Publications3

Title	Year	Journal	Tools
Complex marine microbial communities partition metabolism of scarce resources over the diel cycle	2022	Nature Ecology and Evolution	Github Repository
Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean	2021	The ISME Journal
A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances	2021	The ISME Journal
Revisiting the rules of life for viruses of microorganisms	2021	Nature Reviews Microbiology
Forward-looking serial intervals correctly link epidemic growth to reproduction numbers	2021	PNAS
Fighting microbial pathogens by integrating host ecosystem interactions and evolution	2021	BioEssays
A thermal trade‐off between viral production and degradation drives virus‐phytoplankton population dynamics	2021	Ecology Letters	Github Repository
Estimating the cumulative incidence of SARS-CoV-2 infection and the infection fatality ratio in light of waning antibodies	2021	Epidemiology
Reacting to outbreaks at neighboring localities	2021	Journal of Theoretical Biology	Github Repository
Infect while the iron is scarce: nutrient-explicit phage-bacteria games	2021	Theoretical Ecology	Github Repository
Disease-dependent interaction policies to support health and economic outcomes during the COVID-19 epidemic	2021	iScience	Github Repository
Time-scales modulate optimal lysis-lysogeny decision switches and near-term phage fitness	2021	BioRxiv	Github Repository
Modeling shield immunity to reduce COVID-19 transmission in long-term care facilities	2021	medRxiv	Github Repository
Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing	2021	bioRxiv
Diel population dynamics and mortality of Prochlorococcus in the North Pacific Subtropical Gyre	2021	bioRxiv	Github Repository
Roles of generation-interval distributions in shaping relative epidemic strength, speed, and control of new SARS-CoV-2 variants	2021	medRxiv
Heterogeneity in susceptibility dictates the order of epidemic models	2021	Journal of Theoretical Biology	Github Repository
A framework for monitoring population immunity to SARS-CoV-2	2021	Annals of Epidemiology	Github Repository
Risk factors for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) seropositivity among nursing home staff	2021	Antimicrobial Stewardship & Healthcare Epidemiology
Modeling serological testing to inform relaxation of social distancing for COVID-19 control	2021	Nature Communications
Surveillance-to-Diagnostic Testing Program for Asymptomatic SARS-CoV-2 Infections on a Large, Urban Campus in Fall 2020	2021	Epidemiology	Github Repository
Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage	2021	mSystems	Github Repository
Modeling shield immunity to reduce COVID-19 epidemic spread	2020	Nature Medicine	Github Repository
The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak	2020	Epidemics
Optimizing the Timing and Composition of Therapeutic Phage Cocktails: A Control-Theoretic Approach	2020	Bulletin of Mathematical Biology
Quantitative Models of Phage-Antibiotic Combination Therapy	2020	mSystems	Github repository
Real-time, interactive website for US-county-level COVID-19 event risk assessment	2020	Nature Human Behavior
Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations	2020	The ISME Journal
Linking Light-Dependent Life History Traits with Population Dynamics for Prochlorococcus and Cyanophage	2020	mSystems	Github Repository
A Primer for Microbiome Time-Series Analysis	2020	Frontiers in Genetics	Github Repository

The Weitz Group