School of Graduate Studies

MD-PhD Program

jacob elnaggar

Jacob Elnaggar, Ph.D.
jelnag@lsuhsc.edu

Year:  L3

Hometown:  New Orleans, LA

Education:  B.S. Bioinformatics - Baylor University

Current research interest:  Vaginal Microbiome, Microbial Analysis Techniques, Bioinformatics

Career goal: A physician-scientist that will help move forward personalized treatments for the benefit of patients. 

Best thing about MD/PhD program:  The ability to study and combine my passion of Bioinformatics with the medical field along with the support and guidance of LSUHSC's supportive faculty and physicians.

Hobbies: Tennis, film photography, hiking, web development, and trying new foods.

What makes me unique:  My background is unique. I am a melting pot of culture resulting from my family, hometown, and education.

What makes me common: I love a good cup of coffee.

Research Experience

LSUHSC, MD/PhD Program, New Orleans, LA, June 2018 - Present
• I worked in the Christopher Taylor Lab in the department of Microbiology, Immunology, and Parasitology.
• My goal is to better understand the pathophysiology of bacterial vaginosis to inform diagnosis, treatment, and prevention.
• Learning analysis of longitudinal 16S rRNA and Shotgun Metagenomics Sequencing of the vaginal microbiome of women with bacterial vaginosis.
• Dissertation: Investigating the Temporal Dynamics of the Vaginal Microbiome Prior to Incident Bacterial Vaginosis

MD Anderson Cancer Center, Joint appointed graduate student, Houston, TX, June 2020 – Present
• I worked in the Dr. Lauren Colbert Lab to understand the relationship between the human microbiome and cancer growth and treatment response.
• My project investigated cervical dysbiosis and its relationship with the progression of HPV derived cervical dysplasia to cancer.

MD Anderson Cancer Center, CPRIT-CURE Summer Undergraduate Program, Houston, TX, June 2017 - August 2017
• Worked in the Anil Korkut Lab within the Department of Bioinformatics and Computational Biology.
• There, I implemented a computational model that analyzes treatment resistant melanoma cell lines to nominate novel therapies utilizing proteomics and machine learning.

Baylor University, Bioinformatics Capstone, Waco, TX, August 2016 - December 2016
• Worked with Erich Baker, PhD, on his bioinformatics website, www.Geneweaver.org.
• Created an algorithm for users to compare multiple gene interaction networks, allowing biologists to discover underlying patterns in specific disease models.

LSUHSC Bioinformatics and Genomics Program, New Orleans, LA, June 2016 - August 2016
• Participated in the LSUHSC Undergraduate Research Program in the Chindo Hicks Lab within the Department of Genetics.
• Analyzed public genomic data for predispositions to triple negative breast cancer
• Published manuscript titled, “An Integrative Genomics Approach for Associating Genetic Susceptibility with the Tumor Immune Microenvironment in Triple Negative Breast Cancer”

LSUHSC Summer Undergraduate Research Program, New Orleans, LA, June 2015 - August 2015
• Worked in the Patricia Molina and Liz Simon Labs in the Department of Physiology whose focus is on chronic alcoholism and HIV/AIDS.
• I investigated the combined effects of chronic binge alcohol administration and simian immunodeficiency virus (SIV) on cell apoptosis in the prefrontal cortex of Rhesus macaques.

Selected Publications:

  1. Kim GJ, Elnaggar JH, Varnado M, Feehan AK, Tauzier D, Rose R, Lamers SL, Sevalia M, Nicholas N, Gravois E, Fort D, Crabtree JS, Miele L. A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population. Front Immunol. (2024-05-08). doi:3389/fimmu.2024.1357731
  2. Ardizzone CM, Taylor CM, Toh E, Lillis RA, Elnaggar JH, Lammons JW, Mott PD, Duffy EL, Shen L, Quayle AJ. Association of Chlamydia trachomatis burden with the vaginal microbiota, bacterial vaginosis, and metronidazole treatment. Front Cell Infect Microbiol. (2023-12-12). doi:3389/fcimb.2023.1289449
  3. Colbert LE, El Alam MB, Wang R, Karpinets T, Lo D, Lynn EJ, Harris TA, Elnaggar JH, Yoshida-Court K, Tomasic K, Bronk JK, Sammouri J, Yanamandra AV, Olvera AV, Carlin LG, Sims T, Delgado Medrano AY, Napravnik TC, O’Hara M, Lin D, Abana CO, Li HX, Eifel PJ, Jhingran A, Joyner M, Lin L, Ramondetta LM, Futreal AM, Schmeler KM, Mathew G, Dorta-Estremera S, Zhang J, Wu X, Ajami NJ, Wong M, Taniguchi C, Petrosino JF, Sastry KJ, Okhuysen PC, Martinez SA, Tan L, Mahmud I, Lorenzi PL, Wargo JA, Klopp AH. Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring. Cancer Cell. (2023-11-13). doi:1016/j.ccell.2023.09.012
  4. Muzny CA, Cerca N, Elnaggar JH, Taylor CM, Sobel JD, Van Der Pol B. State of the Art for Diagnosis of Bacterial Vaginosis. Humphries RM, ed. J Clin Microbiol. Published online (2023-05-18). doi:1128/jcm.00837-22
  5. Muzny CA, Van Gerwen OT, Schroeder JA, Kay-Duncan ES, Siwakoti K, Aaron KJ, Eastlund IC, Graves KJ, Elnaggar JH, Tamhane A, Long D, Van Wagoner N, Toh E, Taylor CM. Impact of testosterone use on the vaginal microbiota of transgender men, including susceptibility to bacterial vaginosis: study protocol for a prospective, observational study. BMJ Open. (2023-03-27). doi:1136/bmjopen-2023-073068
  6. Elnaggar JH, Ardizzone CM, Cerca N, Toh E, Łaniewski P, Lillis RA, Herbst-Kralovetz M, Quayle AJ, Muzny CA, Taylor CM. A novel Gardnerella, Prevotella, and Lactobacillus standard that improves accuracy in quantifying bacterial burden in vaginal microbial communities. Cell. Infect. Microbiol Sec. Biofilms. (2023-06-19) doi: 10.3389/fcimb.2023.1198113
  7. Elnaggar JH, Lammons JW, Taylor CM, Toh E, Ardizzone CM, Dong A, Aaron KJ, Luo M, Tamhane A, Lefkowitz EJ, Quayle AJ, Nelson DE, Muzny CA. Characterization of Vaginal Microbial Community Dynamics in the Pathogenesis of Incident Bacterial Vaginosis, a Pilot Study. Sexual Trans Dis. (2023-08-17). doi:1097/OLQ.0000000000001821
  8. Elnaggar JH, Huynh VO, Lin D, Hillman RT, Abana CO, El Alam MB, Tomasic KC, Karpinets TV, Kouzy R, Phan JL, Wargo J, Holliday EB, Das P, Mezzari MP, Ajami NJ, Lynn EJ, Minsky BD, Morris VK, Milbourne A, Messick CA, Klopp AH, Futreal PA, Taniguchi CM, Schmeler KM, Colbert LE. HPV-related anal cancer is associated with changes in the anorectal microbiome during cancer development. Front Immunol. (2023-03-28). doi:3389/fimmu.2023.1051431
  9. Greer M, Elnaggar, JH, Taylor CM, Shen L. Mycoplasma decontamination in Chlamydia trachomatis culture: a curative approach. Pathogens and Disease. (2022-01-12). doi:1093/femspd/ftab056 PMID: 34918079 PMCID: PMC8759436
  10. Baschnagel, A. M., Elnaggar, JH, VanBeek, H. J., Kromke, A. C., Skiba, J. H., Kaushik, S., Abel, L., Clark, P. A., Longhurst, C. A., Nickel, K. P., Leal, T. A., Zhao, S. G., Kimple, R. J. ATR inhibitor M6620 (VX-970) enhances the effect of radiation in non-small cell lung cancer brain metastasis patient derived xenografts. Molecular Cancer Therapeutics. (2021-08-19). https://doi.org/10.1158/1535-7163.MCT-21-0305 PMID: 34413128 PMCID: PMC8571002
  11. Elnaggar J, Tsien F, Yates C, Davis M, Miele L, Hicks C. An Integrative Genomics Approach for Associating Genetic Susceptibility with the Tumor Immune Microenvironment in Triple Negative Breast Cancer. Biomedical Journal of Scientific & Technical Research. (2019-02-25). doi:26717/BJSTR.2019.15.002642.

Complete List of Published Work in My Bibliography:

https://www.ncbi.nlm.nih.gov/myncbi/jacob.elnaggar.2/bibliography/public/  

Find out more about me at www.JacobElnaggar.com