Research

The core of my research program is the use of optimization to design new methods for data analysis.  I also work in areas applying these methods to data, and in other areas of applied optimization.  Application areas include human microbiome research, modeling of bacterial metabolism, public sector operations, scheduling, manufacturing, and inventory management.  I am currently the Statistics and Analysis Team Leader for the VMC MOMS-PI project based at VCU, an NIH-funded project for studying the role of the microbiome during pregnancy and childbirth. 

Selected Publications
  1. "Enumeration and Cartesian Product Decomposition of Alternate Optimal Fluxes in Cellular Metabolism," O Seref, JP Brooks, B Huang, SS Fong, INFORMS Journal on Computing, 2017, 29:197-210.
  2. "The Truth about Metagenomics: Quantifying and Counteracting Bias in 16S rRNA Studies," JP Brooks, DJ Edwards, MD Harwich, Jr., MC Rivera, JM Fettweis, MG Serrano, RA Reris, NU Sheth, B Huang, P Girerd, The Vaginal Microbiome Consortium (additional members), JF Strauss, III, KK Jefferson, GA Buck, BMC Microbiology, 2015, 15:66. Accompanying Code and Data
  3. "Solving a Mixed Integer Programming-Based Constrained Discrimination Model," JP Brooks, EK Lee, INFORMS Journal on Computing, 2014, 26:567-585.
  4. "A Pure L1-Norm Principal Component Analysis," JP Brooks, JH Dula, EL Boone, Computational Statistics & Data Analysis, 2013, 61:83-98. Accompanying Code and Data
  5. "The L1-norm Best-Fit Hyperplane Problem," JP Brooks, JH Dula, Applied Mathematics Letters, 2013, 26:51-55. Data Sets
  6. "Decomposition of Flux Distributions into Metabolic Pathways," O Seref, JP Brooks, SS Fong, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, 10:984-993.
  7. "The Court of Appeals of Virginia Uses Integer Programming and Cloud Computing to Schedule Sessions,'' JP Brooks, Interfaces, 2012, 42:544-553.
  8. "Gap Detection for Genome-Scale Constraint-Based Models," JP Brooks, WP Burns, SS Fong, CM Gowen, SB Roberts, Advances in Bioinformatics, vol 2012, Article ID 876976, 10 pages, 2012.  doi:10.1155/2012/323472.
  9. "Coverings and Matchings in r-Partite Hypergraphs," DS Altner, JP Brooks, Networks, 2012, 59:400-410.
  10. "Support Vector Machines with the Ramp Loss and the Hard Margin Loss," JP Brooks, Operations Research, 2011, 59:467-479.

R Package
pcaL1: L1-Norm PCA Methods.  S Jot, JP Brooks, A Visentin, YW Park, Y-H Zhou.

PCA Tutorial
R Code to Accompany “Principal Component Analysis and Optimization: A Tutorial,” RA Reris, JP Brooks, Operations Research & Computing: Algorithms & Software for Analytics. B Borchers, JP Brooks, LA McLay, editors.  14th INFORMS Computing Society Conference (ICS2015), Richmond, Virginia, January 2015.

Conference Volume
Operations Research & Computing: Algorithms & Software for Analytics.  B Borchers, JP Brooks, LA McLay, editors.  14th INFORMS Computing Society Conference (ICS2015).

https://www.informs.org/Find-Research-Publications/Multimedia-Books/ICS-Proceedings/2015-Conference-Volume


Selected Grants
  • NIJ, "Forensic Body Fluid Identification using Microbiome Signature Attribution," Sp 2017-Fa 2018, co-PI, PI: Baneshwar Singh.
  • NSF Subaward 5100551 of DMS-1127914, "Statistical and Applied Mathematical Sciences Institute," Fa 2014-Sp2015, PI.
  • NSF Award 1416675, "The 2015 INFORMS Computing Society Conference NSF Student Poster Session," Fa 2014-Fa 2015, PI.
  • NIH Award 8U54HD080784, "A Multi-omic Analysis of the Vaginal Microbiome," Fa 2013-Sp 2017, co-investigator, PI: Greg Buck.
  • Jeffress Foundation Trust Awards Program in Interdisciplinary Research, "The Truth about Bacterial Metagenomics: Uncovering Bias using Mixture Effect Models," Fa 2013-Su 2015, co-PI, PI: David Edwards.
  • NIH-NIHMD Award 2P60MD002256-06, "VCU National Institutes on Minority Health and Health Disparities," Su 2012-Sp 2017, co-investigator, PI: Jerry Strauss.
  • Richmond Police Department, "Workforce Assessment and Scheduling," Fa 2010-Su 2012, PI.
  • NASA NNX09AR44A, "NRA research opportunities in space and earth sciences 2008," Fa 2009-Fa 2013, co-PI, PI: Stephen Fong. 
  • NIH-NIAID Award UH2/UH3AI08326-01, "The Vaginal Microbiome: Disease, Genetics, and the Environment,"  Sp 2009-Fa 2013, co-investigator, PIs: Greg Buck, Cindy Cornelissen, Lindon Eaves, Jerry Strauss.

Professional Societies