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List of works by Joshua Weitz

3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture

scientific article published on 11 April 2013

A Primer for Microbiome Time-Series Analysis

scientific article published on 21 April 2020

A framework for monitoring population immunity to SARS-CoV-2

scientific article published in November 2021

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

scientific article published on 30 January 2015

A neutral metapopulation model of biodiversity in river networks

scientific article

A neutral theory of genome evolution and the frequency distribution of genes

scientific article

A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data

scientific article

A null model of morphospace occupation

scientific article published on 21 April 2005

A practical generation-interval-based approach to inferring the strength of epidemics from their speed

scientific article published on 10 January 2019

A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances

scientific article published on 11 September 2020

A thermal trade-off between viral production and degradation drives phytoplankton-virus population dynamics

scientific article published on 18 August 2020

A touch of sleep: biophysical model of contact-mediated dormancy of archaea by viruses.

scientific article

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments.

scientific article published on 21 February 2018

Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations

scientific article published on 27 April 2020

Allometric covariation: a hallmark behavior of plants and leaves

scientific article published on March 2012

Alternative stable states in host–phage dynamics

scientific article published in 2007

An empirical model of carbon flow through marine viruses and microzooplankton grazers

scientific article published on 07 May 2019

An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure

scientific article

An oscillating tragedy of the commons in replicator dynamics with game-environment feedback

scientific article published on 8 November 2016

Attitudes towards booster, testing and isolation, and their impact on COVID-19 response in winter 2022/2023 in France, Belgium, and Italy

scientific article published on 4 January 2023

Author Correction: Caution in inferring viral strategies from abundance correlations in marine metagenomes

scientific article published on 19 February 2019

Author Correction: Re-examination of the relationship between marine virus and microbial cell abundances

scientific article published on 3 October 2017

Awareness-driven behavior changes can shift the shape of epidemics away from peaks and toward plateaus, shoulders, and oscillations

scientific article published on 22 December 2020

Bacteria-phage coevolution with a seed bank

scientific article published in August 2023

Bacterivorous grazers facilitate organic matter decomposition: a stoichiometric modeling approach

scientific article published on 29 April 2009

BiMat : a MATLAB package to facilitate the analysis of bipartite networks

article

Bifurcation Analysis of Gene Regulatory Circuits Subject to Copy Number Variation

scientific article published in January 2010

CRISPR-induced distributed immunity in microbial populations.

scientific article

Caution in inferring viral strategies from abundance correlations in marine metagenomes

scientific article published in Nature Communications

ClearedLeavesDB: an online database of cleared plant leaf images

scientific article (publication date: 28 March 2014)

Coevolution can reverse predator-prey cycles

scientific article

Coevolution with a seed bank

scientific article published on 10 February 2023

Cohort-based approach to understanding the roles of generation and serial intervals in shaping epidemiological dynamics

scientific article published on 5 June 2020

Collective decision making in bacterial viruses

scientific article published on 20 June 2008

Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean

scientific article published on 08 October 2020

Complex marine microbial communities partition metabolism of scarce resources over the diel cycle

scientific article

Conflicting attachment and the growth of bipartite networks. ⬇️

scientific article

Correction for Demory et al., “Linking Light-Dependent Life History Traits with Population Dynamics for Prochlorococcus and Cyanophage”

scientific article published on 26 October 2021

Costs and benefits of reticulate leaf venation

scientific article

Critical cell wall hole size for lysis in Gram-positive bacteria ⬇️

scientific article published on January 9, 2013

Cyanophages from a less virulent clade dominate over their sister clade in global oceans

scientific article published in 2022

Dangerous nutrients: evolution of phytoplankton resource uptake subject to virus attack

scientific article

Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics

scientific article

Disease dynamics in a stochastic network game: a little empathy goes a long way in averting outbreaks

scientific article published on 14 March 2017

Disease-dependent interaction policies to support health and economic outcomes during the COVID-19 epidemic

scientific article published on 01 September 2020

Disentangling niche competition from grazing mortality in phytoplankton dilution experiments

scientific article

Distinguishing between Indirect and Direct Modes of Transmission Using Epidemiological Time Series ⬇️

scientific article published on January 10, 2013

Dynamics of a contact process with ontogeny

scientific article published on 31 August 2004

Dynamics of indirectly transmitted infectious diseases with immunological threshold

scientific article published on 19 December 2008

Dynamics of nutrient uptake strategies: lessons from the tortoise and the hare

scientific article

Dynamics of shigellosis epidemics: estimating individual-level transmission and reporting rates from national epidemiologic data sets

scientific article

Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment

scientific article published on 21 January 2023

Emergence of increased frequency and severity of multiple infections by viruses due to spatial clustering of hosts

scientific article published on 23 January 2017

Estimates of leaf vein density are scale dependent

scientific article (publication date: 2014)

Estimating the cumulative incidence of SARS-CoV-2 infection and the infection fatality ratio in light of waning antibodies

scientific article published on 16 November 2020

Evaluating scaling models in biology using hierarchical Bayesian approaches

scientific article published on 27 April 2009

Evolution, interactions, and biological networks

scientific article

Faculty Opinions recommendation of Emergent biogeography of microbial communities in a model ocean

scientific article published on 15 August 2012

Faculty Opinions recommendation of Marine viruses and their biogeochemical and ecological effects

scientific article published on 15 August 2012

Faculty Opinions recommendation of Transfer of photosynthesis genes to and from Prochlorococcus viruses

scientific article published on 15 August 2012

Faculty Opinions recommendation of Virus-driven nitrogen cycling enhances phytoplankton growth

scientific article published on 15 August 2012

Fighting microbial pathogens by integrating host ecosystem interactions and evolution

scientific article published on 30 December 2020

Fluctuation domains in adaptive evolution

scientific article published on 18 October 2009

Forward-looking serial intervals correctly link epidemic growth to reproduction numbers

scientific article published on 01 January 2021

Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in "Candidatus Liberibacter asiaticus"

scientific article published on 13 November 2019

Functional and comparative genomic analysis of integrated prophage-like sequences in Candidatus Liberibacter asiaticus

scientific article published on 6 June 2019

Functional biogeography of ocean microbes revealed through non-negative matrix factorization

scientific article (publication date: 2012)

Genomic fluidity: an integrative view of gene diversity within microbial populations

scientific article

Genotypic recognition and spatial responses by rice roots

scientific article published on 29 January 2013

GiA Roots: software for the high throughput analysis of plant root system architecture.

scientific article

Heterogeneous Viral Strategies Promote Coexistence in Virus-Microbe Systems

scientific article published on 30 October 2018

Hierarchical ordering of reticular networks

scientific article (publication date: 2012)

How microbes survive in the open ocean.

scientific article

How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics

scientific article published on 22 April 2022

Image-based high-throughput field phenotyping of crop roots

scientific article Plant Physiology (2014)

Image-based high-throughput field phenotyping of crop roots.

scientific article published on 3 September 2014

Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems

scientific article published on 27 January 2010

Inferring phage-bacteria infection networks from time-series data

scientific article

Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2

scientific article published on 30 May 2023

Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2

scientific article published on 5 July 2022

Information sharing for a coordination game in fluctuating environments

scientific article published on 30 June 2018

Information sharing for a coordination game in fluctuating environments

scientific article published on 20 February 2018

Intermediate levels of asymptomatic transmission can lead to the highest epidemic fatalities

Intermediate levels of asymptomatic transmission can lead to the highest levels of epidemic fatalities

scientific article published on 2 August 2022

Intervention Serology and Interaction Substitution: Modeling the Role of 'Shield Immunity' in Reducing COVID-19 Epidemic Spread

scientific article published on 03 April 2020

Large sample spaces do not imply biological systems are 'fine-tuned'

scientific article published on 20 August 2020

Leaf extraction and analysis framework graphical user interface: segmenting and analyzing the structure of leaf veins and areoles

scientific article (publication date: 2011)

Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing

scientific article published in November 2020

Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities

scientific article published on 01 July 2018

Linking Light-Dependent Life History Traits with Population Dynamics for Prochlorococcus and Cyanophage

scientific article published on 31 March 2020

Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage

scientific article published on 11 July 2019

Lysis, lysogeny and virus-microbe ratios

scientific article published on September 2017

Mechanisms of multi-strain coexistence in host-phage systems with nested infection networks

scientific article

Metacommunity Structure Preserves Genome Diversity in the Presence of Gene-specific Selective Sweeps

scientific article published on 19 January 2023

Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone

scientific article published on 27 April 2023

Modeling post-death transmission of Ebola: challenges for inference and opportunities for control

scientific article published on 4 March 2015

Modeling serological testing to inform relaxation of social distancing for COVID-19 control

scientific article published on 01 May 2020

Modeling serological testing to inform relaxation of social distancing for COVID-19 control

scientific article published on 3 December 2021

Modeling shield immunity to reduce COVID-19 epidemic spread

scientific article published on 07 May 2020

Modeling shield immunity to reduce COVID-19 transmission in long-term care facilities

scientific article published in January 2023

Modeling shield immunity to reduce COVID-19 transmission in long-term care facilities

scientific article published on 20 July 2021

Modeling the synergistic elimination of bacteria by phage and the innate immune system

scientific article published on 28 June 2017

Moving Beyond a Peak Mentality: Plateaus, Shoulders, Oscillations and Other 'Anomalous' Behavior-Driven Shapes in COVID-19 Outbreaks

scientific article published on 08 May 2020

Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages ⬇️

scientific article published on November 22, 2012

Multiple regimes of robust patterns between network structure and biodiversity ⬇️

scientific article published on 3 December 2015

Multiscale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin

scientific article published on 19 March 2012

Ocean viruses and their effects on microbial communities and biogeochemical cycles ⬇️

scientific article published on September 5, 2012

Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching

scientific article published in March 2023

Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching

scientific article published on 27 October 2022

Optimizing the Timing and Composition of Therapeutic Phage Cocktails: A Control-Theoretic Approach

scientific article published on 12 June 2020

Overcoming the Law of the Hidden in Cyberinfrastructures

scientific article

Packing-limited growth

scientific article published on 06 May 2002

Packing-limited growth of irregular objects

scientific article published on 29 January 2003

Phage-bacteria infection networks

scientific article published on 14 December 2012

Quantifying enzymatic lysis: estimating the combined effects of chemistry, physiology and physics

scientific article published on 4 October 2010

Quantitative Infection Dynamics of Cafeteria Roenbergensis Virus

article

Quantitative Models of Phage-Antibiotic Combination Therapy

scientific article published on 04 February 2020

Rapid bacteria-phage coevolution drives the emergence of multi-scale networks

scientific article published on 14 April 2023

Rapid bacteria-phage coevolution drives the emergence of multiscale networks

scientific article published on 09 November 2023

Re-examination of the relationship between marine virus and microbial cell abundances.

scientific article

Re-examining the relationship between virus and microbial cell abundances in the global oceans

Reacting to outbreaks at neighboring localities

scientific article published on 29 April 2020

Real-time, interactive website for US-county level Covid-19 event risk assessment

scientific article published on 29 August 2020

Real-time, interactive website for US-county-level COVID-19 event risk assessment

scientific article published on 09 November 2020

Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak

scientific article published on 22 July 2020

Reconciling early-outbreak preliminary estimates of the basic reproductive number and its uncertainty: a new framework and applications to the novel coronavirus (2019-nCoV) outbreak

scientific article published on 2 February 2020

Repeatability and contingency in the evolution of a key innovation in phage lambda

scientific article

Revisiting the rules of life for viruses of microorganisms

scientific article published on 24 March 2021

Robust estimation of microbial diversity in theory and in practice.

scientific article

Roles of generation-interval distributions in shaping relative epidemic strength, speed, and control of new SARS-CoV-2 variants

scientific article published on 5 May 2021

Scale-dependence of resource-biodiversity relationships

scientific article published in November 2003

Scenario-based messages on social media motivate COVID-19 information seeking

scientific article published on 27 April 2023

Small-scale copy number variation and large-scale changes in gene expression.

scholarly article

Spread of COVID-19 through Georgia, USA. Near-term projections and impacts of social distancing via a metapopulation model

scientific article published on 30 May 2020

Statistical structure of host-phage interactions

scientific article

Stochasticity and the limits to confidence when estimating R0 of Ebola and other emerging infectious diseases

scientific article published on 11 August 2016

Surveillance-to-Diagnostic Testing Program for Asymptomatic SARS-CoV-2 Infections on a Large, Urban Campus - Georgia Institute of Technology, Fall 2020

scientific article published on 31 January 2021

Synergy between the Host Immune System and Bacteriophage Is Essential for Successful Phage Therapy against an Acute Respiratory Pathogen

scientific article published on July 2017

Systematic biases in disease forecasting - The role of behavior change

scientific article published on 28 February 2019

Testing the metabolic theory of ecology

scientific article published on 30 August 2012

The Effect of Strain Level Diversity on Robust Inference of Virus-Induced Mortality of Phytoplankton

scientific article published on 03 September 2018

The elemental composition of virus particles: implications for marine biogeochemical cycles

scientific article published on July 2014

The evolution of dispersal in reserve networks

scientific article published on 22 May 2007

The fiber walk: a model of tip-driven growth with lateral expansion

scientific article published in 2014

The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants

scientific article published in June 2022

The metabolic theory of ecology: prospects and challenges for plant biology

scientific article published on 03 September 2010

The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak

scientific article published on 11 May 2020

The virus of my virus is my friend: ecological effects of virophage with alternative modes of coinfection

scientific article published on 21 March 2014

Timescales modulate optimal lysis-lysogeny decision switches and near-term phage reproduction

scientific article published in 2022

To Lyse or Not to Lyse: Transient-Mediated Stochastic Fate Determination in Cells Infected by Bacteriophages ⬇️

scientific article published on March 10, 2011

Topological constraints in early multicellularity favor reproductive division of labor

scientific article published on 17 September 2020

Unsupervised statistical clustering of environmental shotgun sequences.

scientific article

Vaccine Stockpile Sharing For Selfish Objectives

scientific article published in May 2022

Vaccine stockpile sharing for selfish objectives

scientific article published on 5 December 2022

Viral Invasion Fitness Across a Continuum from Lysis to Latency

scientific article published on 6 April 2018

Viral ecology comes of age.

scientific article published on 26 November 2016

Viral invasion fitness across a continuum from lysis to latency

article by Joshua S Weitz et al published January 2019 in Virus Evolution

When to be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny

scientific article published on 22 July 2019

When to be temperate: on the fitness benefits of lysis vs. lysogeny

scientific article published in July 2020

Zero-sum allocational strategies determine the allometry of specific leaf area

scientific article published on 25 October 2010

localcovid19now: processing and mapping COVID-19 case data at subnational scales

scientific article published on 21 January 2023

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