlinear Dynamical System Identification from Biological Time Series.” Physical Review E, Statistical, Nonlinear, and Soft Matter Physics 73 (2006): 021912. Print.

McKinney, Brett et al. “Cytokine Expression Patterns Associated with Systemic Adverse Events Following Smallpox Immunization.” Journal of Infectious Diseases 194.4 (2006): 36092. Print.

McKinney, Brett et al. “N Identical Particles under Quantum Confinement: a Many-Body Dimensional Perturbation Theory Approach.” Annals of Physics 310 (2004): 56. Print.

McKinney, Brett, M. Dunn, and D.K. Watson. “Beyond-Mean-Field Results for Atomic Bose-Einstein Condensates at Interaction Strengths near Feshbach Resonances: A Many-Body Dimensional Perturbation Theory Calculation.” Phys. Rev. A 69 (2004): 043611. Print.

McKinney, Brett, and D.K. Watson. “Bose-Einstein Condensation in Variable Dimensionality.” Phys. Rev. A 65 (2002): 33604. Print.

McKinney, Brett, and D.K. Watson. “Semiclassical Dimensional Perturbation Theory for Two Electrons in a D-Dimensional Quantum Dot.” Phys. Rev. B 61 (2000): 4958. Print.

Watson, D.K., and Brett McKinney. “An Improved Large-N Limit for Bose-Einstein Condensates from Perturbation Theory.” Phys. Rev. A 59 (1999): 4091. Print.

Book Chapter


Lareau, C., and Brett McKinney. “Network Theory for Data-Driven Epistasis Networks.” Epistasis: Method and Protocols, Methods in Molecular Biology. Vol. 1253. 2015. 285–300. Print.

Conference Proceeding


Carley, C. et al. “Using a Shared, Remote Cluster for Teaching HPC.” IEEE Cluster. 2013. Print.


BIOL 6383 Selected Topics in Biological Science
CS 2503 Scientific Programming
CS 4643 Bioinformatics
CS 4971 Research and Computer Sciences Literature
CS 5863 Special Topics
CS 7983 Research and Thesis
CS 9981 Research and Dissertation
ES 2510 Engineering Applications Programming Lab
ES 2513 Engineering Applications Programming
TURC 1981 TURC Junior Scholar