| Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment | Nature Ecology and Evolution | 2024 |
| Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre | Nature Communications | 2024 |
| Design, optimization, and inference of multiphasic decay of infectious virus particles | bioRxiv (preprint) | 2024 |
| Metapopulation model of phage therapy of an acute Pseudomonas aeruginosa lung infection | bioRxiv (preprint) | 2024 |
| Macrophage-induced reduction of bacteriophage density limits the efficacy of in vivo pulmonary phage therapy | bioRxiv (preprint) | 2024 |
| Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes | bioRxiv (preprint) | 2024 |
| Rapid bacteria-phage coevolution drives the emergence of multiscale networks | Science | 2023 |
| Communicating COVID-19 Exposure Risk with an Interactive Website Counteracts Risk Misestimation | PLoS ONE | 2023 |
| localcovid19now: processing and mapping COVID-19 case data at subnational scales | The Journal of Open Source Software | 2023 |
| Personalized Feedback about COVID-19 Immunity Corrects Risk Misestimation and Motivates Booster Vaccinations. | PsyArXiv (preprint) | 2023 |
| Bacteria-phage coevolution with a seed bank | The ISME Journal | 2023 |
| Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2 | PNAS | 2023 |
| Scenario-Based Messages on Social Media Motivate COVID-19 Information Seeking | Journal of Applied Research in Memory and Cognition | 2023 |
| Attitudes towards booster, testing and isolation, and their impact on COVID-19 response in winter 2022/2023 in France, Belgium, and Italy: a cross-sectional survey and modelling study | The Lancet Regional Health- Europe | 2023 |
| How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics | Epidemics | 2023 |
| Epidemic modeling with heterogeneity and social diffusion | J. Math.Biol. | 2023 |
| Intermediate levels of asymptomatic transmission can lead to the highest levels of epidemic fatalities | PNAS Nexus | 2023 |
| Microbial and Viral Genome and Proteome Nitrogen Demand Varies Across Multiple Spatial Scales Within a Marine Oxygen Minimum Zone | mSystems | 2023 |
| Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching | Journal of Theoretical Biology | 2023 |
| The dynamic interplay of bacteriophage, bacteria and the mammalian host during phage therapy | iScience | 2023 |
| Modeling shield immunity to reduce COVID-19 transmission in long-term care facilities | Annals of Epidemiology | 2023 |
| Reasons for Receiving or Not Receiving Bivalent COVID-19 Booster Vaccinations Among Adults — United States, November 1–December 10, 2022 | CDC Morbidity and Mortality Weekly Report (MMWR) | 2023 |
| Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment | bioRxiv (preprint) | 2023 |
| Metacommunity Structure Preserves Genome Diversity in the Presence of Gene-specific Selective Sweeps. | bioRxiv (preprint) | 2023 |
| Vaccine stockpile sharing for selfish objectives | PLOS Global Public Health | 2022 |
| Defective Subviral Particles Modify Ecological Equilibria and Enhance Viral Coexistence | Frontiers in Virology | 2022 |
| Cyanophages from a less virulent clade dominate over their sister clade in global oceans | The ISME Journal | 2022 |
| Quantifying Risk for SARS-CoV-2 Infection among Nursing Home Workers For 2020/2021 Winter Surge of the COVID-19 Pandemic in Georgia, USA | Journal of the American Medical Directors Association. | 2022 |
| The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants | Journal of the Royal Society Interface | 2022 |
| Surveillance-to-Diagnostic Testing Program for Asymptomatic SARS-CoV-2 Infections on a Large, Urban Campus in Fall 2020 | Epidemiology | 2022 |
| Complex marine microbial communities partition metabolism of scarce resources over the diel cycle | Nature Ecology & Evolution. | 2022 |
| Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing. | Ecology Letters | 2022 |
| Modeling serological testing to inform relaxation of social distancing for COVID-19 control. | Nature Communications | 2021 |
| Heterogeneity in susceptibility dictates the order of epidemic models | Journal of Theoretical Biology | 2021 |
| Risk Factors for SARS-CoV-2 Seropositivity Among Nursing Home Staff: A Cross-Sectional Analysis of Participants Enrolled in the COPING Study. | Antimicrobial Stewardship & Healthcare Epidemiology | 2021 |
| A framework for monitoring population immunity to SARS-CoV-2 | Annals of Epidemiolgy | 2021 |
| Time-scales modulate optimal lysis-lysogeny decision switches and near-term phage fitness | BioRxiv (preprint) | 2021 |
| Estimating the Cumulative Incidence of SARS-CoV-2 Infection and the Infection Fatality Ratio in Light of Waning Antibodies | Epidemiology | 2021 |
| Reacting to outbreaks at neighboring localities. | Journal of Theoretical Biology | 2021 |
| Disease-dependent interaction policies to support health and economic outcomes during the COVID-19 epidemic | iScience | 2021 |
| Infect while the iron is scarce: nutrient-explicit phage-bacteria games | Theoretical Ecology | 2021 |
| A thermal trade-off between viral production and degradation drives virus-phytoplankton population dynamics | Ecology Letters | 2021 |
| Fighting microbial pathogens byintegrating host ecosystem interactions and evolution. | BioEssays | 2021 |
| Revisiting the rules of life for viruses of microorganisms | Nature Reviews Microbiology | 2021 |
| A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances | The ISME Journal | 2021 |
| Forward-looking serial intervals correctly link epidemic growth to reproduction numbers. | PNAS | 2021 |
| Large sample spaces do not imply biological systems are ‘fine-tuned’ | Journal of Theoretical Biology | 2020 |
| Awareness-driven Behavior Changes Can Shift the Shape of Epidemics Away from Peaks and Towards Plateaus, Shoulders, and Oscillations | PNAS | 2020 |
| Real-time, interactive website for US-county-level COVID-19 event risk assessment | Nature Human Behavior | 2020 |
| Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean | The ISME Journal | 2020 |
| Population Susceptibility Variation and Its Effect on Contagion Dynamics | arXiv (preprint) | 2020 |
| Seroprevalence of Antibodies to SARS-CoV-2 in 10 Sites in the United States, March 23-May 12, 2020 | JAMA International Medicine | 2020 |
| Topological constraints in early multicellularity favor reproductive division of labor | eLife | 2020 |
| When be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny | Virus Evolution | 2020 |
| Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak | Journal of the Royal Society Interface | 2020 |
| The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak | Epidemics | 2020 |
| Spread of COVID-19 through Georgia, USA. Near-term projections and impacts of social distancing via a metapopulation model | medRxiv (preprint) | 2020 |
| Optimizing the Timing and Composition of Therapeutic Phage Cocktails: A Control-Theoretic Approach | Bulletin of Mathematical Biology | 2020 |
| Modeling shield immunity to reduce COVID-19 epidemic spread | Nature Medicine | 2020 |
| Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations | The ISME Journal | 2020 |
| A Primer for Microbiome Time-Series Analysis | Frontiers in Genetics | 2020 |
| Linking Light-Dependent Life History Traits with Population Dynamics for Prochlorococcus and Cyanophage | mSystems | 2020 |
| Quantitative Models of Phage-Antibiotic Combination Therapy | mSystems | 2020 |
| Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “Candidatus Liberibacter asiaticus” | mSphere | 2019 |
| The ecological and biogeochemical state of the North Pacific Subtropical Gyre is linked to sea surface height | Journal of Marine Research | 2019 |
| A practical generation-interval-based approach to inferring the strength of epidemics from their speed | Epidemics | 2019 |
| Systematic biases in disease forecasting: The role of behavior change | Epidemics | 2019 |
| An empirical model of carbon flow through marine viruses and microzooplankton grazers | Environmental Microbiology | 2019 |
| Contrasting Controls on Microzooplankton Grazing and Viral Infection of Microbial Prey | Frontiers in Marine Science | 2019 |
| Spatial Interactions and Oscillatory Tragedies of the Commons | APS Physics | 2019 |
| Not by (Good) Microbes Alone: Towards Immunocommensal Therapies | Trends in Microbiology | 2019 |
| Heterogeneous viral strategies promote coexistence in virus-microbe systems | Journal of Theoretical Biology | 2019 |
| Viral invasion fitness across a continuum from lysis to latency | Virus Evolution | 2019 |
| Caution in inferring viral strategies from abundance correlations in marine metagenomes | Nature Communications | 2019 |
| Optimal control policies for evolutionary dynamics with environmental feedback | IEEE Conference on Decision and Control | 2018 |
| Information sharing for a coordination game in fluctuating environments | Journal of Theoretical Biology | 2018 |
| The Effect of Strain Level Diversity on Robust Inference of Virus-Induced Mortality of Phytoplankton | Frontiers in Microbiology | 2018 |
| Quantitative Infection Dynamics of Cafeteria Roenbergensis Virus | Viruses | 2018 |
| Limitations of correlation-based inference in complex virus-microbe communities | mSystems | 2018 |
| A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extrem environments | The ISME Journal | 2018 |
| Lysis, lysogeny and virus-microbe ratios | Nature | 2017 |
| Modeling the synergistic elimination of bacteria by phage and the innate immune system | Journal of Theoretical Biology | 2017 |
| How microbes survive the open ocean | Science | 2017 |
| Networked SIS Epidemics With Awareness | IEEE Transactions on Computational Social Systems | 2017 |
| Synergy between the Host Immune System and Bacteriophage Is Essential for Successful Phage Therapy against an Acute Respiratory Pathogen | Cell Host & Microbe | 2017 |
| Disentangling niche competition from grazing mortality in phytoplankton dilution experiments | PloS One | 2017 |
| Disease dynamics in a stochastic network game: a little empathy goes a long way in averting outbreaks | Scientific Reports | 2017 |
| Viral ecology comes of age | Environmental Microbiology Reports | 2017 |
| Overcoming the law of the hidden cyberinfrastructures | Trends in Plant Science | 2017 |
| Stochasticity and the limits to confidence when estimating R0 of Ebola and other emerging infectious diseases | Journal of Theoretical Biology | 2016 |
| An oscillating tragedy of the commons in replicator dynamics with game-environment feedback | PNAS | 2016 |
| Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer | BMC Genomics | 2016 |
| Inferring phage-bacteria infection networks from time-series data | Royal Society Open Science | 2016 |
| A touch of sleep: biophysical model of contact-mediated dormancy of archaea by viruses | Proceedings of the Royal Society B: Biological Sciences | 2016 |
| Conflicting attachment and the growth of bipartite networks | Physical Review E | 2016 |
| Re-examination of the relationship between marine virus and microbial cell abundances | Nature Microbiology | 2016 |
| Multiple regimes of robust patterns between network structure and biodiversity | Scientific Reports | 2015 |
| Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics | Plant Methods | 2015 |
| Reconstructing weighted networks from dynamics | Physical Review E | 2015 |
| Modeling post-death transmission of Ebola: challenges for inference and opportunities for control | Scientific Reports | 2015 |
| A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes | The ISME Journal | 2015 |
| Estimates of leaf vein density are scale dependent | Plant Physiology | 2014 |
| Costs and benefits of reticulate leaf venation | BMC Plant Biology | 2014 |
| The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection | Journal of Theoretical Biology | 2014 |
| Viral tagging reveals discrete populations in Synechococcus viral genome sequence space | Nature | 2014 |
| CRISPR-induced distributed immunity in microbial populations | PloS One | 2014 |
| The elemental composition of virus particles: implications for marine biogeochemical cycles | Nature Reviews Microbiology | 2014 |
| Coevolution can reverse predator-prey cycles | PNAS | 2014 |
| ClearedLeavesDB: an online database of cleared plant leaf images | Plant Methods | 2014 |
| Let my people go (home) to Spain: a genealogical model of Jewish identities since 1492 | PloS One | 2014 |
| Suppression of expression between adjacent genes within heterologous modules in yeast | G3: Genes, Genomes, Genetics | 2014 |
| The fiber walk: a model of tip-driven growth with lateral expansion | PloS One | 2014 |
| Extracting connectivity from dynamics of networks with uniform bidirectional coupling | Physical Review E | 2013 |
| Dynamics of shigellosis epidemics: estimating individual-level transmission and reporting rates from national epidemiologic data sets | American Journal of Epidemiology | 2013 |
| Mechanisms of multi-strain coexistence in host-phage systems with nested infection networks | Journal of Theoretical Biology | 2013 |
| A guide to sensitivity analysis of quantitative models of gene expression dynamics | Methods | 2013 |
| 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture | PNAS | 2013 |
| Critical cell wall hole size for lysis in Gram-positive bacteria | Journal of the Royal Society Interface | 2013 |
| Distinguishing between indirect and direct modes of transmission using epidemiological time series | The American Naturalist | 2013 |
| Phage-bacteria infection networks | Trends in Microbiology | 2013 |
| Genotypic recognition and spatial responses by rice roots | PNAS | 2013 |
| Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages | The ISME Journal | 2012 |
| Scaling and structure of dicotyledonous leaf venation networks | Ecology Letters | 2012 |
| Functional biogeography of ocean microbes revealed through non-negative matrix factorization | PloS One | 2012 |
| Ocean viruses and their effects on microbial communities and biogeochemical cycles | F1000 Biology Reports | 2012 |
| Testing the metabolic theory of ecology | Ecology Letters | 2012 |
| GiA Roots: software for the high throughput analysis of plant root system architecture | BMC Plant Biology | 2012 |
| A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data | Journal of Mathematical Biology | 2012 |
| Hierarchical Ordering of Reticular Networks | PloS One | 2012 |
| A neutral theory of genome evolution and the frequency distribution of genes | BMC Genomics | 2012 |
| Repeatability and contingency in the evolution of a key innovation in phage lambda | Science | 2012 |
| Allometric covariation: a hallmark behavior of plants and leaves | New Phytologist | 2012 |
| Analysing threshold effects in the sexual dynamics of cyclically parthenogenetic rotifer populations | Hydrobiologia | 2011 |
| Statistical structure of host-phage interactions | PNAS | 2011 |
| To lyse or not to lyse: transient-mediated stochastic fate determination in cells infected by bacteriophages | PLoS Computational Biology | 2011 |
| Dynamics of nutrient uptake strategies: lessons from the tortoise and the hare | Theoretical Ecology | 2011 |
| Genomic fluidity: an integrative view of gene diversity within microbial populations | BMC Genomics | 2011 |
| Quantifying enzymatic lysis: estimating the combined effects of chemistry, physiology and physics | Physical Biology | 2010 |
| The metabolic theory of ecology: prospects and challenges for plant biology | New Phytologist | 2010 |
| Fluctuation domains in adaptive evolution | Theoretical Population Biology | 2010 |
| Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems | Plant Physiology | 2010 |
| Unsupervised statistical clustering of environmental shotgun sequences | BMC Bioinformatics | 2009 |
| Bacterivorous grazers facilitate organic matter decomposition: a stoichiometric modeling approach | FEMS Microbiology Ecology | 2009 |
| Small-scale copy number variation and large-scale changes in gene expression | PNAS | 2008 |
| Collective decision making in bacterial viruses | Biophysical Journal | 2008 |
| Alternative stable states in host-phage dynamics | Theoretical Ecology | 2008 |
| Evolutionary ecology of bacterial viruses | Microbe | 2008 |
| The evolution of dispersal in reserve networks | The American Naturalist | 2007 |
| A neutral metapopulation model of biodiversity in river networks | Journal of Theoretical Biology | 2007 |
| Evolution, interactions, and biological networks | PLoS One Biology | 2007 |
| Phage in the time of cholera | The Lancet: Infectious Diseases | 2006 |
| Ontogenetically stable hydraulic design in woody plants | Functional Ecology | 2006 |
| Size and scaling of predator-prey dynamics | Ecology Letters | 2006 |
| A null model of morphospace occupation | The American Naturalist | 2005 |
| Coevolutionary arms races between bacteria and bacteriophage | PNAS | 2005 |
| Dynamics of a contact process with ontogeny | Physical Review E | 2004 |
| Scale-dependence of resource-biodiversity relationships | Journal of Theoretical Biology | 2003 |
| Packing-limited growth of irregular objects | Physical Review E | 2003 |
| Explaining mortality rate plateaus | PNAS | 2001 |
| Re-examination of the “3/4” law of metabolism | Journal of Theoretical Biology | 2001 |
