Bio


Aly is a PhD student in the Emmett Interdisciplinary Program in Environment & Resources, studying how climate instability impacts infectious disease dynamics. She uses tools in computation and network science to study the effect of anthropogenic change on underlying transmission networks in an effort to prevent widening disease disparities and to address the socio-political drivers of disease distribution.

Prior to coming to Stanford, Aly was a Data Science Fellow at the Centers for Disease Control and Prevention where she developed analytic tools for outbreak detection and triage of multiple pathogens and supported the CDC’s Novel Coronavirus (COVID-19) Response. She also worked at the People, Place & Health Collective at the Brown University School of Public Health while earning her undergraduate (BS, Applied Mathematics) and master's degrees (MA, Biostatistics). Outside of science she loves exploring the world through backcountry travel, rollerblading, and live music events.

Honors & Awards


  • Delta Omega Honorary Society in Public Health, Epsilon Iota Chapter, Brown University School of Public Health
  • Honors in Applied Mathematics, Brown University

Education & Certifications


  • MA, Brown University, Biostatistics (2020)
  • BS, Brown University, Applied Mathematics (2019)

All Publications


  • Survey of incidence, lifetime prevalence, and treatment of self-reported vulvovaginal candidiasis, United States, 2020. BMC women's health Benedict, K., Singleton, A. L., Jackson, B. R., Molinari, N. A. 2022; 22 (1): 147

    Abstract

    Vulvovaginal candidiasis (VVC) is a common gynecologic problem in the United States but estimates of its true incidence and prevalence are lacking. We estimated self-reported incidence and lifetime prevalence of healthcare provider-diagnosed VVC and recurrent VVC (RVVC), assessed treatment types, and evaluated demographic and health-related risk factors associated with VVC.An online survey sent to 4548 U.S. adults; data were weighted to be representative of the population. We conducted descriptive and bivariate analyses to examine demographic characteristics and health related factors associated with having VVC in the past year, lifetime prevalence of VVC, and over-the-counter (OTC) and prescription antifungal treatment use. We conducted multivariate analyses to assess features associated with 1) having VVC in the past year, 2) number of VVC episodes in the past year, and 3) lifetime prevalence of VVC.Among the subset of 1869 women respondents, 98 (5.2%) had VVC in the past year; of those, 5 (4.7%) had RVVC. Total, 991 (53%) women reported healthcare provider-diagnosed VVC in their lifetime. Overall, 72% of women with VVC in the past year reported prescription antifungal treatment use, 40% reported OTC antifungal treatment use, and 16% reported both. In multivariate analyses, odds of having VVC in the past year were highest for women with less than a high school education (aOR = 6.30, CI: 1.84-21.65), with a child/children under 18 years old (aOR = 3.14, CI: 1.58-6.25), with diabetes (aOR = 2.93, CI: 1.32-6.47), who were part of a couple (aOR = 2.86, CI: 1.42-5.78), and with more visits to a healthcare provider for any reason (aOR = 2.72, CI: 1.84-4.01). Similar factors were associated with increasing number of VVC episodes in the past year and with lifetime prevalence of VVC.VVC remains a common infection in the United States. Our analysis supports known clinical risk factors for VVC and suggests that antifungal treatment use is high, underscoring the need to ensure appropriate diagnosis and treatment.

    View details for DOI 10.1186/s12905-022-01741-x

    View details for PubMedID 35538480

    View details for PubMedCentralID PMC9092842

  • Network structure and rapid HIV transmission among people who inject drugs: A simulation-based analysis EPIDEMICS Singleton, A. L., Marshall, B. L., Bessey, S., Harrison, M. T., Galvani, A. P., Yedinak, J. L., Jacka, B. P., Goodreau, S. M., Goedel, W. C. 2021; 34: 100426

    Abstract

    As HIV incidence among people who inject drugs grows in the context of an escalating drug overdose epidemic in North America, investigating how network structure may affect vulnerability to rapid HIV transmission is necessary for preventing outbreaks. We compared the characteristics of the observed contact tracing network from the 2015 outbreak in rural Indiana with 1000 networks generated by an agent-based network model with approximately the same number of individuals (n = 420) and ties between them (n = 913). We introduced an initial HIV infection into the simulated networks and compared the subsequent epidemic behavior (e.g., cumulative HIV infections over 5 years). The model was able to produce networks with largely comparable characteristics and total numbers of incident HIV infections. Although the model was unable to produce networks with comparable cohesiveness (where the observed network had a transitivity value 35.7 standard deviations from the mean of the simulated networks), the structural variability of the simulated networks allowed for investigation into their potential facilitation of HIV transmission. These findings emphasize the need for continued development of injection network simulation studies in tandem with empirical data collection to further investigate how network characteristics played a role in this and future outbreaks.

    View details for DOI 10.1016/j.epidem.2020.100426

    View details for Web of Science ID 000632640900003

    View details for PubMedID 33341667

    View details for PubMedCentralID PMC7940592

  • Added Benefits of Pre-Exposure Prophylaxis Use on HIV Incidence with Minimal Changes in Efficiency in the Context of High Treatment Engagement Among Men Who Have Sex with Men AIDS PATIENT CARE AND STDS Singleton, A. L., Marshall, B. L., Zang, X., Nunn, A. S., Goedel, W. C. 2020; 34 (12): 506-515

    Abstract

    Although there is ongoing debate over the need for substantial increases in pre-exposure prophylaxis (PrEP) use when antiretroviral treatment confers the dual benefits of reducing HIV-related morbidity and mortality and the risk of HIV transmission, no studies to date have quantified the potential added benefits of PrEP use and changes in its efficiency in the context of high treatment engagement across multiple US subpopulations. We used a previously published agent-based model to simulate HIV transmission in a dynamic network of Black/African American and White men who have sex with men (MSM) in Atlanta, Georgia (2015-2024) to understand how reductions in HIV incidence attributable to varying levels of PrEP use change when United Nations Joint Programme on HIV/AIDS (UNAIDS) "90-90-90" goals for HIV treatment are achieved and maintained. Even at achievement of "90-90-90" goals, 75% PrEP coverage further reduced incidence by 67.9% and 74.2% to 1.53 [simulation interval (SI): 1.39-1.70] and 0.355 (SI: 0.316-0.391) per 100 person-years for Black/African American and White MSM, respectively, compared with the same scenario with no PrEP use. Increasing PrEP coverage from 15% to 75% under "90-90-90" goals only increased the number of person-years of PrEP use per infection averted by 8.1% and 10.5% to 26.7 (SI: 25.6-28.0) and 73.3 (SI: 70.6-75.7) among Black/African American MSM and White MSM, respectively. Even with high treatment engagement, substantial expansion of PrEP use contributes to meaningful decreases in HIV incidence among MSM with minimal changes in efficiency.

    View details for DOI 10.1089/apc.2020.0151

    View details for Web of Science ID 000592966300001

    View details for PubMedID 33216618

    View details for PubMedCentralID PMC7757534

  • Potential effectiveness of long-acting injectable pre-exposure prophylaxis for HIV prevention in men who have sex with men: a modelling study LANCET HIV Marshall, B. L., Goedel, W. C., King, M. F., Singleton, A., Durham, D. P., Chan, P. A., Townsend, J. P., Galvani, A. P. 2018; 5 (9): E498-E505

    Abstract

    Oral pre-exposure prophylaxis (PrEP) prevents HIV infection in men who have sex with men (MSM); however, adherence is an ongoing concern. Long-acting injectable PrEP is being tested in phase 3 trials and could address challenges associated with adherence. We examined the potential effectiveness of long-acting injectable PrEP compared with oral PrEP in MSM.We used an agent-based model to simulate HIV transmission in a dynamic network of 11 245 MSM in Atlanta, GA, USA. We used raw data from studies in macaque models and pharmacokinetic data from safety trials to estimate the time-varying efficacy of long-acting injectable PrEP. The effect of long-acting injectable PrEP on the cumulative number of new HIV infections over 10 years (2015-24) was compared with no PrEP and daily oral PrEP across a range of coverage levels. Sensitivity analyses were done with varying maximum efficacy and drug half-life values.In the absence of PrEP, the model predicted 2374 new HIV infections (95% simulation interval [SI] 2345-2412) between 2015 and 2024. The cumulative number of new HIV infections was reduced in all scenarios in which MSM received long-acting injectable PrEP compared with oral PrEP. At a coverage level of 35%, compared with no PrEP, long-acting injectable PrEP led to a 44% reduction in new HIV infections (1044 new infections averted [95% SI 1018-1077]) versus 33% (792 infections averted [763-821]) for oral PrEP. The relative benefit of long-acting injectable PrEP was sensitive to the assumed efficacy of injections received every 8 weeks, discontinuation rates, and terminal drug half-life.Long-acting injectable PrEP has the potential to produce larger reductions in HIV transmission in MSM than oral PrEP. However, the real-world, population-level impact of this approach will depend on uptake of this prevention method and its effectiveness, as well as retention of patients in clinical care.National Institute on Drug Abuse and National Institute of Mental Health.

    View details for DOI 10.1016/S2352-3018(18)30097-3

    View details for Web of Science ID 000443740400012

    View details for PubMedID 29908917

    View details for PubMedCentralID PMC6138558