Publications

For additional publications see my NCBI bibliography

2025

  1. Manuscript
    Investigating Bacterial Vaginosis Pathogenesis Using Peptide Nucleic Acid-Fluorescence In Situ Hybridization with a Focus on the Roles of Gardnerella Species, Prevotella bivia, and Fannyhessea vaginae
    Sheridan D. George, Megan H. Amerson-Brown, Lúcia G. V. Sousa, and 15 more authors
    Open Forum Infectious Diseases, Sep 2025
    Published 03 September 2025
  2. Manuscript
    Predicting Bacterial Vaginosis Development Using Artificial Neural Networks
    Jacob H. Elnaggar, John W. Lammons, Caleb M. Ardizzone, and 12 more authors
    medRxiv, May 2025
    Preprint; PMID: 40385447; PMCID: PMC12083586
  3. Manuscript
    The Impact of Testosterone Therapy on the Vaginal Microbiota of Transgender Men and Non-Binary People: A Prospective Study
    Olivia T. Van Gerwen, Kristal J. Aaron, Emma Sophia Kay, and 13 more authors
    Journal of Infectious Diseases, Sep 2025
    Published 15 September 2025
  4. Poster presentation
    Gene Expression of Gardnerella vaginalis in Clinical Specimens Reflects Polymicrobial Interactions in Bacterial Vaginosis
    Lúcia G. V. Sousa, Jacob H. Elnaggar, John Lammons, and 3 more authors
    Oct 2025
  5. Poster presentation
    Developing a Foundation Model of the Vaginal Microbiome: Early Prediction of Bacterial Vaginosis
    Urbi Chakravarty, John Lammons, Jacob Elnaggar, and 6 more authors
    Jul 2025
  6. Poster presentation
    Littoral Cell Angioma: A Rare Diagnosis
    Jacob Elnaggar, Donnel White, Christopher Cunningham, and 1 more author
    Apr 2025
  7. Poster presentation
    Navigating Diagnostic and Therapeutic Challenges in Small Lymphocytic Lymphoma: A Case with Multifocal Involvement
    Donnel White, Jacob Elnaggar, Christopher Cunningham, and 1 more author
    Feb 2025
  8. Poster presentation
    Enlarged Mystery: Unveiling Littoral Cell Angioma
    Jacob Elnaggar, Daniel White, Christopher Cunningham, and 1 more author
    Jan 2025

2024

  1. Manuscript
    A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population
    Grace J. Kim, Jacob H. Elnaggar, Mallory Varnado, and 10 more authors
    Frontiers in Immunology, May 2024
    eCollection 2024
  2. Manuscript
    The Role of Prevotella Species in Female Genital Tract Infections
    Sheridan D. George, Olivia T. Van Gerwen, Chaoling Dong, and 5 more authors
    Pathogens, Apr 2024
    Featured cover article
  3. Manuscript
    Microbial interactions among Gardnerella, Prevotella and Fannyhessea prior to incident bacterial vaginosis: protocol for a prospective, observational study
    Christina A. Muzny, Jacob H. Elnaggar, Lúcia G. V. Sousa, and 11 more authors
    BMJ Open, Feb 2024
    Published 05 February 2024
  4. Oral presentation
    Leveraging Machine Learning Techniques to Investigate the Pathogenesis of Incident Bacterial Vaginosis
    Jacob H. Elnaggar, Clayton Jacobs, Caleb M. Ardizzone, and 12 more authors
    Aug 2024

2023

  1. Manuscript
    Association of Chlamydia trachomatis burden with the vaginal microbiota, bacterial vaginosis, and metronidazole treatment
    Caleb M. Ardizzone, Christopher M. Taylor, Evelyn Toh, and 7 more authors
    Frontiers in Cellular and Infection Microbiology, Dec 2023
    eCollection 2023
  2. Manuscript
    Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring
    Lauren E. Colbert, Molly B. El Alam, Rui Wang, and 42 more authors
    Cancer Cell, Nov 2023
    Epub 19 Oct 2023
  3. Manuscript
    State of the Art for Diagnosis of Bacterial Vaginosis
    Christina A. Muzny, Nuno Cerca, Jacob H. Elnaggar, and 3 more authors
    Journal of Clinical Microbiology, Aug 2023
    Epub 18 May 2023
  4. Manuscript
    A novel Gardnerella, Prevotella, and Lactobacillus standard that improves accuracy in quantifying bacterial burden in vaginal microbial communities
    Jacob H. Elnaggar, Caleb M. Ardizzone, Nuno Cerca, and 7 more authors
    Frontiers in Cellular and Infection Microbiology, Jun 2023
    eCollection 2023
  5. Manuscript
    Characterization of Vaginal Microbial Community Dynamics in the Pathogenesis of Incident Bacterial Vaginosis, a Pilot Study
    Jacob H. Elnaggar, John W. Lammons, Christopher M. Taylor, and 10 more authors
    Sexually Transmitted Diseases, Aug 2023
    Epub 17 Apr 2023
  6. Manuscript
    HPV-related anal cancer is associated with changes in the anorectal microbiome during cancer development
    Jacob H. Elnaggar, Victoria O. Huynh, Daniel Lin, and 22 more authors
    Frontiers in Immunology, Mar 2023
    eCollection 2023
  7. Manuscript
    Impact of testosterone use on the vaginal microbiota of transgender men, including susceptibility to bacterial vaginosis: study protocol for a prospective, observational study
    Christina A. Muzny, Olivia T. Van Gerwen, Julia A. Schroeder, and 11 more authors
    BMJ Open, Mar 2023
    Published 27 March 2023
  8. Oral presentation
    Leveraging Machine Learning Techniques to Investigate the Pathogenesis of Incident Bacterial Vaginosis
    Jacob H. Elnaggar, Clayton Jacobs, Caleb M. Ardizzone, and 12 more authors
    Nov 2023
  9. Poster presentation
    A Preliminary Analysis of Vaginal Microbial Changes Prior to Incident Bacterial Vaginosis
    Jacob Elnaggar, Christopher M. Taylor, Caleb M. Ardizzone, and 9 more authors
    Jul 2023
  10. Poster presentation
    A Preliminary Analysis of Vaginal Microbial Changes Prior to Incident Bacterial Vaginosis as Determined by qPCR and Inferred Absolute Abundance
    Jacob Elnaggar, Christopher M. Taylor, Caleb M. Ardizzone, and 7 more authors
    Oct 2023

2022

  1. Manuscript
    Precision combination therapies based on recurrent oncogenic co-alterations
    Xubin Li, Elisabeth K. Dowling, Gonghong Yan, and 11 more authors
    Cancer Discovery, Jun 2022
    Published 02 June 2022
  2. Manuscript
    Microbiome Dynamics During Chemoradiotherapy for Anal Cancer
    Daniel Lin, Molly B. El Alam, Joseph Abi Jaoude, and 20 more authors
    International Journal of Radiation Oncology, Biology, Physics, Aug 2022
    Epub 02 May 2022
  3. Manuscript
    Mycoplasma decontamination in Chlamydia trachomatis culture: a curative approach
    Madison Greer, Jacob H. Elnaggar, Christopher M. Taylor, and 1 more author
    Pathogens and Disease, Jan 2022
    Published 12 January 2022
  4. Oral presentation
    Is Lactobacillus Phage Involved in the Pathogenesis of Bacterial Vaginosis?
    Jacob Elnaggar, John Lammons, Evelyn Toh, and 8 more authors
    Feb 2022
  5. Oral presentation
    Shotgun Metagenomic Sequencing of Longitudinal Vaginal Specimens: Is Lactobacillus Phage Involved in the Pathogenesis of Bacterial Vaginosis?
    Jacob Elnaggar, John Lammons, Evelyn Toh, and 8 more authors
    Jan 2022
  6. Poster presentation
    Changes in the Anorectal Microbiome of Anal Cancer and Anal Dysplasia
    Daniel Lin, Tyler Hillman, Molly El Alam, and 7 more authors
    Oct 2022
  7. Poster presentation
    Is Lactobacillus Phage Involved in the Pathogenesis of Bacterial Vaginosis?
    Jacob Elnaggar, Christopher M. Taylor, Evelyn Toh, and 8 more authors
    Aug 2022
  8. Poster presentation
    Precision Combination Therapies Based on Recurrent Oncogenic Co-Alterations
    Anil Korkut, Xubin Li, Emily Kong, and 11 more authors
    Apr 2022

2021

  1. Manuscript
    ATR Inhibitor M6620 (VX-970) Enhances the Effect of Radiation in Non-Small Cell Lung Cancer Brain Metastasis Patient-Derived Xenografts
    Andrew M. Baschnagel, Jacob H. Elnaggar, Haley J. VanBeek, and 10 more authors
    Molecular Cancer Therapeutics, Nov 2021
    Epub 19 Aug 2021
  2. Manuscript
    Integrating GWAS with Gene Expression Data to Map the Landscape of Luminal Androgen Receptor and Mesenchymal Subtypes of Triple Negative Breast Cancer
    Chindo Hicks, Jacob Elnaggar, and Jiande Wu
    Journal of Oncology Research and Therapy, Jan 2021
    Published 18 January 2021
  3. Poster presentation
    Shotgun Metagenomic Sequencing of Vaginal Specimens Suggests Potential Involvement of Lactobacillus Phage Preceding Incident Bacterial Vaginosis
    Jacob Elnaggar, Christopher M. Taylor, Evelyn Toh, and 7 more authors
    Apr 2021

2020

  1. Poster presentation
    Use of Shotgun Metagenomics to Investigate the Pathogenesis of Incident Bacterial Vaginosis
    Christopher M. Taylor, Evelyn Toh, Qun Dong, and 6 more authors
    Jul 2020

2019

  1. Manuscript
    An Integrative Genomics Approach for Associating Genetic Susceptibility with the Tumor Immune Microenvironment in Triple Negative Breast Cancer
    Jacob Elnaggar, Fei Tsien, Catherina Yates, and 3 more authors
    Biomedical Journal of Scientific & Technical Research, Feb 2019
  2. Poster presentation
    Assessing the Vaginal Bacterial Community Leading up to Incident Bacterial Vaginosis Using Shotgun Metagenomics Sequencing
    Jacob Elnaggar, Christina Muzny, and Christopher Taylor
    Oct 2019

2017

  1. Poster presentation
    Investigation of Adaptive Responses to Targeted Therapy in BRAF Inhibitor-Resistant Melanoma Cells
    Jacob Elnaggar, Xubin Li, and Anil Korkut
    Aug 2017

2015

  1. Poster presentation
    Chronic Binge Alcohol Administration Enhances Pre-frontal Cortex Apoptotic Signaling in SIV-Infected Rhesus Macaques
    Jacob Elnaggar, J. Maxi, and Patricia Molina
    Jul 2015