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Joshua Nugent, PhD

joshua.r.nugent@kp.org

Kaiser Permanente Researcher Profiles

Nugent, Joshua R.

​Joshua R. Nugent, PhD, is a biostatistician at the Kaiser Permanente Northern California Division of Research. His research focuses on causal inference methods with a particular interest in leveraging semiparametric statistics and machine learning to efficiently estimate policy-relevant effects. Recent projects include the evaluation of randomized trials to reduce the incidence of HIV and TB in settings with complex clustered data and observational studies examining risk factors for COVID-19 infection. Dr. Nugent received his PhD in biostatistics from the University of Massachusetts Amherst. Before earning his doctorate, he served as a public high school math teacher for eight years.

Current Positions

  • Research Scientist I

Section Affiliations

Primary Research Interests

  • Causal inference
  • Statistical methods for clustered data
  • Machine learning
  • Infectious disease prevention

Publications

Country of Birth, Race, Ethnicity, and Prenatal Depression

Authors: Kelly-Taylor K;Aghaee S;Nugent J;Oberman N;Kubo A;Kurtovich E;Quesenberry CP;Sujan AC;Erickson-Ridout K;Bhalala MM;Avalos LA

JAMA Netw Open. 2025 Sep 02;8(9):e2531844. Epub 2025-09-02.

PubMed abstract

COVID-19 Vaccine Booster Uptake and Effectiveness Among US Adults With Cancer

Authors: Skarbinski J;Skarbinski, Jacek;Elkin, Eric P;Hsiao, Crystal A;Nugent, Joshua R;Kushi, Lawrence H;Figueiredo JC; et al.

JAMA Oncol. 2025 Sep 01;11(9):999-1010.

PubMed abstract

Developing and Validating Models to Predict Suboptimal Early Glycemic Control Among Individuals With Younger Onset Type 2 Diabetes

Authors: Gopalan A;Board CA;Alexeeff SE;Nugent JR;Mishra P;Karter AJ;Grant RW

Med Care. 2025 Aug 01;63(8):614-623. Epub 2025-05-09.

PubMed abstract

Diabetes Deprescribing in Older Adults: A Randomized Clinical Trial

Authors: Grant RW;Peterson I;McCloskey JM;Lipska KJ;Nugent J;Karter AJ;Gilliam LK

JAMA Intern Med. 2025 Aug 01;185(8):926-935.

PubMed abstract

Prenatal Depression and Symptom Severity by Maternal Race and Ethnicity

Authors: Kelly-Taylor, Kendria;Aghaee, Sara;Nugent, Joshua;Oberman, Nina;Kubo, Ai;Kurtovich, Elaine;Quesenberry, Charles P;Sujan, Ayesha C;Erickson-Ridout, Kathryn;Bhalala, Mibhali M;Avalos, Lyndsay A

JAMA Netw Open. 2025 Mar 03;8(3):e250743. Epub 2025-03-03.

PubMed abstract

Risk of Incident Tuberculosis Disease in a Large Integrated Health Care System in California, 2004-2022

Authors: Skarbinski, Jacek;Ni, Yuching;Halmer, Nicole;Bruxvoort, Katia J;Nugent, Joshua R;Fischer, Heidi;Qian, Lei;Ackerson, Bradley K;Amsden, Laura B;Shaw, Sally F;Spence, Brigitte;Tartof, Sara Y

Open Forum Infect Dis. 2025 Mar;12(3):ofaf103. Epub 2025-03-20.

PubMed abstract

Sociodemographic differences in modes of cannabis use among pregnant individuals in Northern California

Authors: Young-Wolff, Kelly C;Cortez, Catherine A;Nugent, Joshua R;Adams, Sara R;Slama, Natalie;Does, Monique;Campbell, Cynthia I;Brown, Qiana L; et al.

Drug Alcohol Depend. 2025 Feb 01;267:112546. Epub 2024-12-28.

PubMed abstract

On- and Off-Label Atypical Antipsychotic Prescription Trends Across a Nine-Year Period Among Adolescents Pre- to Post-COVID-19

Authors: Costales, Brianna;Slama, Natalie E;Penfold, Robert B;Nugent, Joshua R;Spalding, Scott R;Sterling, Stacy A;Iturralde, Esti

Acad Pediatr. 2024 Mar 06.

PubMed abstract

Community-Wide Universal Human Immunodeficiency Virus (HIV) Test and Treat Intervention Reduces Tuberculosis Transmission in Rural Uganda: A Cluster-Randomized Trial

Authors: Marquez, Carina;Nugent, Joshua;Balzer, Laura B;et al.

Clin Infect Dis. 2024 Jan 16.

PubMed abstract

Development and External Validation of a Prediction Model for Colorectal Cancer Among Patients Awaiting Surveillance Colonoscopy Following Polypectomy

Authors: Levin, Theodore R;Jensen, Christopher D;Marks, Amy R;Schlessinger, David;Liu, Vincent;Udaltsova, Natalia;Badalov, Jessica;Layefsky, Evan;Corley, Douglas A;Nugent, Joshua R;Lee, Jeffrey K

Gastro Hep Adv. 2024;3(5):671-683. Epub 2024-03-15.

PubMed abstract

Impact of COVID-19 on myalgic encephalomyelitis/chronic fatigue syndrome-like illness prevalence: A cross-sectional survey

Authors: Wood, Mariah S;Nugent, Joshua R;Skarbinski, Jacek;for STOP-ME/CFS and COVID-SELECT,;et al.

PLoS One. 2024;19(9):e0309810. Epub 2024-09-18.

PubMed abstract

Relative contribution of COVID-19 vaccination and SARS-CoV-2 infection to population-level seroprevalence of SARS-CoV-2 spike antibodies in a large integrated health system

Authors: Chervo, Tyler C;Nugent, Joshua R;Ergas, Isaac J;Quesenberry, Charles P;Corley, Douglas A;Habel, Laurel A;Kushi, Lawrence H;Skarbinski, Jacek;Skarbinski, Jacek;et al.

PLoS One. 2024;19(6):e0303303. Epub 2024-06-20.

PubMed abstract

Blurring cluster randomized trials and observational studies: Two-Stage TMLE for subsampling, missingness, and few independent units

Authors: Nugent, Joshua R;Marquez, Carina;Charlebois, Edwin D;Abbott, Rachel;Balzer, Laura B;SEARCH COLLABORATION,

Biostatistics. 2023 Aug 02.

PubMed abstract

SARS-CoV-2 Delta variant genomic variation associated with breakthrough infection in Northern California: A retrospective cohort study

Authors: Skarbinski, Jacek;Wyman, Stacia K;et al.

J Infect Dis. 2023 May 17.

PubMed abstract

A demonstration of Modified Treatment Policies to evaluate shifts in mobility and COVID-19 case rates in U.S. counties

Authors: Nugent, Joshua R; Balzer, Laura B

Am J Epidemiol. 2023 May 05;192(5):762-771.

PubMed abstract

Type I error control for cluster randomized trials under varying small sample structures.

Authors: Nugent, Joshua R; Kleinman, Ken P

BMC Med Res Methodol. 2021 Apr 3;21(1):65. doi: 10.1186/s12874-021-01236-7.

PubMed abstract

HIV incidence after pre-exposure prophylaxis initiation among women and men at elevated HIV risk: A population-based study in rural Kenya and Uganda.

Authors: Koss, Catherine A; Havlir, Diane V; Ayieko, James; Kwarisiima, Dalsone; Kabami, Jane; Chamie, Gabriel; Atukunda, Mucunguzi; Mwinike, Yusuf; Mwangwa, Florence; Owaraganise, Asiphas; Peng, James; Olilo, Winter; Snyman, Katherine; Awuonda, Benard; Clark, Tamara D; Black, Douglas; Nugent, Joshua; Brown, Lillian B; Marquez, Carina; Okochi, Hideaki; Zhang, Kevin; Camlin, Carol S; Jain, Vivek; Gandhi, Monica; Cohen, Craig R; Bukusi, Elizabeth A; Charlebois, Edwin D; Petersen, Maya L; Kamya, Moses R; Balzer, Laura B

PLoS Med. 2021 Feb 9;18(2):e1003492. doi: 10.1371/journal.pmed.1003492. eCollection 2021 Feb.

PubMed abstract

A mid-level health manager intervention to promote uptake of isoniazid preventive therapy among people with HIV in Uganda: a cluster randomised trial.

Authors: Kakande, Elijah; Christian, Canice; Balzer, Laura B; Owaraganise, Asiphas; Nugent, Joshua R; DiIeso, William; Rast, Derek; Kabami, Jane; Johnson Peretz, Jason; Camlin, Carol S; Shade, Starley B; Geng, Elvin H; Kwarisiima, Dalsone; Kamya, Moses R; Havlir, Diane V; Chamie, Gabriel

Lancet HIV. 2022 Sep;9(9):e607-e616. doi: 10.1016/S2352-3018(22)00166-7. Epub 2022 Jul 28.

PubMed abstract

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