Paul Brooks

Peer-Reviewed Journal Articles

  • Decomposition of Flux Distributions into Metabolic Pathways, O Seref, JP Brooks, and SS Fong. Accepted to IEEE/ACM Transactions on Computational Biology and Bioinformatics, September 2013.
  • Solving a Mixed Integer Programming-Based Constrained Discrimination Model, JP Brooks and EK Lee. Accepted to INFORMS Journal on Computing, February 2013.
  • Workforce Assessment Method for an Urban Police Department: Using Analytics to Estimate Patrol Staffing, S Srinivasan, TP Sorrell, JP Brooks, DJ Edwards, RL Diehl. Accepted to Policing: An International Journal of Police Strategies & Managment, February 2013.
  • Relaxing Support Vectors for Classification. O Seref, WA Chaovlitwongse, JP Brooks. Accepted to Annals of Operations Research, July 2012.
  • Another Look at Foldover for Two-Level Nonregular Designs. DJ Edwards and JP Brooks. Communications in Statistics: Simulation and Computation, 2014, 43:209-224.
  • A Pure L1-Norm Principal Component Analysis. JP Brooks, JH Dula, and EL Boone. Computational Statistics and Data Analysis, 2013, 61:83-98.
  • The L1-norm best-fit hyperplane problem. JP Brooks and JH Dula. Applied Mathematics Letters, 2013, 26:51-55.
  • Uncertainty quantification for a Middle East water supply system. RE Bullene, JP Brooks, EL Boone, C Lipchin, TP Sorrell, CR Stewart. Journal of Water Resources Planning and Management, 2013, 139:223-234.
  • Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data. PS LaRosa, JP Brooks, E Deych, EL Boone, DJ Edwards, Q Wang, E Sodergren, G Weinstock and W Shannon. PLOS ONE, 2012, 7, e52078.
  • Species-level classification of the vaginal microbiome. JM Fettweis, MG Serrano, NU Sheth, CM Mayer, AL Glascock, JP Brooks, KK Jefferson, Vaginal Microbiome Consortium, and GA Buck. BMC Genomics, 2012, 13, S17.
  • The Court of Appeals of Virginia uses integer programming and cloud computing to schedule sessions. JP Brooks. Accepted to Interfaces, May 2011.
  • Gap detection for genome-scale constraint-based models. JP Brooks, WP Burns, SS Fong, CM Gowen, SB Roberts. Accepted to Advances in Bioinformatics, vol 2012, Article ID 876976. doi:10.1155/2012/323472.
  • Structure, function and diversity of the human microbiome in an adult reference population. The Human Microbiome Consortium. Nature, 2012, 486:207-214.
  • A framework for human microbiome research. The Human Microbiome Consortium. Nature, 2012, 486:215-221.
  • Coverings and matchings in r-partite hypergraphs. DS Altner and JP Brooks. Networks, 2012, 59:349-410.
  • Analyzing the volume and nature of emergency medical calls during severe weather events using regression methodologies. LA McLay, JP Brooks, EL Boone. Socio-Economic Planning Sciences, 2012, 46:55-66.
  • Support vector machines with the ramp loss and the hard margin loss. JP Brooks. Operations Research, 59:467-479, 2011.
  • Outlier-resistant L1 orthogonal regression via the reformulation-linearization technique. JP Brooks, EL Boone. Advances in Operations Research, 2011, doi:10.1155/2011/263762, available here.
  • Genome-scale metabolic modeling and analysis of clostridium thermocellulm for bioethanol production. SB Roberts, CM Gowen, JP Brooks, and SS Fong. BMC Systems Biology, 4:31, 2010.
  • Analysis of the consistency of a mixed integer programming-based multi-category constrained discriminant model. JP Brooks and EK Lee. Annals of Operations Research, 174:147-168, 2010.
  • Measurable notions of complexity and their relationship to biological complexity. JP Brooks. Chemistry and Biodiversity, 4:2656-2660, 2007.
  • Automated planning volume definition in soft-tissue sarcoma adjuvant brachytherapy. EK Lee, AYC Fung, JP Brooks, and M Zaider. Physics in Medicine and Biology, 47:1891-1910, 2002.

    Conference Proceedings Papers

  • Simulating calls for service for an urban police department. JP Brooks, DJ Edwards, TP Sorrell, S Srinivasan, and RL Diehl. Proceedings of the Winter Simulation Conference, Phoenix, AZ, December 2011.
  • Methods for the analysis of microbioime data. JP Brooks, M Rivera, EL Boone, DJ Edwards, Q Wang, P LaRosa, W Shannon, Proceedings of the Workshop on Data Mining and Health Informatics, INFORMS Annual Meeting, Charlotte, NC, November 2011.
  • Locally linear support vector machines and other local models. V Kecman and JP Brooks. International Joint Conference on Neural Networks, July 2010.
  • A Bayesian simulation model for Middle East water distribution. EL Boone, JP Brooks, RE Bullene, and C Lipchin, Center for Integrative Mediterranean Studies Conference, Richmond, VA, September 2009.
  • Robust support vector machines via integer programming. JP Brooks, R Shioda, and A Spencer. Proceedings of the Artificial Intelligence and Data Mining Workshop, INFORMS Annual Meeting, November 2007.
  • Mixed integer programming constrained discrimination model for credit screening. JP Brooks and EK Lee. Proceedings of the Business and Industry Symposium, Spring Simulation Multiconference, Norfolk, VA, March 2007.
  • Solving a mixed-integer programming formulation of a multi-category constrained discrimination model. JP Brooks and EK Lee. Proceedings of the Artificial Intelligence and Data Mining Workshop, INFORMS Annual Meeting, November 2006.

    R Package, Book Review, Book Chapter

  • pcaL1: Three L1-norm PCA methods, R package. S Jot and JP Brooks. Available here, released April 2012.
  • Review of Data Analysis with Open Source Tools by P.K. Janert. JP Brooks. INFORMS Journal on Computing, 23:BR1-BR4, 2011, available here.
  • Transportation algorithms. DS Altner and JP Brooks. Wiley Encyclopedia of Operations Research and Management Science, Ed. JJ Cochran, Wiley, 2011.

    Funded Research

  • Jeffress Foundation Trust Awards Program in Interdisciplinary Research, Fall 2013-Summer 2014, co-PI, PI: David Edwards.
  • NIH U54, A Multi-omic Analysis of the Vaginal Microbiome, Fall 2013-Summer 2016, co-investigator, PI: Greg Buck.
  • NIH P60, VCU National Institutes on Minority Health and Health Disparities, Summer 2012-Spring 2017, co-investigator, PI: Jerry Strauss.
  • Richmond Police Department, Workforce Assessment and Scheduling, Fall 2010-Summer 2011, PI.
  • NASA NNX09AR44A, NRA research opportunities in space and earth sciences 2008, Fall 2009-Fall 2012, co-PI, PI: Stephen Fong.
  • NIH-NIAID Award UH2/UH3AI08326-01, The vaginal microbiome: disease, genetics, and the environment, Spring 2009-Fall 2013, co-investigator, PIs: Greg Buck, Cindy Cornelissen, Lindon Eaves, Jerry Strauss.
  • VCU College of Humanities and Sciences Career Scholarship Enhancement Award, Optimization-based metabolic models for biofuel development, Spring 2008-Summer 2009, PI.

    Thesis Supervision (completed)

  • Radha Koripalli, M.S., Statistics
  • Katherine Perry, M.S., Operations Research
  • Umaporn Siangphoe, M.S., Bioinformatics
  • Sapan Jot, M.S., Statistics
  • Rachel Bullene, M.S., Operations Research
  • Michael Hobson, M.S., Operations Research
  • Charles Stewart, M.S., Operations Research
  • Yasser Tanvir, M.S., Operations Research
  • Yonathan Negash, M.S., Operations Research
  • Bandana Kumari, M.S., Operations Research

    Professional Societies, etc.

    INFORMS - Institute for Operations Research and the Management Sciences
    INFORMS Section on Data Mining
    INFORMS Computing Society
    INFORMS Optimization Society
    Mathematical Optimization Society
    KDnuggets
    Biomathematics at VCU
    Vaginal Microbiome Consortium

    VCU Research Guide for Operations Research and Statistics

    VCU Research Guide

    Analytics Magazine

    Analytics, a digital magazine published by the Institute for Operations Research and the Management Science (INFORMS), provides readers with real-life examples of how data, modeling and mathematical analysis is used to drive better business decisions and provide concrete competitive advantage.

    Paul Brooks
    Date last modified: September 17, 2013.