Weitz Lab

PI: Joshua Weitz



  • K. (Joey) Leung 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) Nature Microbiology
  • #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.
  • 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.
  • #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.
  • #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.
  • 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


  • 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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