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.

Selected Publications

1. "Conjecturing-Based Disccovery of Patterns in Data," JP Brooks, DJ Edwards, CE Larson, N Van Cleemput, INFORMS Journal on Data Science, accepted December 2023. 

2. "Addressing Economic/Environmental Sustainability Tradeoffs in Procurement Episodes with Industrial Suppliers,"  LW Saunders, JP Brooks, J Merrick, CW Autry, Production and Operations Management Journal, 2020, 29:1256-1269.

3. "Racioethnic Diversity in the Dynamics of the Vaginal Microbiome during Pregnancy," MG Serrano, HI Parikh, JP Brooks, DJ Edwards, TJ Arodz, L Edupuganti, B Huang, PH Girerd, YA Bokhari, SP Bradley, JL Brooks, MR Dickinson, JI Drake, RA Duckworth, III, SS Fong, AL Glascock, S Jean, NR Jimenez, J Khoury, VN Koparde, AM Lara, V Lee, AV Matveyev, SH Milton, SD Mistry, SK Rozycki, NU Sheth, E Smirnova, SC Vividelli, NR Wijesooriya, J Xu, P Xu, DO Chaffin, AL Sexton, MG Gravett, CE Rubens, KD Hendricks-Munoz, KK Jefferson, JF Strauss, III, JM Fettweis, GA Buck, Nature Medicine, 2019, 25:1001-1011.

4. "The Vaginal Microbiome and Preterm Birth,"  JM Fettweis, MG Serrano, JP Brooks, DJ Edwards, PH Girerd, HI Parikh, B Huang, TJ Arodz, L Edupuganti, AL Glascock, J Xu, NR Jimenez, SC Vividelli, SS Fong, NU Sheth, S Jean, V Lee, YA Bokhari, AM Lara, SD Mistry, RA Duckworth, III, SP Bradley, VN Koparde, XV Orenda, SH Milton, SK Rozycki, AV Matveyev, ML Wright, SV Huzurbazar, EM Jackson, E Smirnova, J Korlach, Y-C Tsai, MR Dickinson, JL Brooks, JI Drake, DO Chaffin, AL Sexton, MG Gravett, CE Rubens, NR Wijesooriya, KD Hendricks-Munoz, KK Jefferson, JF Strauss, III, GA Buck, Nature Medicine, 2019, 25:1012-1021.

5. "Identifying Hospital Antimicrobial Resistance Targets via Robust Ranking,” JP Brooks, JH Dula, AL Pakyz, RE Polk, IISE Transactions on Healthcare Systems Engineering, 2017, 7:121-128. 

6. "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.

7. "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

8. "Solving a Mixed Integer Programming-Based Constrained Discrimination Model," JP Brooks, EK Lee, INFORMS Journal on Computing, 2014, 26:567-585.

9. "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

10. "The L1-norm Best-Fit Hyperplane Problem," JP Brooks, JH Dula, Applied Mathematics Letters, 2013, 26:51-55. Data Sets

11. "The Court of Appeals of Virginia Uses Integer Programming and Cloud Computing to Schedule Sessions,'' JP Brooks, Interfaces, 2012, 42:544-553.

12. "Coverings and Matchings in r-Partite Hypergraphs," DS Altner, JP Brooks, Networks, 2012, 59:400-410.

13. "Support Vector Machines with the Ramp Loss and the Hard Margin Loss," JP Brooks, Operations Research, 2011, 59:467-479.

Publication List on Google Scholar

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.

Editorial Activities

Area Editor, INFORMS Journal on Computing, Applications in Biology, Medicine, & Healthcare.

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