Publications

Highlighted

Clinical and Epidemiological Aspects of Diphtheria: A Systematic Review and Pooled Analysis.
Clinical and Epidemiological Aspects of Diphtheria: A Systematic Review and Pooled Analysis.
Shaun A Truelove, Lindsay T Keegan, William J Moss, Lelia H Chaisson, Emilie Macher, Andrew S Azman, Justin Lessler
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America   ·   24 Jun 2020   ·   pmid:31425581

All

2024

The Effectiveness of Face Mask Mandates on COVID-19 Transmission in Utah
The Effectiveness of Face Mask Mandates on COVID-19 Transmission in Utah
Alicia C. Horn, Holly E. Shoemaker, Lindsay T. Keegan
Public Health Reports®   ·   30 Oct 2024   ·   doi:10.1177/00333549241290676
A theoretical framework to quantify the tradeoff between individual and population benefits of expanded antibiotic use
A theoretical framework to quantify the tradeoff between individual and population benefits of expanded antibiotic use
Cormac R. LaPrete, Sharia M. Ahmed, Damon J.A. Toth, Jody R. Reimer, Valerie M. Vaughn, Frederick R. Adler, Lindsay T. Keegan
Cold Spring Harbor Laboratory   ·   28 Aug 2024   ·   doi:10.1101/2024.08.28.24312731
Importance of underlying mechanisms for interpreting relative risk of Clostridioides difficile infection among antibiotic-exposed patients in healthcare facilities
Importance of underlying mechanisms for interpreting relative risk of Clostridioides difficile infection among antibiotic-exposed patients in healthcare facilities
Christopher Mitchell, Lindsay T. Keegan, Thuy T. T. Le, Karim Khader, Alexander Beams, Matthew H. Samore, Damon J. A. Toth
PLOS ONE   ·   08 Aug 2024   ·   doi:10.1371/journal.pone.0306622
Model-based estimates of age-structured SARS-CoV-2 epidemiology in households
Model-based estimates of age-structured SARS-CoV-2 epidemiology in households
Damon J.A. Toth, Theresa R. Sheets, Alexander B. Beams, Sharia M. Ahmed, Nathan Seegert, Jay Love, Lindsay T. Keegan, Matthew H. Samore
Cold Spring Harbor Laboratory   ·   19 Apr 2024   ·   doi:10.1101/2024.04.18.24306047

2023

Assessing the Impact of Mask Mandates on SARS-CoV-2 Transmission: A Case Study of Utah
Assessing the Impact of Mask Mandates on SARS-CoV-2 Transmission: A Case Study of Utah
Alicia C. Horn, Holly E. Shoemaker, Lindsay T. Keegan
Cold Spring Harbor Laboratory   ·   13 Nov 2023   ·   doi:10.1101/2023.11.13.23298464

2022

432. Ward-level Variation in Transmission of MRSA in Veterans Affairs Hospitals
432. Ward-level Variation in Transmission of MRSA in Veterans Affairs Hospitals
Karim Khader, Vanessa W Stevens, Alun Thomas, Damon Toth, Lindsay T Keegan, Michael Rubin, Matthew H Samore
Open Forum Infectious Diseases   ·   01 Dec 2022   ·   doi:10.1093/ofid/ofac492.507
Are<i>Staphylococcus aureus</i>Carrier Types Evidence of Population Heterogeneity?
AreStaphylococcus aureusCarrier Types Evidence of Population Heterogeneity?
Alexander Beams, Lindsay T Keegan, Frederick R Adler, Matthew H Samore, Karim Khader, Damon J A Toth
American Journal of Epidemiology   ·   17 Nov 2022   ·   doi:10.1093/aje/kwac201
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States.
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States.
Estee Y Cramer, Evan L Ray, Velma K Lopez, Johannes Bracher, Andrea Brennen, ..., Jo W Walker, Rachel B Slayton, Michael A Johansson, Matthew Biggerstaff, Nicholas G Reich
Proceedings of the National Academy of Sciences of the United States of America   ·   08 Apr 2022   ·   pmid:35394862

2021

Analysis of Vaccine Effectiveness Against COVID-19 and the Emergence of Delta and Other Variants of Concern in Utah
Analysis of Vaccine Effectiveness Against COVID-19 and the Emergence of Delta and Other Variants of Concern in Utah
Lindsay T. Keegan, Shaun Truelove, Justin Lessler
JAMA Network Open   ·   23 Dec 2021   ·   doi:10.1001/jamanetworkopen.2021.40906
High variability in transmission of SARS-CoV-2 within households and implications for control
High variability in transmission of SARS-CoV-2 within households and implications for control
Damon J. A. Toth, Alexander B. Beams, Lindsay T. Keegan, Yue Zhang, Tom Greene, Brian Orleans, Nathan Seegert, Adam Looney, Stephen C. Alder, Matthew H. Samore
PLOS ONE   ·   10 Nov 2021   ·   doi:10.1371/journal.pone.0259097
The United States COVID-19 Forecast Hub dataset
The United States COVID-19 Forecast Hub dataset
Estee Y Cramer, Yuxin Huang, Yijin Wang, Evan L Ray, Matthew Cornell, ..., Ariane Stark, Apurv Shah, Nutcha Wattanchit, Martha W Zorn, Nicholas G Reich
Cold Spring Harbor Laboratory   ·   04 Nov 2021   ·   doi:10.1101/2021.11.04.21265886
Comparison of antigen- and RT-PCR-based testing strategies for detection of SARS-CoV-2 in two high-exposure settings.
Comparison of antigen- and RT-PCR-based testing strategies for detection of SARS-CoV-2 in two high-exposure settings.
Jay Love, Megan T Wimmer, Damon J A Toth, Arthi Chandran, Dilip Makhija, Charles K Cooper, Matthew H Samore, Lindsay T Keegan
PloS one   ·   07 Sep 2021   ·   pmid:34492025
Comparison of antigen- and RT-PCR-based testing strategies for detection of Sars-Cov-2 in two high-exposure settings
Comparison of antigen- and RT-PCR-based testing strategies for detection of Sars-Cov-2 in two high-exposure settings
Jay Love, Megan T. Wimmer, Damon J.A. Toth, Arthi Chandran, Dilip Makhija, Charles K. Cooper, Matthew H. Samore, Lindsay T. Keegan
Cold Spring Harbor Laboratory   ·   06 Jun 2021   ·   doi:10.1101/2021.06.03.21258248
Modeling transmission of pathogens in healthcare settings
Modeling transmission of pathogens in healthcare settings
Anna Stachel, Lindsay T. Keegan, Seth Blumberg
Current Opinion in Infectious Diseases   ·   25 May 2021   ·   doi:10.1097/QCO.0000000000000742
Modeling of Future COVID-19 Cases, Hospitalizations, and Deaths, by Vaccination Rates and Nonpharmaceutical Intervention Scenarios — United States, April–September 2021
Modeling of Future COVID-19 Cases, Hospitalizations, and Deaths, by Vaccination Rates and Nonpharmaceutical Intervention Scenarios — United States, April–September 2021
Rebecca K. Borchering, Cécile Viboud, Emily Howerton, Claire P. Smith, Shaun Truelove, ..., Rachel B. Slayton, Matthew Biggerstaff, Michael A. Johansson, Katriona Shea, Justin Lessler
MMWR. Morbidity and Mortality Weekly Report   ·   14 May 2021   ·   doi:10.15585/mmwr.mm7019e3
Coordinated Strategy for a Model-Based Decision Support Tool for Coronavirus Disease, Utah, USA.
Coordinated Strategy for a Model-Based Decision Support Tool for Coronavirus Disease, Utah, USA.
Hannah R Meredith, Emerson Arehart, Kyra H Grantz, Alexander Beams, Theresa Sheets, ..., Shannon Frattaroli, Matthew H Samore, Justin Lessler, Elizabeth C Lee, Lindsay T Keegan
Emerging infectious diseases   ·   01 May 2021   ·   pmid:33900179
Coordinated Strategy for a Model-Based Decision Support Tool for Coronavirus Disease, Utah, USA
Coordinated Strategy for a Model-Based Decision Support Tool for Coronavirus Disease, Utah, USA
Hannah R. Meredith, Emerson Arehart, Kyra H. Grantz, Alexander Beams, Theresa Sheets, ..., Shannon Frattaroli, Matthew H. Samore, Justin Lessler, Elizabeth C. Lee, Lindsay T. Keegan
Emerging Infectious Diseases   ·   01 May 2021   ·   doi:10.3201/eid2705.203075
A scenario modeling pipeline for COVID-19 emergency planning.
A scenario modeling pipeline for COVID-19 emergency planning.
Joseph C Lemaitre, Kyra H Grantz, Joshua Kaminsky, Hannah R Meredith, Shaun A Truelove, ..., Josh Wills, Kathryn Kaminsky, Javier Perez-Saez, Justin Lessler, Elizabeth C Lee
Scientific reports   ·   06 Apr 2021   ·   pmid:33824358
A scenario modeling pipeline for COVID-19 emergency planning
A scenario modeling pipeline for COVID-19 emergency planning
Joseph C. Lemaitre, Kyra H. Grantz, Joshua Kaminsky, Hannah R. Meredith, Shaun A. Truelove, ..., Josh Wills, Kathryn Kaminsky, Javier Perez-Saez, Justin Lessler, Elizabeth C. Lee
Scientific Reports   ·   06 Apr 2021   ·   doi:10.1038/s41598-021-86811-0
Association Between Contact Precautions and Transmission of Methicillin-Resistant <i>Staphylococcus aureus</i> in Veterans Affairs Hospitals
Association Between Contact Precautions and Transmission of Methicillin-Resistant Staphylococcus aureus in Veterans Affairs Hospitals
Karim Khader, Alun Thomas, Vanessa Stevens, Lindsay Visnovsky, McKenna Nevers, Damon Toth, Lindsay T. Keegan, Makoto Jones, Michael Rubin, Matthew H. Samore
JAMA Network Open   ·   15 Mar 2021   ·   doi:10.1001/jamanetworkopen.2021.0971
The Effects of Using a Clinical Prediction Rule to Prioritize Diagnostic Testing on Transmission and Hospital Burden: A Modeling Example of Early Severe Acute Respiratory Syndrome Coronavirus 2
The Effects of Using a Clinical Prediction Rule to Prioritize Diagnostic Testing on Transmission and Hospital Burden: A Modeling Example of Early Severe Acute Respiratory Syndrome Coronavirus 2
Jody R Reimer, Sharia M Ahmed, Ben J Brintz, Rashmee U Shah, Lindsay T Keegan, Matthew J Ferrari, Daniel T Leung
Clinical Infectious Diseases   ·   23 Feb 2021   ·   doi:10.1093/cid/ciab177
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US
Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US
Estee Y Cramer, Evan L Ray, Velma K Lopez, Johannes Bracher, Andrea Brennen, ..., Jo W Walker, Rachel B Slayton, Michael A Johansson, Matthew Biggerstaff, Nicholas G Reich
Cold Spring Harbor Laboratory   ·   05 Feb 2021   ·   doi:10.1101/2021.02.03.21250974
Robust Testing in Outpatient Settings to Explore COVID-19 Epidemiology: Disparities in Race/Ethnicity and Age, Salt Lake County, Utah, 2020
Robust Testing in Outpatient Settings to Explore COVID-19 Epidemiology: Disparities in Race/Ethnicity and Age, Salt Lake County, Utah, 2020
Sharia M. Ahmed, Rashmee U. Shah, Valerie Fernandez, Sara Grineski, Benjamin Brintz, Matthew H. Samore, Matthew J. Ferrari, Daniel T. Leung, Lindsay T. Keegan
Public Health Reports®   ·   04 Feb 2021   ·   doi:10.1177/0033354920988612
Transmission Dynamics of <i>Clostridioides difficile</i> in 2 High-Acuity Hospital Units
Transmission Dynamics of Clostridioides difficile in 2 High-Acuity Hospital Units
Karim Khader, L Silvia Munoz-Price, Ryan Hanson, Vanessa Stevens, Lindsay T Keegan, Alun Thomas, Liliana E Pezzin, Ann Nattinger, Siddhartha Singh, Matthew H Samore
Clinical Infectious Diseases   ·   15 Jan 2021   ·   doi:10.1093/cid/ciaa1580
Effectiveness of Contact Precautions to Prevent Transmission of Methicillin-Resistant <i>Staphylococcus aureus</i> and Vancomycin-Resistant Enterococci in Intensive Care Units
Effectiveness of Contact Precautions to Prevent Transmission of Methicillin-Resistant Staphylococcus aureus and Vancomycin-Resistant Enterococci in Intensive Care Units
Karim Khader, Alun Thomas, W Charles Huskins, Vanessa Stevens, Lindsay T Keegan, Lindsay Visnovsky, Matthew H Samore
Clinical Infectious Diseases   ·   15 Jan 2021   ·   doi:10.1093/cid/ciaa1603
Continued need for non-pharmaceutical interventions after COVID-19 vaccination in long-term-care facilities
Continued need for non-pharmaceutical interventions after COVID-19 vaccination in long-term-care facilities
Jay Love, Lindsay T. Keegan, Frederick J. Angulo, John McLaughlin, Kimberly M. Shea, David L. Swerdlow, Matthew H. Samore, Damon J.A. Toth
Cold Spring Harbor Laboratory   ·   06 Jan 2021   ·   doi:10.1101/2021.01.06.21249339

2020

Seasonal patterns of dengue incidence in Thailand across the urban-rural gradient
Seasonal patterns of dengue incidence in Thailand across the urban-rural gradient
Qifang Bi, Derek AT Cummings, Nicholas G. Reich, Lindsay T. Keegan, Joshua Kaminsky, Henrik Salje, Hannah Clapham, Pawinee Doung-ngern, Sopon Iamsirithaworn, Justin Lessler
Cold Spring Harbor Laboratory   ·   27 Nov 2020   ·   doi:10.1101/2020.11.25.20186056
A modular approach to integrating multiple data sources into real-time clinical prediction for pediatric diarrhea
A modular approach to integrating multiple data sources into real-time clinical prediction for pediatric diarrhea
Ben J. Brintz, Benjamin Haaland, Joel Howard, Dennis L. Chao, Joshua L. Proctor, ..., James A. Platts-Mills, Eric J. Nelson, Adam C. Levine, Andrew T. Pavia, Daniel T. Leung
Cold Spring Harbor Laboratory   ·   27 Oct 2020   ·   doi:10.1101/2020.10.26.20210385
Ensemble Forecasts of Coronavirus Disease 2019 (COVID-19) in the U.S.
Ensemble Forecasts of Coronavirus Disease 2019 (COVID-19) in the U.S.
Evan L Ray, Nutcha Wattanachit, Jarad Niemi, Abdul Hannan Kanji, Katie House, ..., Rachel Slayton, Velma Lopez, Matthew Biggerstaff, Michael A Johansson, Nicholas G Reich
Cold Spring Harbor Laboratory   ·   22 Aug 2020   ·   doi:10.1101/2020.08.19.20177493
Modeling the potential impact of administering vaccines against Clostridioides difficile infection to individuals in healthcare facilities
Modeling the potential impact of administering vaccines against Clostridioides difficile infection to individuals in healthcare facilities
Damon J.A. Toth, Lindsay T. Keegan, Matthew H. Samore, Karim Khader, Justin J. O'Hagan, Holly Yu, Alvaro Quintana, David L. Swerdlow
Vaccine   ·   01 Aug 2020   ·   doi:10.1016/j.vaccine.2020.06.081
Modeling reductions in SARS-CoV-2 transmission and hospital burden achieved by prioritizing testing using a clinical prediction rule
Modeling reductions in SARS-CoV-2 transmission and hospital burden achieved by prioritizing testing using a clinical prediction rule
Jody R. Reimer, Sharia M. Ahmed, Benjamin Brintz, Rashmee U. Shah, Lindsay T. Keegan, Matthew J. Ferrari, Daniel T. Leung
Cold Spring Harbor Laboratory   ·   08 Jul 2020   ·   doi:10.1101/2020.07.07.20148510
Clinical and Epidemiological Aspects of Diphtheria: A Systematic Review and Pooled Analysis.
Clinical and Epidemiological Aspects of Diphtheria: A Systematic Review and Pooled Analysis.
Shaun A Truelove, Lindsay T Keegan, William J Moss, Lelia H Chaisson, Emilie Macher, Andrew S Azman, Justin Lessler
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America   ·   24 Jun 2020   ·   pmid:31425581
Planning for the aftershocks: a model of post-acute care needs for hospitalized COVID-19 patients
Planning for the aftershocks: a model of post-acute care needs for hospitalized COVID-19 patients
Matthew Maloney, Ryan Morley, Robert Checketts, Peter Weir, Darryl Barfuss, Hannah R. Meredith, Michelle G. Hofmann, Matthew H. Samore, Lindsay T. Keegan
Cold Spring Harbor Laboratory   ·   13 Jun 2020   ·   doi:10.1101/2020.06.12.20129551
The real time effective reproductive number for COVID-19 in the United States
The real time effective reproductive number for COVID-19 in the United States
Yue Zhang, Lindsay T Keegan, Qiu Yuqing, Matthew H Samore
Cold Spring Harbor Laboratory   ·   13 May 2020   ·   doi:10.1101/2020.05.08.20095703

2019

Clinical and Epidemiological Aspects of Diphtheria: A Systematic Review and Pooled Analysis
Clinical and Epidemiological Aspects of Diphtheria: A Systematic Review and Pooled Analysis
Shaun A Truelove, Lindsay T Keegan, William J Moss, Lelia H Chaisson, Emilie Macher, Andrew S Azman, Justin Lessler
Clinical Infectious Diseases   ·   19 Aug 2019   ·   doi:10.1093/cid/ciz808

2018

Perfect Counterfactuals for Epidemic Simulations
Perfect Counterfactuals for Epidemic Simulations
Joshua Kaminsky, Lindsay T. Keegan, C. Jessica E. Metcalf, Justin Lessler
Cold Spring Harbor Laboratory   ·   26 Oct 2018   ·   doi:10.1101/451153
Prospective forecasts of annual dengue hemorrhagic fever incidence in Thailand, 2010–2014
Prospective forecasts of annual dengue hemorrhagic fever incidence in Thailand, 2010–2014
Stephen A. Lauer, Krzysztof Sakrejda, Evan L. Ray, Lindsay T. Keegan, Qifang Bi, ..., Suthanun Suthachana, Yongjua Laosiritaworn, Derek A.T. Cummings, Justin Lessler, Nicholas G. Reich
Proceedings of the National Academy of Sciences   ·   20 Feb 2018   ·   doi:10.1073/pnas.1714457115

2017

Quantifying Zika: Advancing the Epidemiology of Zika With Quantitative Models
Quantifying Zika: Advancing the Epidemiology of Zika With Quantitative Models
Lindsay T Keegan, Justin Lessler, Michael A Johansson
The Journal of Infectious Diseases   ·   15 Dec 2017   ·   doi:10.1093/infdis/jix437

2016

Estimating finite-population reproductive numbers in heterogeneous populations
Estimating finite-population reproductive numbers in heterogeneous populations
Lindsay T. Keegan, Jonathan Dushoff
Journal of Theoretical Biology   ·   01 May 2016   ·   doi:10.1016/j.jtbi.2016.01.022

2014

Analytic Calculation of Finite-Population Reproductive Numbers for Direct- and Vector-Transmitted Diseases with Homogeneous Mixing
Analytic Calculation of Finite-Population Reproductive Numbers for Direct- and Vector-Transmitted Diseases with Homogeneous Mixing
Lindsay Keegan, Jonathan Dushoff
Bulletin of Mathematical Biology   ·   23 Apr 2014   ·   doi:10.1007/s11538-014-9950-x

2013

Population-level effects of clinical immunity to malaria
Population-level effects of clinical immunity to malaria
Lindsay T Keegan, Jonathan Dushoff
BMC Infectious Diseases   ·   11 Sep 2013   ·   doi:10.1186/1471-2334-13-428