Samuel Jenness, PhD

Assistant Professor // Department of Epidemiology

Rollins School of Public Health // Emory University

I am an infectious disease epidemiologist specializing in mathematical and computational approaches for studying the drivers of and prevention strategies for infectious disease through the framework of dynamic transmission networks.

As an Assistant Professor in the Department of Epidemiology at the Rollins School of Public Health of Emory University, I lead the EpiModel Research Lab and also collaborate on several projects in both methods and applications for infectious disease epidemiology.

Research Interests

My methodological research focuses on the development of an open-souce software platform for epidemic modeling, EpiModel, which allows users to build, simulate, and analyze complex mechanistic models for transmission of arbitrarily defined infectious disease systems. EpiModel provides a powerful toolkit for modeling dynamic contact networks that are often fundamental for representing transmission of diseases requiring direct contact. EpiModel has been used in over 50 scientific publications, both by my group and modeling researchers around the world!

My applied research focuses on the epidemiology of HIV, sexually transmitted infections, and other infectious diseases. I am interested in how we can use mechanistic modeling and network science frameworks to understand the drivers of these diseases, and to design and evaluate effective prevention strategies. Recent applications have used models to simulate the co-circulation of multiple co-circulating pathogens within the same population, since the risk factors for acquiring one disease may depend on the epidemic dynamics of other infections transmitted along the same contact network.

More broadly, the work of my EpiModel Research Lab involves addressing these questions with research in the following domains:

  • Infectious disease epidemiology
  • Mechanistic/mathematical modeling of infectious disease
  • Network science
  • Causal inference methods for epidemiology
  • Survey research design and analysis
  • Computational epidemiology & scientific software development
I actively support and mentor PhD students, post-docs, and research staff who work with me in these areas.

News

2020-11-15

New paper published in AIDS: Modeling an Integrated HIV Prevention and Care Continuum to Achieve the Ending the HIV Epidemic Goals

2020-09-30

New pre-print in medRxiv: Projected HIV and Bacterial STI Incidence Following COVID-Related Sexual Distancing and Clinical Service Interruption

2020-09-03

New paper led by Kevin Maloney published in Journal of Infectious Diseases: Projected Impact of Concurrently Available Long-Acting Injectable and Daily-Oral HIV Pre-Exposure Prophylaxis

2020-09-30

New pre-print in medRxiv: Modeling Dynamic Network Strategies for SARS-CoV-2 Control on a Cruise Ship

2020-07-23

New paper led by Christina Chandra published in Clinical Infectious Diseases: Gaps in Screening of Sexually Transmitted Infections among Men Who Have Sex with Men during PrEP Care in the United States

2020-07-01

New paper led by Kristin Nelson published in the American Journal of Epidemiology: Modeling Missing Cases and Transmission Links in Networks of Extensively Drug-Resistant Tuberculosis in KwaZulu-Natal, South Africa

2020-03-01

New paper led by Kevin Weiss published in JAIDS: Estimated Number of Men Who Have Sex With Men With Indications for HIV Pre-exposure Prophylaxis in a National Sexual Network Study

2020-03-01

New paper led by Stephen Uong published in Epidemiology: Assessing the Validity of Sexual Network Degree among Men Who Have Sex with Men using Prospective Cohort Data

2020-01-24

New paper led by Kevin Weiss published in Epidemics: Egocentric Sexual Networks of Men Who Have Sex with Men in the United States: Results from the ARTnet Study

2019-11-01

New paper led by Kevin Weiss published in Sexually Transmitted Diseases: Epidemiological Impact of Expedited Partner Therapy for Men Who Have Sex with Men: A Modeling Study

2019-10-25

New paper led by Kevin Weiss published in Open Forum Infectious Diseases: Optimizing Coverage versus Frequency for Sexually Transmitted Infection Screening of Men Who Have Sex with Men

2019-06-07

New paper led by Jeb Jones published in Sexually Transmitted Diseases: Proportion of Incident HIV Cases among Men Who Have Sex with Men Attributable to Gonorrhea and Chlamydia: A Modeling Analysis.

2018-10-11

New paper published in American Journal of Epidemiology: Addressing Gaps in HIV Preexposure Prophylaxis Care to Reduce Racial Disparities in HIV Incidence in the United States.

2018-07-29

New paper published in Sexually Transmitted Diseases: Bacterial STI Screening Rates by Symptomatic Status among Men Who Have Sex with Men in the United States: A Hierarchical Bayesian Analysis.

2018-07-12

Received new major research funding (my first R01 funding as a PI) from NIH/NIAID (R01 AI138783) for a project to develop and extend the EpiModel platform to address the next generation of important HIV/STI prevention science questions.

2018-06-18

New commentary published in Clinical Infectious Diseases: Moving Forward With Treatment of Gonorrhea for Users of Human Immunodeficiency Virus Preexposure Prophylaxis Given the Threat of Antimicrobial Resistance.

2018-04-20

New paper published in the Journal of Statistical Software: EpiModel: An R Package for Mathematical Modeling of Infectious Disease over Networks.

2017-09-01

New paper published in Clinical Infectious Diseases: Incidence of Gonorrhea and Chlamydia Following Human Immunodeficiency Virus Preexposure Prophylaxis Among Men Who Have Sex With Men: A Modeling Study.

2017-02-15

Received my first NIH funding as a PI (R21 MH112449) for a new study to collect a national sample of network-based data on MSM for local modeling of HIV/STI transmission dynamics and opportunities for prevention.

2017-01-06

New paper published in PLoS One: Individual HIV Risk versus Population Impact of Risk Compensation after HIV Preexposure Prophylaxis Initiation among Men Who Have Sex with Men.

2016-12-01

Journal of Infectious Disease issue with our HIV PrEP model was published in the December 15 issue, and featured artwork from our study on the cover of the issue.

2016-09-01

Started a new affiliation with the Northwestern Center for Prevention Implementation Methodology (CePIM) as an Early Stage Investigator, with funding to conduct network and implementation science research over the next 5 years.

2016-07-14

New paper published in the Journal of Infectious Diseases: Impact of the Centers for Disease Control's HIV Preexposure Prophylaxis Guidelines for Men Who Have Sex with Men in the United States

2016-06-13

New paper published in the journal Sexually Transmitted Infections: Effectiveness of combination packages for HIV-1 prevention in sub-Saharan Africa depends on partnership network structure: a mathematical modelling study