Weitz Lab

PI: Joshua Weitz

 

Papers

2020
  • Azimi, S., Roberts, A.E.L., #Peng, S., Weitz, J.S., McNally, A., Brown, S.P., Diggle, S.P., Allelic polymorphism shapes collective phenotypes in evolving Pseudomonas aeruginosa ISME J
  • #Coenen, A.R., Hu, S., Luo, E., #Muratore, D., Weitz, J.S. A primer on analyzing microbiome high-resolution time series. Frontiers in Genetics
  • #Demory, D. Liu, R., Chen, Y., Zhao, F., #Coenen, A., Zeng, Q, and Weitz, J.S. (in press) Linking light dependent life history traits with population dynamics for Prochlorococcus and cyanophage.
  • #Rodriguez-Gonzalez, R.A., #Leung, C-Y., Chan, B., Turner, P.E., Weitz, J.S. (2020) Quantitative models of phage-antibiotic combination therapy. mSystems. 5: e00756-19.
2019
  • Barone, B, #Coenen, A., #Beckett, S.J., Dennis J. McGillicuddy, Jr., Weitz, J.S., and Karl, D. (2019) The impact of sea surface height on biogeochemical dynamics at Station ALOHA. Journal of Marine Research. 77 S1:215-245
  • #Dominguez-Mirazo, M., #Jin, R., Weitz, J.S. (2019) Functional and comparative genomic analysis of integrated prophage-like sequences in Candidatus Liberibacter asiaticus. mSphere
  • Weitz, J.S., #Li, G., #Gulbudak, H., #Cortez, M.H., and Whitaker, R.J. (2019) Viral invasion fitness across a continuum from lysis to latency. Virus Evolution. 5: vez006
  • Talmy, D., #Beckett, S.J., Taniguchi, D., Brussaard, C.P.D., Weitz, J.S., and Follows, M.J. (2019) An empirical model of carbon flow through marine viruses and microzooplankton grazers. Environmental Microbiology. doi: 10.111/1462-2920.14626
  • Talmy, D., #Beckett, S.J., #Zhang, A, Taniguchi, D., Weitz, J.S., and Follows, M.J. (2019) Contrasting controls on microzooplankton grazing and viral infection of microbial prey. Frontiers in Marine Science. 6: 182.
  • #Lin, Y. and Weitz, J.S. (2019) Spatial interactions and oscillatory tragedies of the commons. Physical Review Letters. 122: 148102
  • #Eksin, C., #Paarporn, K., and Weitz, J.S. (2019) Systematic biases in disease forecasting – the role of behavior change. doi: 10.1016/j.epidem.2019.02.004
  • Park, S.W., Champredon, D., Weitz, J.S., and Dushoff, J. (2019) Exploring how generation intervals link strength and speed of epidemics. doi: 10.1016/j.epidem.2018.12.002.
  • #Leung, C.Y. and Weitz, J.S. (2019) Not by (good) microbes alone: towards immunocommensal therapies. Trends in Microbiology. 27: 294-302.
  • #Al-Rasheed, H., #Jin, R., and Weitz, J.S. (2019) Caution in inferring viral strategies from abundance correlations in marine metagenomes. Nature Communications. 10: 501.
  • #Gulbudak, H. & Weitz, J.S. (2019) Heterogeneous virus strategies promote coexistence in virus-microbe systems, Theor. Biol. 462: 65-84.
2018
  • #Paarporn, K., #Eksin, C., Weitz, J.S., and Wardi, Y. Optimal control policies for evolutionary dynamics with environmental feedback. IEEE Conference on Decision and Control
  • #Taylor, B.P, Weitz, J.S., Brussaard, C.P.D., and Fischer, M.G. (2018) Quantitative infection dynamics of Cafeteria roenbergensis Viruses 10: 468.
  • #Beckett, S.J. and Weitz, J.S. (2018) The effect of strain level diversity on robust inference of virus-induced mortality. Microbiol. 9: 1850.
  • #Coenen, A and Weitz, J.S. Limitations of correlation-based inference in complex virus-microbe communities. mSystems 3: e00084-18.
  • #Paarporn, K., #Eksin, C. Weitz, J.S. (2018) Information sharing for a coordination game in fluctuating environment. Theor. Biol. 454: 376-385.
  • Munson-McGee, J.H, #Peng, S., Dewerff, S, Stepanauskas, R., Whitaker, R.J, Weitz, J.S., Young, M.J. (2018) A virus or more in (nearly) every cell: ubiquitous virus-host interactions in extreme environments. The ISME Journal. 12: 1706-1714.
2017
  • Weitz, J.S., #Beckett, S.J., Brum, J.R., Cael, B.B., and Dushoff, J. (2017) Lysis, lysogeny, and virus-microbe ratios. 549: E1-E3.
  • Zehr, J., Weitz, J.S., Joint, I. (2017) How microbes survive in the open ocean. 357: 646-647.
  • #Leung, C.Y. & Weitz, J.S. (2017) Modeling the synergistic elimination of bacteria by phage and the innate immune system. Theor. Biol. 429: 241-252.
  • Roach, D.R., #Leung, C.Y., Henry, M., Morello, E., #Singh, D., Di Santo, J.P., *Weitz, J.S., and *Debarbieux, L. (2017). Synergy between the host immune system and bacteriophage is essential for successful phage therapy against an acute respiratory pathogen. Cell Host and Microbe. (*co-corresponding). 22: 38-47.
  • #Paarporn, K., #Eksin, C., Weitz, J.S. and Shamma, J. (2017) Networked SIS epidemics with awareness. IEEE Transactions on Computational Social Systems. 4: 93-103
  • #Beckett, S.J. and Weitz, J.S. (2017) Disentangling niche competition from grazing mortality in phytoplankton dilution experiments. PLoS One. 12: e0177517
  • #Eksin, C., Shamma, J., and Weitz, J.S. (2017) Disease dynamics in a stochastic network game: a little empathy goes a long way in averting outbreaks. Scientific Reports 7: 44122.
  • #Bucksch, A., Schneider, H., Merchant, N. and Weitz, J.S. (2017) Overcoming the law of the hidden in cyberinfrastructures. Trends in Plant Science. 22: 117-123.
  • Sullivan, M.B., Weitz, J.S., Wilhelm, S.W. (2017) Viral ecology comes of age. Environmental Microbiology Reports. 9: 33-35.
2016
  • #Taylor, B.P., Penington, C., and Weitz, J.S. (2016) Emergence of increased frequency and severity of multiple infections by viruses due to spatial clustering of hosts. Physical Biology.
  • Weitz, J.S., #Eksin, C., #Paarporn, K., Brown, S.P., and Ratcliff, W.C. (2016) An oscillatory tragedy of the commons in replicator dynamics with game-environment feedback. Proceedings of the National Academy of Sciences USA. doi:10.1073/pnas.1604096113
  • Gregory, A.C., Solonenko, S.A., Ignacio-Espinoza, J.C., LaButti, K., Copeland, A., Sudek, S., Maitland, A., Chittick, L., dos Santos, F., Weitz, J.S., Worden, A.Z., Woyke, T., and Sullivan, M.B. (2016) Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics 17:930.
  • #Jover, L.F., Romberg, J. and Weitz, J.S. (2016) Inferring phage-bacteria infection networks from time-series data. Soc. Open Sci. 3: 160654.
  • #Gulbudak, H and Weitz, J.S. (2016) A touch of sleep: biophysical model of contact-mediated dormancy of archaea by viruses. doi: 10.1098/rspb.2016.1037
  • #Taylor, B.P., Dushoff, J. and Weitz, J.S. (2016) Stochasticity and the limits to confidence when estimating R0 of Ebola and other emerging infectious diseases. Theor. Biol. 408: 145-154.
  • #Leung, C.Y. and Weitz, J.S. (2016) Conflicting attachment and the growth of bipartite networks. Physical Review E. 93: 032303.
  • Charles H Wigington, Derek L Sonderegger, Corina PD Brussaard, Alison Buchan, Jan F Finke, Jed Fuhrman, Jay T Lennon, Mathias Middelboe, Curtis A Suttle, Charles Stock, William H Wilson, K Eric Wommack, Steven W Wilhelm, Weitz, J.S. (2016) Re-examination of the relationship between marine virus and microbial cell abundances. Nature Microbiology 1:15024.
  • #Flores, C.O, Poisot, T., Valverde, S and Weitz, J.S. (2016) BiMat: a MATLAB package to facilitate the analysis of bipartite networks. Methods in Ecology and Evolution. 7:127-132.
2015
  • Weitz, JS. (2015) Quantitative Viral Ecology: Dynamics of Viruses and Their Microbial Hosts. Princeton University Press, 360 pp.
  • #Das A, Schneider H, Burridge J, Ascanio AKM, Wojciechowski T, Topp CN, Lynch JP, Weitz JS, #Bucksch A. (2015). Digital Imaging of Root Traits (DIRT): a high-throughput computing and collaboration platform for field-based plant phenomics. Plant Methods. 11:51.
  • #Jover, L.F., #Flores, C.O., #Cortez, M.H. and Weitz, J.S. (2015) Multiple regimes of robust patterns between network structure and biodiversity. Scientific Reports. 5:17856.
  • Weitz, J.S. Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A, Follows MJ, Fuhrman JA, #Jover LF, Lennon JT, Middelboe M, Sonderegger DL, Suttle CA, #Taylor BP, Frede Thingstad T, Wilson WH, Eric Wommack K. (2015). Multitrophic model of virus effects on marine surface microbial communities. ISME J. 9:1352-1364.
  • Weitz, J.S. & Dushoff, J. (2015) Modeling post-death transmission of Ebola virus disease: challenges for inference and opportunities for control. Scientific Reports 5: 8751.
2014
  • #Bucksch A, Burridge J, York LM, Das A, Noord E, Weitz JS, and Lynch JP. (2014).  Image-based high-throughput field phenotyping of crop roots. Plant Physiology. 166:470-486.
  • #Childs LM, England W, Weitz JS, Whitaker, RW. (2014) CRISPR-induced distributed immunity in microbial populations. PLoS One. 9:e101710
  • Deng, L, Ignacio-Espinazo, J., Poulous B. Weitz JS, Hugenholtz P and Sullivan MB.  (2014) Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. 513: 242-245.
  • #Jover, L, Effler, TC, Buchan A, Wilhelm SW, and Weitz JS. (2014) An elemental view of virus particles: implications for marine biogeochemical cycles. Nat Rev Microbiol. 12: 519-528.
  • #Das A, #Bucksch A, #Price CA and Weitz JS. (2014) ClearedLeavesDB: an online database of cleared plant leaf images. Plant Methods. 10:8
  • #Taylor, B.P. #Cortez, MH and Weitz, JS. (2014) The virus of my virus is my friend: ecological effects of virophage with alternative modes of coinfection. Journal of Theoretical Biology. 354: 124-136.
  • #Cortez, MH and Weitz, JS. (2014) Coevolution can reverse predator-prey cycles, Proceedings of the National Academy of Sciences USA. 111: 7486-7491
  • #Price, CA, and Weitz, J.S. (2014) Costs and benefits of reticulate leaf venation. BMC Plant Biology. 14: 234
  • Weitz JS. (2014) Let my people go (home) to Spain: a genealogical model of Jewish identities since 1492. PLoS One. 9:e85673
  • #Bucksch A, Turk G and Weitz, J.S. (2014) The Fiber Walk: A Model of Tip-Driven Growth with Lateral Expansion. PLoS One, 9: e85585.
  • #Price CA, Munro, P and Weitz JS, (2014) Estimates of leaf vein density are scale dependent. Plant Physiology . 164:173-180
  • #Lee, T., Parikh, R., Weitz, J.S., Kim, H. (2014) Quantifying the interaction between adjacent genes within heterologous modules in yeast. 4: 109-116.
2013
  • #Joh, R.I, Barzilay, E., Mintz, E., Weiss, H. and Weitz, J.S. (2013) Dynamics of shigellosis epidemics: estimating individual-level transmission and reporting rate from national epidemiological datasets. Am J. Epidemiol 178: 1319-1326.
  • #Taylor, B, #Lee, T. and Weitz, JS. (2013) Multi-scale sensitivity analyses of models of complex gene regulatory networks. 62: 109-120.
  • Held, NL, #Childs, LM, Davison, M, Weitz, JS, Whitaker, RJ & Bhaya, D. (2013) CRISPR-Cas systems to probe ecological diversity and host-viral interactions. CRISPR-Cas systems, editors: Barrangou and van der Oost, Springer. 221-250.
  • Topp CN, Iyer-Pascuzzi AS, Anderson JT, Lee C-R, Zurek PR, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore BT, Harer J, Edelsbrunner H, Mitchell-Olds T, Weitz JS, Benfey PN. (2013) 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. Natl. Acad. Sci. USA. 110: E1695-E1704.
  • #Jover, L., #Cortez, MH, and Weitz, JS. (2013) Mechanisms of multi-strain coexistence in host-phage systems with nested infection networks. Theor. Biol. 332: 65-77
  • Haegeman, B, Hamelin, J., Moriary, J., Neal, P., Dushoff, J. and Weitz, J.S. (2013) Robust estimation of microbial diversity in theory and in practice. ISME Journal. 7: 1092-11101.
  • #Mitchell, G.J., Nelson, D.C., Wiesenfeld, K. and Weitz, J.S. (2013) Critical cell wall hole size for enzymatic lysis in Gram-positive bacteria. Roy. Soc. Interface. 10: 20120892.
  • #Flores, CA, Valverde, S and Weitz, JS (2013), Multi-scale structure and geographic drivers of cross-infection within marine bacteria and phages. ISME Journal. 7: 520-532.
  • #Cortez, M.H. and Weitz, J.S. (2013) Distinguishing between indirect and direct modes of transmission using epidemiological time series. American Naturalist. 181: E43-E54.
  • Held, NL, #Childs, LM, Davison, M, Weitz, JS, Whitaker, RJ & Bhaya, D. (2013) CRISPR-Cas systems to probe ecological diversity and host-viral interactions. CRISPR-Cas systems, editors: Barrangou and van der Oost, Springer.
  • Fang, S., Clark, R.T., Zheng, Y., Iyer-Pascuzzi, A.S., Weitz, J.S., Kochian, L.V., Edelsbrunner, H., Liao, H., and Benfey, P.N.. (2013) Evidence for genotype-dependent recognition by rice roots. Natl. Acad. Sci. USA. 110: 2670-2675.
  • Weitz, J.S., Poisot, T., Meyer, J.R., #Flores, C.O., Valverde, S., Sullivan, M.B., and Hochberg, M.E. (2013) Phage-bacteria infection networks. Trends in Microbiology. 21: 82-91.
2012
  • Price, C.A, Weitz, J.S, Savage, V., Stegen, J., Clarke, A., Coomes, D., Dodds, P.S., Etienne, R., Kerkhoff, A., McCulloh, K., Niklas, K., Olff, H., Swenson, N. (2012) Testing the metabolic theory of ecology. Ecology Letters. 15: 1465-1474.
  • #Price, C.A. and Weitz, J.S. (2012) Mini-review: Allometric covariation: a hallmark behavior of plants and leaves. New Phytologist. 192: 882-889.
  • Weitz, J.S. and Wilhelm, S.W. (2012) Ocean Viruses and Their Dynamical Effects on Microbial Communities and Biogeochemical Cycles. F1000 Biology Reports. 4:17
  • Jiang, X., Langille, M.G.I., Neches, R.Y., Elliot, M. Levin, S.A., Eisen, J.A., Weitz, J.S. and Dushoff, J. (2012). Functional biogeography of ocean microbes: dimension reduction of metagenomic data identifies biological patterns across scales. PLoS One. 7: e43866
  • #Mileyko, Y, Edelsbrunner, H, #Price, C.A., and Weitz, J.S. (2012) Hierarchical ordering of reticular networks. PLoS One. 7: e36715.
  • #Galkovskyi, T, #Mileyko, Y., Bucksch, A., Moore, B., #Symonova, O., #Price, C.A., Topp, C.N., Iyer-Pascuzzi, A.S., Zurek, P.R., Fang, S., Harer, J., Benfey, P.N. and Weitz, J.S. (2012) GiA Roots: software for the high-throughput analysis of plant root system architecture. BMC Plant Biology. 12:116.
  • Haegeman, B and Weitz, J.S. (2012) Neutral theory of genome evolution and the frequency distribution of genes.  BMC Genomics. 13: 196.
  • #Childs, LM, Held, NL, Young, MJ, Whitaker, RJ and Weitz, J.S. (2012) Multi-scale Model of CRISPR-induced Coevolutionary Dynamics: Diversification at the Interface of Lamarck and Darwin. 66: 2015-2029.
  • Meyer, J.R., Dobias, D.T., Weitz, J.S. , Barrick, J.E., Quick, R.T. and Lenski, R.E. (2012) Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335:428-432.
  • #Price, C.A., Wing, S. and Weitz, J.S. (2012) Scaling and structure of dicotyledenous leaf venation networks. Ecology Letters 15: 87-95.
  • Jeng, X., Weitz, J.S., Dushoff, J. (2012). A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data. Journal of Mathematical Biology. 64: 697-711.

(# indicates Weitz group grad student/postdoc; @ indicates undergraduate author)

Google Scholar profile at http://bit.ly/jsweitz_gscholar

Awards

  • 2014-2017       Simons Foundation Investigator in Ocean Ecology Processes
  • 2014-2017       Advisory Board Member, National Institute for Mathematical and Biological Synthesis
  • 2013-2014       Visiting Associate Professor, Department of Ecology and Evolutionary Biology, University of Arizona
  • 2012    Opponent, PhD Defense, Niels Bohr Institute

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