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Joshua Nugent, PhD

Kaiser Permanente Researcher Profiles

Joshua  Nugent, PhD

​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


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

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

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

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

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