| 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 |
