Weitz Group

Investigating how viruses transform human health and the fate of our planet

Investigating how viruses transform human health and the fate of our planet.      

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    • Foundations of Quantitative Viral Ecology
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    • Viral Ecology of Marine Systems
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    • Joshua Weitz
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Title Authors Journal Tools
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 G. de Meijere, E. Valdano, C. Castellano, M. Debin, C. Kengne-Kuetche, C. Turbelin, H. Noël, J.S. Weitz, D. Paolotti, L. Hermans, N. Hens, V. Colizza The Lancet Regional Health- Europe Github Repository
Microbial and Viral Genome and Proteome Nitrogen Demand Varies Across Multiple Spatial Scales Within a Marine Oxygen Minimum Zone D. Muratore, A. D. Bertagnolli, L. A. Bristow, B. Thamdrup, J. S. Weitz, F. J. Stewart mSystems Github Repository
How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics J. Harris, S.W. Park, J. Dushoff, J.S. Weitz Epidemics Github Repository
The dynamic interplay of bacteriophage, bacteria and the mammalian host during phage therapy J. Marchi, S. Zborowsky, L. Debarbieux, J.S.Weitz iScience
Reasons for Receiving or Not Receiving Bivalent COVID-19 Booster Vaccinations Among Adults A.H. Sinclair, M.K. Taylor, J.S. Weitz, S.J. Beckett, G.R. Samanez-Larkin CDC Morbidity and Mortality Weekly Report
localcovid19now: processing and mapping COVID-19 case data at subnational scales S.J. Beckett, F.A. Brandel-Tanis, Q. Nguyen, A.T. Chande, L. Rishishwar, C. Andris, J.S. Weitz The Journal of Open Source Software Github Repository
Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching A. Măgălie, D. A. Schwartz, J. T. Lennon, J. S. Weitz Journal of Theoretical Biology
Modeling shield immunity to reduce COVID-19 transmission in long-term care facilities A. Lucia-Sanz, A. Magalie, R. Rodriguez-Gonzalez, C.-Y. Leung, J. S.Weitz Annals of Epidemiology

Title Authors Journal Tools
Vaccine stockpile sharing for selfish objectives S. Shivam, J.S. Weitz, Y. Wardi PLOS Global Public Health
The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants S.W. Park , B.M. Bolker, S. Funk, C.J.E. Metcalf , J.S. Weitz , B.T. Grenfell, J. Dushoff Journal of the Royal Society Interface Github Repository
Cyanophages from a less virulent clade dominate over their sister clade in global oceans I. Maidanik, S. Kirzner, I. Pekarski, L. Arsenieff, R. Tahan, M.C.G. Carlson, D. Shitrit, N. Baran, S. Goldin, J.S. Weitz, D. Lindell The ISME Journal
Time-Scales Modulate Optimal Lysis-Lysogeny Decision Switches and Near-Term Phage Reproduction S. Shivam, G. Li, A. Lucia-Sanz, J.S. Weitz Virus Evolution Github Repository
Quantifying Risk for SARS-CoV-2 Infection Among Nursing Home Workers for the 2020-2021 Winter Surge of the COVID-19 Pandemic in Georgia, USA W.C. Dub, T.J Kellogg, C. Adams, M.H. Collins, B.A Lopman, T.M. Johnson, A.B. Amin, J.S. Weitz, S.K. Fridkin Journal of the American Medical Directors Association
Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing A. Gupta, S. Peng, C.Y. Leung, J.M. Borin, S.J. Medina, J.S. Weitz, J.R. Meyer Ecology Letters
Complex marine microbial communities partition metabolism of scarce resources over the diel cycle A.D. Muratore, A.K. Boysen, M.J. Harke, K.W. Becker, J.R. Casey, S.N. Coesel, D.R. Mende, S.T. Wilson, F.O. Aylward, J.M. Eppley, A. Vislova, S. Peng, R.A. Rodriguez-Gonzalez, S.J. Beckett, E.V. Armbrust, E.F. DeLong, D.M. Karl, A.E. White, J.P. Zehr, B.A.S. Van Mooy, S.T. Dyhrman, A.E. Ingalls, J.S. Weitz Nature Ecology and Evolution Github Repository
Surveillance-to-Diagnostic Testing Program for Asymptomatic SARS-CoV-2 Infections on a Large, Urban Campus in Fall 2020 G. Gibson, J.S. Weitz, M.P. Shannon, B. Holton, A. Bryksin, B. Liu, M. Sieglinger, A.R. Coenen, C. Zhao, S.J. Beckett, S. Bramblett, J. Williamson, M. Farrell, A. Ortiz, C.T. Abdallah, A.J. Garcia Epidemiology Github Repository

Title Authors Journal Tools
Linking light-dependent life history traits with population dynamics for Prochlorococcus and cyanophage D. Demory, R. Liu, Y. Chen, F. Zhao, A.R. Coenen, Q. Zeng, J.S. Weitz mSystems Github Repository
Modeling serological testing to inform relaxation of social distancing for COVID-19 control A.N.M. Kraay, K.N. Nelson, C.Y. Zhao, D. Demory, J.S. Weitz, B.A. Lopman Nature Communications
Risk factors for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) seropositivity among nursing home staff A.B. Amin, J.T. Kellogg, C. Adams, W.C. Dube, M.H. Collins, B.A. Lopman, T.M. Johnson II, J.S. Weitz, S.K. Fridkin Antimicrobial Stewardship & Healthcare Epidemiology
A framework for monitoring population immunity to SARS-CoV-2 B.A. Lopman, K. Shioda, Q. Nguyen, S.J. Beckett, A.J. Siegler, P.S. Sullivan, J.S. Weitz Annals of Epidemiology Github Repository
Heterogeneity in susceptibility dictates the order of epidemic models C. Rose, A.J. Medford, C.F Goldsmith, T. Vegge, J.S.Weitz, A.A. Petersonac Journal of Theoretical Biology Github Repository
Reacting to outbreaks at neighboring localities Ceyhun Eksin, Martial Ndeffo-Mbah, Joshua S.Weitz Journal of Theoretical Biology Github Repository
Infect while the iron is scarce: nutrient-explicit phage-bacteria games Daniel Muratore, Joshua S. Weitz Theoretical Ecology Github Repository
Disease-dependent interaction policies to support health and economic outcomes during the COVID-19 epidemic Guanlin Li, Shashwat Shivam, Michael E. Hochberg, Yorai Wardi, Joshua S. Weitz iScience Github Repository
Estimating the cumulative incidence of SARS-CoV-2 infection and the infection fatality ratio in light of waning antibodies Kayoko Shioda, Max S.Y. Lau, Alicia N.M. Kraay, Kristin N. Nelson, Aaron J. Siegler, Patrick S. Sullivan, Matthew H. Collins, Joshua S. Weitz, Benjamin A. Lopman Epidemiology
A thermal trade‐off between viral production and degradation drives virus‐phytoplankton population dynamics David Demory, Joshua S. Weitz, Anne‐Claire Baudoux, Suzanne Touzeau, Natalie Simon, Sophie Rabouille, Antoine Sciandra, Olivier Bernard Ecology Letters Github Repository
Fighting microbial pathogens by integrating host ecosystem interactions and evolution Alita R. Burmeister, Elsa Hansen, Jessica J. Cunningham, E. Hesper Rego, Paul E. Turner, Joshua S. Weitz, Michael E. Hochberg BioEssays
Forward-looking serial intervals correctly link epidemic growth to reproduction numbers Sang Woo Park, Kaiyuan Sun, David Champredon, Michael Li, Benjamin M. Bolker, David J. D. Earn, Joshua S. Weitz, Bryan T. Grenfell, Jonathan Dushoff PNAS
Revisiting the rules of life for viruses of microorganisms Adrienne M.S. Correa, Cristina Howard-Varona, Samantha R. Coy, Alison Buchan, Matthew B. Sullivan, Joshua S. Weitz Nature Reviews Microbiology
A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances Noor Mruwat, Michael C. G. Carlson, Svetlana Goldin, François Ribalet, Shay Kirzner, Yotam Hulata, Stephen J. Beckett, Dror Shitrit, Joshua S. Weitz, E. Virginia Armbrust, Debbie Lindell The ISME Journal
Combined pigment and metatranscriptomic analysis reveals highly synchronized diel patterns of phenotypic light response across domains in the open oligotrophic ocean Kevin W. Becker, Matthew J. Harke, Daniel R. Mende, Daniel Muratore, Joshua S. Weitz, Edward F. DeLong, Sonya T. Dyhrman, Benjamin A. S. Van Mooy The ISME Journal

Title Authors Journal Tools
A single-cell polony method reveals low levels of infected Prochlorococcus in oligotrophic waters despite high cyanophage abundances Noor Mruwat, Michael C. G. Carlson, Svetlana Goldin, François Ribalet, Shay Kirzner, Yotam Hulata, Stephen J. Beckett, Dror Shitrit, Joshua S. Weitz, E. Virginia Armbrust, Debbie Lindell The ISME Journal
Large sample spaces do not imply biological systems are ‘fine-tuned’ Joseph Lachance, Corinne N.Simonti, Joshua S.Weitz Journal of Theoretical Biology
Awareness-driven behavior changes can shift the shape of epidemics away from peaks and toward plateaus, shoulders, and oscillations Joshua S. Weitz, Sang Woo Park, Ceyhun Eksin, Jonathan Dushoff PNAS
Modeling shield immunity to reduce COVID-19 epidemic spread Joshua S. Weitz, Stephen .J Beckett, Ashley R. Coenen, David Demory, Marian Dominguez-Mirazo, Jonathan Dushoff, Chung-Yin Leung, Guanlin Li, Andreea Măgălie, Sang Woo Park, Rogelio Rodriguez-Gonzalez, Shashwat Shivam, Conan Y. Zhao Nature Medicine Github Repository
The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak Sang Woo Park, Daniel M. Cornforth, Jonathan Dushoff, Joshua S. Weitz Epidemics
Optimizing the Timing and Composition of Therapeutic Phage Cocktails: A Control-Theoretic Approach Guanlin Li, Chung-Yin Leung, Yorai Wardi, Laurent Debarbieux, Joshua S. Weitz Bulletin of Mathematical Biology
Quantitative Models of Phage-Antibiotic Combination Therapy Rogelio A. Rodriguez-Gonzalez, Chung-Yin Leung, Benjamin K. Chan, Paul E. Turner, Joshua S. Weitz mSystems Github repository
Real-time, interactive website for US-county-level COVID-19 event risk assessment Aroon Chande, Seolha Lee, Mallory Harris, Quan Nguyen, Stephen J. Beckett, Troy Hilley, Clio Andris, Joshua S. Weitz Nature Human Behavior
Allelic polymorphism shapes community function in evolving Pseudomonas aeruginosa populations Sheyda Azimi, Aled E. L. Roberts, Shengyun Peng, Joshua S. Weitz, Alan McNally, Samuel P. Brown, Stephen P. Diggle The ISME Journal
Linking Light-Dependent Life History Traits with Population Dynamics for Prochlorococcus and Cyanophage David Demory, Riyue Liu, Yue Chen, Fangxin Zhao, Ashley R. Coenen, Qinglu Zeng, Joshua S. Weitz mSystems Github Repository
A Primer for Microbiome Time-Series Analysis Ashley R. Coenen, Sarah K. Hu, Elaine Luo, Daniel Muratore, Joshua S. Weitz Frontiers in Genetics Github Repository
Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak Sang Woo Park, Benjamin M. Bolker, David Champredon, David J. D. Earn, Michael Li, Joshua S. Weitz, Bryan T. Grenfell, Jonathan Dushoff Journal of the Royal Society Interface
Topological constraints in early multicellularity favor reproductive division of labor David Yanni, Shane Jacobeen, Pedro Márquez-Zacarías, Joshua S Weitz, William C Ratcliff, Peter J Yunker eLife
When to be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny Guanlin Li, Michael H. Cortez, Jonathan Dushoff, Joshua S. Weitz Virus Evolution Github Repository

Title Authors Journal Tools
Heterogeneous viral strategies promote coexistence in virus-microbe systems Heyriye Gulbudak, Joshua S. Weitz Journal of Theoretical Biology
The ecological and biogeochemical state of the North Pacific Subtropical Gyre is linked to sea surface height Benedetto Barone, Ashley R. Coenen, Stephen J. Beckett, Dennis J. McGillicuddy, Joshua S. Weitz, David M. Karl Journal of Marine Research
Spatial Interactions and Oscillatory Tragedies of the Commons Yu-Hui Lin, Joshua S. Weitz Physical Review Letters Github Repository
An empirical model of carbon flow through marine viruses and microzooplankton grazers David Talmy, Stephen J. Beckett, Darcy A. Taniguchi, Corina P.D. Brussaard, Joshua S. Weitz, Michael J. Follows  Environmental Microbiology
Viral invasion fitness across a continuum from lysis to latency Joshua S. Weitz, Guanlin Li, Hayriye Gulbudak, Michael H. Cortez, Rachel J. Whitaker Virus Evolution Github Repository
Caution in inferring viral strategies from abundance correlations in marine metagenomes Hend Alrasheed, Rong Jin, Joshua S. Weitz Nature Communications
Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “Candidatus Liberibacter asiaticus” Marian Dominguez-Mirazo, Rong Jin, Joshua S. Weitz mSphere Github Repository
Contrasting Controls on Microzooplankton Grazing and Viral Infection of Microbial Prey David Talmy, Stephen J. Beckett, Adam B. Zhang, Darcy A. A. Taniguchi, Joshua S. Weitz, Michael J. Follows Frontiers in Marine Science
Systematic biases in disease forecasting – The role of behavior change Ceyhun Eksin, Keith Paarporn, Joshua S.Weitz Epidemics
Not by (Good) Microbes Alone: Towards Immunocommensal Therapies Chung-Yin Leung, Joshua S. Weitz Trends in Microbiology Github Repository
A practical generation-interval-based approach to inferring the strength of epidemics from their speed Sang WooPark, David Champredon, Joshua S.Weitz, Jonathan Dushoff Epidemics

Title Authors Journal Tools
Information sharing for a coordination game in fluctuating environments Keith Paarporn, Ceyhun Eksin, Joshua S.Weitz Journal of Theoretical Biology Github Repository
Limitations of correlation-based inference in complex virus-microbe communities Ashley R. Coenen, Joshua S. Weitz mSystems Github Repository
The Effect of Strain Level Diversity on Robust Inference of Virus-Induced Mortality of Phytoplankton Stephen J. Beckett, Joshua S. Weitz Frontiers in Microbiology
A virus or more in (nearly) every cell: ubiquitous networks of virus–host interactions in extreme environments Jacob H. Munson-McGee, Shengyun Peng, Samantha Dewerff, Ramunas Stepanauskas, Rachel J. Whitaker, Joshua S. Weitz, Mark J. Young The ISME Journal
Optimal control policies for evolutionary dynamics with environmental feedback Keith Paarporn, Ceyhun Eksin, Joshua S.Weitz, Yorai Wardi IEEE Conference on Decision and Control
Quantitative Infection Dynamics of Cafeteria Roenbergensis Virus Bradford P. Taylor, Joshua S. Weitz, Corina P.D. Brussaard, Matthias G. Fischer Viruses Github Repository

Title Authors Journal Tools
Modeling the synergistic elimination of bacteria by phage and the innate immune system Chung-Yin Leung, Joshua S. Weitz Journal of Theoretical Biology Github Repository
Networked SIS Epidemics With Awareness Keith Paarporn, Ceyhun Eksin, Joshua S. Weitz, Jeff S. Shamma IEEE Transactions on Computational Social Systems
Lysis, lysogeny and virus–microbe ratios Joshua S. Weitz, Stephen J. Beckett, Jennifer R. Brum, B. B. Cael, Jonathan Dushoff Nature Github Repository
How microbes survive the open ocean Johnathan P. Zehr, Joshua S. Weitz Science
Synergy between the Host Immune System and Bacteriophage Is Essential for Successful Phage Therapy against an Acute Respiratory Pathogen Dwayne R. Roach, Chung- Yin Leung, Marine Henry, Eric Morello, Devika Singh, James P. Di Santo, Joshua S. Weitz, Laurent Debarbieux Cell Host & Microbe Github Repository
Viral ecology comes of age Matthew B. Sullivan, Joshua S. Weitz, Steven Wilhelm Environmental Microbiology Reports
Disease dynamics in a stochastic network game: a little empathy goes a long way in averting outbreaks Ceyhun Eksin, Jeff S. Shamma, Joshua S. Weitz Scientific Reports Github Repository
Overcoming the law of the hidden cyberinfrastructures Alexander Bucksch, Abhiram Das, Hannah Schneider, Nirav Merchant, Joshua S. Weitz Trends in Plant Science
Disentangling niche competition from grazing mortality in phytoplankton dilution experiments Stephen J. Beckett, Joshua S. Weitz PloS One Github Repository

Title Authors Journal Tools
Re-examination of the relationship between marine virus and microbial cell abundances Charles H. Wigington, Derek Sonderegger, Corina P. D. Brussaard, Alison Buchan, Jan F. Finke, Jed A. Fuhrman, Jay T. Lennon, Mathias Middelboe, Curtis A. Suttle, Charles Stock, William H. Wilson, K. Eric Wommack, Steven W. Wilhelm, Joshua S. Weitz Nature Microbiology Github Repository
Stochasticity and the limits to confidence when estimating R0 of Ebola and other emerging infectious diseases Bradford P. Taylor, Jonathan Dushoff, Joshua S.Weitz Journal of Theoretical Biology Github Repository
A touch of sleep: biophysical model of contact-mediated dormancy of archaea by viruses Hayriye Gulbudak, Hoshua S. Weitz Proceedings of the Royal Society B: Biological Sciences
Conflicting attachment and the growth of bipartite networks Chung-Yin Leung, Joshua S. Weitz Physical Review E Github Repository
Inferring phage–bacteria infection networks from time-series data Luis F. Jover, Justin Romberg, Joshua S. Weitz Royal Society Open Science
An oscillating tragedy of the commons in replicator dynamics with game-environment feedback Joshua S. Weitz, Ceyhun Eksin, Keith Paarporn, Sam P. Brown, William C. Ratcliff PNAS
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer Ann C. Gregory, Sergei A. Solonenko, J. Cesar Ignacio-Espinoza, Kurt LaButti, Alex Copeland, Sebastian Sudek, Ashley Maitland, Lauren Chittick, Filipa dos Santos, Joshua S. Weitz, Alexandra Z. Worden, Tanja Woyke, Matthew B. Sullivan BMC Genomics

Title Authors Journal Tools
Multiple regimes of robust patterns between network structure and biodiversity Luis F. Jover, Cesar O. Flores, Michael H. Cortez, Joshua S. Weitz Scientific Reports Github Repository
Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics Abhiram Das, Hannah Schneider, James Burridge, Ana Karine Martinez Ascanio, Tobias Wojciechowski, Christopher N. Topp, Jonathan P. Lynch, Joshua S. Weitz, Alexander Bucksch Plant Methods Github Repository
Reconstructing weighted networks from dynamics Emily S. C. Ching, Pik-Yin Lai, Chung-Yin Leung Physical Review E
A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes Joshua S. Weitz, Charles A. Stock, Steven W. Wilhelm, Lydia Bourouiba, Maureen L. Coleman, Alison Buchan, Michael J. Follows, Jed A. Fuhrman, Luis F. Jover, Jay T. Lennon, Mathias Middelboe, Derek L. Sonderegger, Curtis A. Suttle, Bradford P. Taylor, T. Frede Thingstad, William H. Wilson, K. Eric Wommack The ISME Journal
Modeling post-death transmission of Ebola: challenges for inference and opportunities for control Joshua S. Weitz, Johnathan Dushoff Scientific Reports Github Respository

Title Authors Journal Tools
ClearedLeavesDB: an online database of cleared plant leaf images Abhiram Das, Alexander Bucksch, Charles A Price, Joshua S Weitz Plant Methods
The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection Bradford P. Taylor, Michael H. Cortez, Joshua S. Weitz Journal of Theoretical Biology
Let my people go (home) to Spain: a genealogical model of Jewish identities since 1492 Joshua S. Weitz PloS One
The fiber walk: a model of tip-driven growth with lateral expansion Alexander Bucksch, Greg Turk, Joshua S. Weitz PloS One
Estimates of leaf vein density are scale dependent Charles A. Price, Peter R.T. Munro, Joshua S. Weitz Plant Physiology
Suppression of expression between adjacent genes within heterologous modules in yeast Tae J. Lee, Rasesh Y. Parikh, Joshua S. Weitz, Harold D. Kim G3: Genes, Genomes, Genetics
Costs and benefits of reticulate leaf venation Charles A. Price, Joshua S. Weitz BMC Plant Biology
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space Li Deng, J. Cesar Ignacio-Espinoza, Ann C. Gregory, Bonnie T. Poulos, Joshua S. Weitz, Philip Hugenholtz, Matthew B. Sullivan Nature
The elemental composition of virus particles: implications for marine biogeochemical cycles Luis F. Jover, T. Chad Effler, Alison Buchan, Steven W. Wilhelm, Joshua S. Weitz Nature Reviews Microbiology
CRISPR-induced distributed immunity in microbial populations Lauren M. Childs, Whitney E. England, Mark J. Young, Joshua S. Weitz, Rachel J. Whitaker PloS One
Coevolution can reverse predator–prey cycles Michael H. Cortez, Joshua S. Weitz PNAS

Title Authors Journal Tools
Critical cell wall hole size for lysis in Gram-positive bacteria Gabriel J. Mitchell, Kurt Wiesenfeld, Daniel C. Nelson, Joshua S. Weitz Journal of the Royal Society Interface
Distinguishing between indirect and direct modes of transmission using epidemiological time series Michael H. Cortez, Joshua S. Weitz The American Naturalist
Dynamics of shigellosis epidemics: estimating individual-level transmission and reporting rates from national epidemiologic data sets Richard I. Joh, Robert M. Hoekstra, Ezra J. Barzilay, Anna Bowen, Eric D. Mintz, Howard Weiss, Joshua S. Weitz American Journal of Epidemiology
3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture Christopher N. Topp, Anjali S. Iyer-Pascuzzi, Jill T. Anderson, Cheng-Ruei Lee, Paul R. Zurek, Olga Symonova, Ying Zheng, Alexander Bucksch, Yuriy Mileyko, Taras Galkovskyi, Brad T. Moore, John Harer, Herbert Edelsbrunner, Thomas Mitchell-Olds, Joshua S. Weitz, Philip N. Benfey PNAS
A guide to sensitivity analysis of quantitative models of gene expression dynamics Bradford Taylor, Tae J. Lee, Joshua S. Weitz Methods
Mechanisms of multi-strain coexistence in host–phage systems with nested infection networks Luis F. Jover, Michael H. Cortez, Joshua S. Weitz Journal of Theoretical Biology
Genotypic recognition and spatial responses by rice roots Suqin Fang, Randy T. Clark, Ying Zheng, Anjali S. Iyer-Pascuzzi, Joshua S. Weitz, Leon V. Kochian, Herbert Edelsbrunner, Hong Liao, Philip N. Benfey PNAS
Phage–bacteria infection networks Joshua S. Weitz, Timothée Poisot, Justin R. Meyer, Cesar O. Flores, Sergi Valverde, Matthew B. Sullivan, Michael E. Hochberg Trends in Microbiology
Extracting connectivity from dynamics of networks with uniform bidirectional coupling Emily S. C. Ching, Pik-Yin Lai, Chung-Yin Leung Physical Review E

Title Authors Journal Tools
Scaling and structure of dicotyledonous leaf venation networks Charles A. Price, Scott Wing, Joshua S. Weitz Ecology Letters
A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data Xingpeng Jiang, Joshua S. Weitz, Jonathan Dushoff Journal of Mathematical Biology
Repeatability and contingency in the evolution of a key innovation in phage lambda Justin R. Meyer, Devin T. Dobias, Joshua S. Weitz, Jeffrey E. Barrick, Ryan T. Quick, Richard E. Lenski Science
Allometric covariation: a hallmark behavior of plants and leaves Charles A. Price, Joshua S. Weitz New Phytologist
Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages Cesar O. Flores, Sergi Valverde, Joshua S. Weitz The ISME Journal
Testing the metabolic theory of ecology Charles A. Price, Joshua S Weitz, Van M. Savage, James Stegen, Andrew Clarke, David A. Coomes, Peter S. Dodds, Rampal S. Etienne, Andrew J. Kerkhoff, Katherine McCulloh, Karl J. Niklas, Han Olff, Nathan G. Swenson Ecology Letters
Functional biogeography of ocean microbes revealed through non-negative matrix factorization Xingpeng Jiang, Morgan G.I. Langille, Russell Y. Neches, Marie Elliot, Simon A. Levin, Jonathan A. Eisen, Joshua S. Weitz, Jonathan Dushoff PloS One
GiA Roots: software for the high throughput analysis of plant root system architecture Taras Galkovskyi, Yuriy Mileyko, Alexander Bucksch, Brad Moore, Olga Symonova, Charles A. Price, Christopher N. Topp, Anjali S. Iyer-Pascuzzi, Paul R. Zurek, Suqin Fang, John Harer, Philip N. Benfey, Joshua S. Weitz BMC Plant Biology
A neutral theory of genome evolution and the frequency distribution of genes Bart Haegeman, Joshua S. Weitz BMC Genomics Github Repository
Ocean viruses and their effects on microbial communities and biogeochemical cycles Joshua S. Weitz, Steven W. Wilhelm F1000 Biology Reports
Hierarchical Ordering of Reticular Networks Yuriy Mileyko, Herbert Edelsbrunner, Charles A. Price, Joshua S. Weitz PloS One

Title Authors Journal Tools
Genomic fluidity: an integrative view of gene diversity within microbial populations Andrey O. Kislyuk, Bart Haegeman, Nicholas H. Bergman, Joshua S. Weitz BMC Genomics Github Repository
To lyse or not to lyse: transient-mediated stochastic fate determination in cells infected by bacteriophages Richard I. Joh, Joshua S. Weitz PLoS Computational Biology Github Repository
Analysing threshold effects in the sexual dynamics of cyclically parthenogenetic rotifer populations Manuel Serra, Hilary A. Smith, Joshua S. Weitz, Terry W. Snell Hydrobiologia
Dynamics of nutrient uptake strategies: lessons from the tortoise and the hare Duncan N.L. Menge, Ford Ballantyne, Joshua S. Weitz Theoretical Ecology
Statistical structure of host–phage interactions Cesar O. Flores, Justin R. Meyer, Sergi Valverde, Lauren Farr, Joshua S. Weitz PNAS

Title Authors Journal Tools
Fluctuation domains in adaptive evolution Carl Boettiger, Johnathan Dushoff, Joshua S. Weitz Theoretical Population Biology Github Repository
Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems Anjali S. Iyer-Pascuzzi, Olga Symonova, Yuriy Mileyko, Yueling Hao, Heather Belcher, John Harer, Joshua S. Weitz, Philip N. Benfey Plant Physiology
The metabolic theory of ecology: prospects and challenges for plant biology Charles A. Price, James F. Gilooly, Andrew P. Allen, Joshua S. Weitz, Karl J. Niklas New Phytologist
Quantifying enzymatic lysis: estimating the combined effects of chemistry, physiology and physics Gabriel J. Mitchell, Daniel C. Nelson, Joshua S. Weitz Physical Biology

Title Authors Journal Tools
Bacterivorous grazers facilitate organic matter decomposition: a stoichiometric modeling approach Hao Wang, Lin Jiang, Joshua S. Weitz FEMS Microbiology Ecology
Unsupervised statistical clustering of environmental shotgun sequences Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff, Joshua S. Weitz BMC Bioinformatics

Title Authors Journal Tools
Alternative stable states in host–phage dynamics Joshua S. Weitz, Johnathan Dushoff Theoretical Ecology
Collective decision making in bacterial viruses Joshua S. Weitz, Yuriy Mileyko, Richard I. Joh, Eberhard O. Voit Biophysical Journal
Small-scale copy number variation and large-scale changes in gene expression Yuriy Mileyko, Richard I. Joh, Joshua S. Weitz PNAS
Evolutionary ecology of bacterial viruses Joshua S. Weitz Microbe

Title Authors Year Journal Tools
Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment R. Pineau, D. Demory, E. Libby, D.T. Lac, T. Day, P. Bravo, J.S. Weitz, P.J. Yunker, G.O. Bozdag, W.C. Ratcliff 2023 bioRxiv
Attitudes towards booster, testing and isolation, and their impact on COVID-19 response in winter 2022/2023 in France, Belgium, and Italy G. de Meijere, E. Valdano, C. Castellano, M. Debin, C. Kengne-Kuetche, C. Turbelin, H. Noël, J.S. Weitz, D. Paolotti, L. Hermans, N. Hens, V. Colizza 2023 medRxiv
Coevolution with a seed bank D.A. Schwartz, W.R. Shoemaker, A.Magalie, J.S. Weitz, J.T. Lennon 2023 bioRxiv
Metacommunity Structure Preserves Genome Diversity in the Presence of Gene-specific Selective Sweeps. S. Pompei, E. Bella, J.S. Weitz, J. Grilli, M. Cosentino Lagomarsino 2023 bioRxiv Github Repository
Counteracting COVID-19 Risk Misestimation with an Interactive Website: An Online Informational Intervention A.H. Sinclair, M. Taylor, F. Brandel-Tanis, A. Davidson, A.T. Chande, L. Rishishwar, C.M. Andris, R.A. Adcock, J.S. Weitz, G. Samanez-Larkin, S.J. Beckett 2022 PsyArXiv Covid-19 risk tool user data
How time-scale differences in asymptomatic and symptomatic transmission shape SARS-CoV-2 outbreak dynamics J. Harris, S.W. Park, J. Dushoff, J.S. Weitz 2022 medRxiv Github Repository
Scenario-Based Messages on Social Media Motivate COVID-19 Information Seeking A.H. Sinclair, M. Taylor, A. Davidson, J.S. Weitz, S.J. Beckett, G. Samanez-Larkin 2022 PsyArXiv COVID-19 Event Risk Tool: User Data
Intermediate levels of asymptomatic transmission can lead to the highest levels of epidemic fatalities S.W. Park, J. Dushoff, B. Grenfell, J.S. Weitz 2022 medRxiv Github Repository
Microbial and Viral Genome and Proteome Nitrogen Demand Varies Across Multiple Spatial Scales Within a Marine Oxygen Minimum Zone D. Muratore, A. D. Bertagnolli, L. A. Bristow, B. Thamdrup, J. S. Weitz, F. J. Stewart 2022 bioRxiv Github Repository
Real-time Interventions Counteract COVID-19 Risk Misestimation in the United States AH Sinclair, M Taylor, F Brandel-Tanis, A Davidson, AT Chande, L Rishishwar, CM Andris, RA Adcock, JS Weitz, G Samanez-Larkin, SJ Beckett 2022 PsyArXiv
Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2 Sang Woo Park, Kaiyuan Sun, Sam Abbott, Ron Sender, Yinon Bar-on, Joshua S. Weitz, Sebastian Funk, Bryan T. Grenfell, Jantien A Backer, Jacco Wallinga, Cecile Viboud, Jonathan Dushoff 2022 MedRxiv
Communicating COVID-19 Exposure Risk with an Interactive Website Counteracts Risk Misestimation A.H. Sinclair, M. Taylor, F.A. Brandel-Tanis, A. Davidson, A.T. Chande, L. Rishishwar, C.M. Andris, R.A. Adcock, J.S. Weitz, G. Samanez-Larkin, S. Beckett 2022 PsyArXiv
Diel population dynamics and mortality of Prochlorococcus in the North Pacific Subtropical Gyre S.J. Beckett, D. Demory, A.R. Coenen, J.R. Casey, M. Dugenne, C.L. Follett, P. Connell, M.C.G. Carlson, S.K. Hu, S.T. Wilson, A.D. Muratore, R.A. Rodriguez-Gonzalez, S. Peng, K.W. Becker, D.R. Mende, E.V. Armbrust, D.A. Caron, D. Lindell, M.J. Follows, A.E. White, F. Ribalet, J.S. Weitz 2021 bioRxiv Github Repository
Spread of COVID-19 through Georgia, USA. Near-term projections and impacts of social distancing via a metapopulation model S.J. Beckett, M. Dominguez-Mirazo, S. Lee, C.M. Andris, J.S. Weitz 2020 medRxiv Github Repository

The Weitz Group

Investigating how viruses transform human health and the fate of our planet

310 Ferst Dr
School of Biological Sciences
Georgia Institute of Technology
Atlanta, GA 30332, USA

Website developed by Audra Davidson for the Weitz Group, 2021. For more information on the group, contact Dr. Gabi Steinbach: gabi.steinbach (@) biosci.gatech.edu

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