Publications

Reduced effectiveness of repeat influenza vaccination: distinguishing among within-season waning, recent clinical infection, and subclinical infection.

Author(s): Bi Q, Dickerman BA, Nguyen HQ, Martin ET, Gaglani M, Wernli KJ, Balasubramani GK, Flannery B, Lipsitch M, Cobey S, US Flu Vaccine Effectiveness Network Investigators|Journal: J Infect Dis|PMID: 38687898| June 2024

Studies have reported that prior-season influenza vaccination is associated with higher risk of clinical influenza infection among vaccinees. This effect…

Correction: Practical considerations for measuring the effective reproductive number, Rt.

Author(s): Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S|Journal: PLoS Comput Biol|PMID: 34879070| December 2021

[This corrects the article DOI: 10.1371/journal.pcbi.1008409.].

Investigate the origins of COVID-19.

Author(s): Bloom JD, Chan YA, Baric RS, Bjorkman PJ, Cobey S, Deverman BE, Fisman DN, Gupta R, Iwasaki A, Lipsitch M, Medzhitov R, Neher RA, Nielsen R, Patterson N, Stearns T, van Nimwegen E, Worobey M, Relman DA|Journal: Science|PMID: 33986172| May 2021

Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination.

Author(s): Cobey S, Larremore DB, Grad YH, Lipsitch M|Journal: Nat Rev Immunol|PMID: 33795856| April 2021

When vaccines are in limited supply, expanding the number of people who receive some vaccine, such as by halving doses…

Model-informed COVID-19 vaccine prioritization strategies by age and serostatus.

Author(s): Bubar KM, Reinholt K, Kissler SM, Lipsitch M, Cobey S, Grad YH, Larremore DB|Journal: Science|PMID: 33479118| January 2021

Limited initial supply of SARS-CoV-2 vaccine raises the question of how to prioritize available doses. Here, we used a mathematical…

Practical considerations for measuring the effective reproductive number, Rt.

Author(s): Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey S|Journal: PLoS Comput Biol|PMID: 33301457| December 2020

Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During the Coronavirus…

Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine.

Author(s): Cai FY, Fussell T, Cobey S, Lipsitch M|Journal: PLoS Comput Biol|PMID: 30273332| October 2018

For encapsulated bacteria such as Streptococcus pneumoniae, asymptomatic carriage is more common and longer in duration than disease, and hence…

Host population structure and treatment frequency maintain balancing selection on drug resistance.

Author(s): Cobey S, Baskerville EB, Colijn C, Hanage W, Fraser C, Lipsitch M|Journal: J R Soc Interface|PMID: 28835542| August 2017

It is a truism that antimicrobial drugs select for resistance, but explaining pathogen- and population-specific variation in patterns of resistance…

Viral factors in influenza pandemic risk assessment.

Author(s): Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA|Journal: Elife|PMID: 27834632| November 2016

The threat of an influenza A virus pandemic stems from continual virus spillovers from reservoir species, a tiny fraction of…

Pathogen diversity and hidden regimes of apparent competition.

Author(s): Cobey S, Lipsitch M|Journal: Am Nat|PMID: 23234842| January 2013

Competition through cross-reacting host immune responses, a form of apparent competition, is a major driver of pathogen evolution and diversity.…