| Title | Authors | Journal | Tools |
|---|---|---|---|
| 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 |
|---|---|---|---|
| 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 |
| 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 | |
| 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 | |
| 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 |
| 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 |
| 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 | |
| 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 | |
| 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 |
| 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 | |
| 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 | |
| When 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 |
|---|---|---|---|
| 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 |
|---|---|---|---|
| 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 | |
| Estimates of leaf vein density are scale dependent | Charles A. Price, Peter R.T. Munro, Joshua S. Weitz | Plant Physiology | |
| The fiber walk: a model of tip-driven growth with lateral expansion | Alexander Bucksch, Greg Turk, Joshua S. Weitz | PloS One | |
| Let my people go (home) to Spain: a genealogical model of Jewish identities since 1492 | Joshua S. Weitz | PloS One | |
| 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 | |
| ClearedLeavesDB: an online database of cleared plant leaf images | Abhiram Das, Alexander Bucksch, Charles A Price, Joshua S Weitz | Plant Methods | |
| Coevolution can reverse predator–prey cycles | Michael H. Cortez, Joshua S. Weitz | PNAS | |
| CRISPR-induced distributed immunity in microbial populations | Lauren M. Childs, Whitney E. England, Mark J. Young, Joshua S. Weitz, Rachel J. Whitaker | PloS One | |
| 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 | |
| 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 | |
| Costs and benefits of reticulate leaf venation | Charles A. Price, Joshua S. Weitz | BMC Plant Biology |
| 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 |
|---|---|---|---|
| Allometric covariation: a hallmark behavior of plants and leaves | Charles A. Price, Joshua S. Weitz | New Phytologist | |
| 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 | |
| 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 | |
| Scaling and structure of dicotyledonous leaf venation networks | Charles A. Price, Scott Wing, Joshua S. Weitz | Ecology Letters | |
| Hierarchical Ordering of Reticular Networks | Yuriy Mileyko, Herbert Edelsbrunner, Charles A. Price, Joshua S. Weitz | PloS One | |
| Ocean viruses and their effects on microbial communities and biogeochemical cycles | Joshua S. Weitz, Steven W. Wilhelm | F1000 Biology Reports | |
| A neutral theory of genome evolution and the frequency distribution of genes | Bart Haegeman, Joshua S. Weitz | BMC Genomics | Github Repository |
| 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 | |
| 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 | |
| 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 | |
| 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 |
| 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 |
