About

Timothy P. Flanigan is a Professor of Health Services, Policy and Practice, and a Professor of Medicine at Brown University. He is a member of the Division of Infectious Diseases at The Miriam and Rhode Island Hospitals and Alpert Medical School of Brown University. Dr. Flanigan joined Brown Medical School in 1991 with the goal of establishing a primary care network for individuals living with HIV, with particular attention to women, people who inject drugs, and those leaving prison. He developed the HIV Care Program at the State Prison to provide care for people with HIV and facilitate their linkage to community-based resources upon release, resulting in over 70% of individuals with HIV in Rhode Island linking with primary medical care at The Immunology Center. His research and clinical work have included developing models of combined therapy for people who inject drugs and have HIV, as well as linkage-to-care programs for HIV-positive individuals leaving jail. Dr. Flanigan has received recognition for his contributions to community health, including a community health leadership award from The Robert Wood Johnson Foundation and an honorary doctorate from Salve Regina University. His efforts extend to global health, exemplified by his training of healthcare workers in Liberia during the Ebola epidemic. His recent research projects focus on Lyme Disease and Tickborne Illnesses, and he is involved in NIH training programs aimed at developing investigators in HIV and infectious diseases, especially related to substance use disorders. Additionally, Dr. Flanigan is a permanent deacon in the Catholic Diocese of Providence.

Research topics

• Internal medicine
• Virology
• Medicine
• Pediatrics

Selected publications

• P-470. CD4 Testing in HIV Care: Uncovering Patterns of Over-Monitoring

  Open Forum Infectious Diseases · 2025-01-29

  articleOpen accessSenior author

  Abstract Background In the realm of HIV care, CD4 monitoring guidelines serve as a cornerstone for managing the health and treatment plans of individuals living with HIV. Various authoritative bodies, including the U.S. Department of Health and Human Services (HHS) offer nuanced guidelines tailored to the latest research and clinical best practices. In our study, we aimed to investigate the frequency of unnecessary CD4 testing and assess healthcare providers' comfort level of less frequent monitoring.Figure 1:Healthcare Provider Comfort Levels with Deferring CD4 Count Testing above 500 Methods We conducted a retrospective cohort study of HIV patients under active care at the Lifespan Immunology Clinic, Miriam Hospital, Providence, Rhode Island, from 2021 to 2023, with undetectable viral loads (< 200 VL) and CD4 counts over 500. Data were extracted from electronic health records, including demographics and clinical measures. Additionally, we conducted qualitative surveys among key healthcare providers to determine adherence to guidelines and to identify any patterns of unnecessary CD4 testing.Figure 2:Awareness of Costs Associated with CD4 Count and HIV Viral Load Testing Among Healthcare Providers Results In our first phase of the study, a cohort of 1,929 active unique patients was monitored for their immunological status in 2021. Among these, 1,226 individuals underwent CD4 testing as the event date, with 825 achieving CD4 counts >500. Further analysis highlighted a subgroup of 712 patients who exhibited undetectable viral loads over a three-year span with CD4 counts >500 in 2021. Additionally, 610 of these patients continued to undergo regular CD4 testing after the event date. This group represents approximately 86% of those who were undetectable from 2021 to 2023. In the second phase of the study, a survey involving 40 healthcare providers at the immunology clinic assessed practices in monitoring with CD4 counts >500. The survey revealed 77% were comfortable not performing further CD4 tests, regardless of the patient's viral load status and 90% preferred not testing patients with undetectable viral loads for 1-2 years. Conclusion Our study observed significant increasing frequency with unnecessary monitoring of CD4 above 500 with undetectable viral loads. This highlights the importance of implementing future guidelines for minimizing CD4 testing in stable patients, aligning clinical practices and improving outcomes. Disclosures All Authors: No reported disclosures

  PublisherOA PDFDOI

• Social Determinants of Health and Linkage to HIV Care Among Groups at High Risk for Not Linking to HIV Care

  Research Square · 2025-05-16

  preprintOpen access
  PublisherOA PDFDOI

• Burden of Kidney Disease in an Aging Population Living with HIV in the United States

  AIDS Patient Care and STDs · 2024-11-11 · 1 citations

  article

  Antiretroviral therapy (ART) has significantly improved mortality rates for individuals living with HIV, but kidney disease remains prevalent, especially among older adults. Our study analyzed the burden of kidney disease in individuals aged 65 and older at The Miriam Hospital Immunology Center in Rhode Island. We calculated estimated glomerular filtration rates using the last creatinine values from 2019 and identified chronic kidney disease (CKD) stages. Results showed a 19% prevalence of moderate or severe CKD among adults living with HIV, rising to 39% for those aged 75 and older. Particularly striking was the increased prevalence among African American adults aged 65+, at 30.4%, rising to 50% for those over 75. In comparison, the National Institute of Diabetes and Digestive and Kidney Diseases reports that CKD stage 3 affects 20.1% of adults aged 65+, compared with just 1.2% in those younger than 65. Gender and racial disparities are evident; CKD stage 3 is more prevalent in females (5.8%) than males (4.4%). Our findings indicate that 32% of HIV-positive females have moderate-to-severe kidney disease, compared with 14% of males. Importantly, we did not account for hypertension, diabetes, and hepatitis C virus infection, which may influence renal outcomes. Our study shows that ART has reduced mortality, as more people with HIV now live longer, while also revealing the disproportionate burden of kidney disease among older adults and racial minorities, as well as a concerning trend among women; therefore, emphasizing the need for targeted health care strategies for high-risk groups.

  PublisherDOI

• What patients tell us: Assessing feedback and perspectives of patients with post-treatment Lyme disease symptoms.

  Medical Research Archives · 2024-01-01 · 1 citations

  articleOpen accessSenior author

  While most patients with Lyme disease fully recover within 6 months, a minority of patients develop significant and persistent symptoms after appropriate antibiotic treatment. With no clear pathophysiology or treatment, post-treatment Lyme disease (PTLDS) (also sometimes referred to as chronic Lyme) is a highly contested condition within the medical community. After conducting a phone survey of 25 patients who had visited an outpatient, academic center for Lyme and other tick-borne diseases, we collected and summarized patients’ perspectives and feedback of the care they received for ongoing Lyme-related symptoms. Findings from this phone survey demonstrated an extremely varied history with regards to experiences with diagnosis, treatment, and management of long-term symptoms. Key themes include a wide-ranging but life-altering self-reported symptomatology, pervasive doubts/frustrations in the medical system regarding treatment of PTLDS symptoms, and how often patients tried unconventional and nontraditional treatment methods. Importantly, patients were unified in their appreciation for an approachable and validating healthcare team even if they did not find complete resolution in their symptoms.

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• Going to the Source: Discussions With Early and Mid-Career Faculty From Groups Underrepresented in Biomedical Research to Develop and Enhance CFAR Services

  JAIDS Journal of Acquired Immune Deficiency Syndromes · 2023-09-14 · 1 citations

  articleOpen access

  BACKGROUND: To include, sustain, and retain HIV-focused early career faculty from groups historically excluded from biomedical research, the Providence/Boston Center for AIDS Research (CFAR) conducted focus groups and individual interviews with early and mid-career faculty to discern their needs. METHODS: We conducted focus groups and interviews with 15 faculty at institutions affiliated with Providence/Boston CFAR from groups underrepresented in biomedical research. The discussion was guided using the domains of an Asset Bundle Model encompassing scientific human capital, social capital, and financial capital. RESULT: Participants' identities, including their race, ethnicity, gender, sexual orientation, and being a parent affected their vision of themselves as scientists. Participants reported confusion or limited training on or access to resources for professional development, hiring staff, meeting NIH reporting requirements, international research, support for working parents, sabbaticals, and addressing workplace conflict or unsupportive work environments. Some described feeling like they were a burden on their mentors who seemed overextended. They identified attributes of effective mentors, such as believing in and investing in the mentee; having the requisite content area expertise and self-confidence; being able to identify mentees needs and meet them where they are; and being consistent, communicative, respectful, and kind. They described a need for additional education and support preresearch and postresearch grant award management. CONCLUSIONS: To learn how to equitably serve all interested in HIV research, CFARs should engage and include perspectives from scientists who have historically been excluded from biomedical research. Our future work will test, implement, and disseminate the ideas generated by these focus group discussions.

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• Exploratory qualitative study examining acceptability of strategies to improve access to substance use treatment and HIV prevention services for young adults on probation in Ukraine

  BMJ Open · 2022-11-01

  articleOpen access

  OBJECTIVE: Adults <30 years' of age experience elevated HIV-rates in Ukraine. Young adults (YA) involved in the criminal justice system (CJS) are at an increased HIV-risk given elevated rates of substance use, engagement in high-risk sexual behaviour and insufficient healthcare access. The objective of this exploratory study was to investigate the acceptability of strategies to refer and link CJS-involved YA to HIV-prevention and substance use treatment services from CJS settings. DESIGN: We conducted qualitative individual interviews with CJS-involved YA (18-24 years), and CJS stakeholders. Interviews were guided by the Social Ecological Model. Interviews with YA explored substance use and sexual behaviour, and acceptability of strategies to link YA to HIV-prevention and substance use treatment services from CJS. Stakeholder interviews explored system practices addressing HIV-prevention and substance use and addiction. Data were analysed using Inductive Thematic Analysis. SETTING: Data were collected in three locales, prior to the 2022 Russian-Ukrainian conflict. PARTICIPANTS: Thirty YA and 20 stakeholders. RESULTS: =23 years. YA were receptive to linkage to HIV-prevention services from CJS; this was shaped by self-perceived HIV-risk and lack of access to HIV-prevention services. YA were less receptive to being referred to substance use treatment services, citing a lack of self-perceived need and mistrust in treatment efficacy. Stakeholders identified multilevel contextual factors shaping acceptability of HIV-prevention and substance use treatment from CJS (eg, stigma). CONCLUSIONS: Findings should be reviewed as a historical record of the pre-conflict context. In that context, we identified strategies that may have been used to help curtail the transmission of HIV in a population most-at-risk, including CJS-involved YA. This study demonstrates that improving access to substance use treatment and HIV-prevention services via CJS linkage were acceptable if provided in the right conditions (eg, low or no-cost, confidential).

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• Police abuse and care engagement of people with HIV who inject drugs in Ukraine

  Global Public Health · 2022-03-28 · 4 citations

  articleOpen access

  Police abuse affects people who inject drugs (PWID), including those with HIV, and negatively impacts care engagement. This cross-sectional study evaluated police abuse among PWID receiving MOUD (medication for opioid use disorder) living with HIV and associations with HIV treatment adherence and receipt of NGO services. We assessed lifetime and past six-month rates of police abuse among a cohort of Ukrainian PWID with HIV receiving MOUD (n = 190) from August to September 2017. Logistic regression models evaluated associations between past six-month police abuse and past 30-day antiretroviral therapy (ART) adherence, and past six-month NGO service receipt. Almost all (90%) participants reported lifetime police abuse: 77% reported physical violence and 75% reported paying the police to avoid arrest. One in four females (25%) reported police-perpetrated sexual violence. Recent police abuse was reported by 16% of males and 2% of females and was not associated with ART adherence (aOR: 1.1; 95% CI:0.3–5.0) or NGO service receipt (aOR: 3.4; 95% CI:0.6–18.3). While lifetime police abuse rates were high, few participants reported recent police abuse, which was not linked to care engagement. These trends should encourage the Ukrainian government for public health-public safety partnerships and legal interventions to eliminate human rights violations against PWID living with HIV.

  PublisherOA PDFDOI

• Development of benchmark datasets for text mining and sentiment analysis to accelerate regulatory literature review

  Regulatory Toxicology and Pharmacology · 2022-11-11 · 5 citations

  articleOpen access

  In the field of regulatory science, reviewing literature is an essential and important step, which most of the time is conducted by manually reading hundreds of articles. Although this process is highly time-consuming and labor-intensive, most output of this process is not well transformed into machine-readable format. The limited availability of data has largely constrained the artificial intelligence (AI) system development to facilitate this literature reviewing in the regulatory process. In the past decade, AI has revolutionized the area of text mining as many deep learning approaches have been developed to search, annotate, and classify relevant documents. After the great advancement of AI algorithms, a lack of high-quality data instead of the algorithms has recently become the bottleneck of AI system development. Herein, we constructed two large benchmark datasets, Chlorine Efficacy dataset (CHE) and Chlorine Safety dataset (CHS), under a regulatory scenario that sought to assess the antiseptic efficacy and toxicity of chlorine. For each dataset, ∼10,000 scientific articles were initially collected, manually reviewed, and their relevance to the review task were labeled. To ensure high data quality, each paper was labeled by a consensus among multiple experienced reviewers. The overall relevance rate was 27.21% (2,663 of 9,788) for CHE and 7.50% (761 of 10,153) for CHS, respectively. Furthermore, the relevant articles were categorized into five subgroups based on the focus of their content. Next, we developed an attention-based classification language model using these two datasets. The proposed classification model yielded 0.857 and 0.908 of Area Under the Curve (AUC) for CHE and CHS dataset, respectively. This performance was significantly better than permutation test (p < 10E-9), demonstrating that the labeling processes were valid. To conclude, our datasets can be used as benchmark to develop AI systems, which can further facilitate the literature review process in regulatory science.

  PublisherDOI

• Evaluating Barriers to Viral Suppression among People with HIV in Santiago, Dominican Republic

  Journal of the International Association of Providers of AIDS Care (JIAPAC) · 2022-01-01 · 3 citations

  articleOpen access

  The Dominican Republic (DR) has the second-highest prevalence of HIV infection in the Caribbean, but viral suppression and treatment adherence are not well understood. We conducted a cross-sectional study among people living with HIV/AIDS(PLWHA) to fill in the knowledge gap. Questionnaire was used to collect demographic data, antiretroviral therapy (ART) adherence, and barriers and facilitators to HIV care. Viral load and other clinical information were extracted through chart reviews. Descriptive analyzes and logistic regression were conducted to explore factors associated with non-viral suppression and imperfect ART adherence. Of 193 PLWHA 83.9% were virally suppressed. Those that were non-virally suppressed were more likely of being male (odds ratio [OR]: 2.55, 95% confidence interval [CI]: 1.17-5.58) and less likely of being unemployed (OR: 0.28, 95% CI: 0.08-0.96). However, being male (OR: 0.78, 95% CI:0.40-1.53) and unemployed (OR: 0.28, 95% CI:0. 08-1.21) were less likely to report imperfect adherence. Tailored interventions are needed to improve adherence and viral suppression in DR.

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• Utility of linking survey and registry data to evaluate interventions and policies to address disparities in breast cancer survivorship among young women

  Evaluation and Program Planning · 2021-05-29

  articleOpen access
  PublisherOA PDFDOI

Recent grants

• NIH Grant N01HB057117

  NIH · $755k · 2000

• HIV and Other Infectious Consequences of Substance Use

  NIH · $9.0M · 2001–2028

• NIH Grant R01DA013767

  NIH · $2.6M · 2005

• Brown University Community and Clinical Research Training Program

  NIH · $3.7M · 2008–2027

• Emerging Infectious Disease and HIV Scholars Program at Brown University

  NIH · $2.6M · 2018–2028

Frequent coauthors

• Josiah D. Rich

  Rhode Island Hospital

  210 shared

• Kenneth H. Mayer

  Fenway Health

  130 shared

• Susan Cu‐Uvin

  Brown University

  128 shared

• Curt G. Beckwith

  Brown University

  127 shared

• Charles C. J. Carpenter

  122 shared

• Antonella Castagna

  Istituto di Ricovero e Cura a Carattere Scientifico San Raffaele

  82 shared

• Stuart H. Cohen

  82 shared

• Jennifer Cunningham

  National Institute of Allergy and Infectious Diseases

  81 shared

Education

• M.D.

  Brown University

• B.A.

  Brown University

Awards & honors

• Community health leadership award from The Robert Wood Johns…