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Title Journal Year
Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment Nature Ecology and Evolution 2024
Design, optimization, and inference of multiphasic decay of infectious virus particles bioRxiv (preprint) 2024
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes bioRxiv (preprint) 2024
Rapid bacteria-phage coevolution drives the emergence of multiscale networks Science 2023
Bacteria-phage coevolution with a seed bank The ISME Journal 2023
Optimal dormancy strategies in fluctuating environments given delays in phenotypic switching Journal of Theoretical Biology 2023
Metacommunity Structure Preserves Genome Diversity in the Presence of Gene-specific Selective Sweeps. bioRxiv (preprint) 2023
Defective Subviral Particles Modify Ecological Equilibria and Enhance Viral Coexistence Frontiers in Virology 2022
Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing. Ecology Letters 2022
Infect while the iron is scarce: nutrient-explicit phage-bacteria games Theoretical Ecology 2021
A thermal trade-off between viral production and degradation drives virus-phytoplankton population dynamics Ecology Letters 2021
Revisiting the rules of life for viruses of microorganisms Nature Reviews Microbiology 2021
Large sample spaces do not imply biological systems are ‘fine-tuned’ Journal of Theoretical Biology 2020
When be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny Virus Evolution 2020
A Primer for Microbiome Time-Series Analysis Frontiers in Genetics 2020
Viral invasion fitness across a continuum from lysis to latency Virus Evolution 2019
Information sharing for a coordination game in fluctuating environments Journal of Theoretical Biology 2018
Quantitative Infection Dynamics of Cafeteria Roenbergensis Virus Viruses 2018
Lysis, lysogeny and virus-microbe ratios Nature 2017
Disentangling niche competition from grazing mortality in phytoplankton dilution experiments PloS One 2017
Viral ecology comes of age Environmental Microbiology Reports 2017
Conflicting attachment and the growth of bipartite networks Physical Review E 2016
Multiple regimes of robust patterns between network structure and biodiversity Scientific Reports 2015
Reconstructing weighted networks from dynamics Physical Review E 2015
The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection Journal of Theoretical Biology 2014
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space Nature 2014
Extracting connectivity from dynamics of networks with uniform bidirectional coupling Physical Review E 2013
Mechanisms of multi-strain coexistence in host-phage systems with nested infection networks Journal of Theoretical Biology 2013
A guide to sensitivity analysis of quantitative models of gene expression dynamics Methods 2013
Distinguishing between indirect and direct modes of transmission using epidemiological time series The American Naturalist 2013
Phage-bacteria infection networks Trends in Microbiology 2013
Testing the metabolic theory of ecology Ecology Letters 2012
A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data Journal of Mathematical Biology 2012
Hierarchical Ordering of Reticular Networks PloS One 2012
To lyse or not to lyse: transient-mediated stochastic fate determination in cells infected by bacteriophages PLoS Computational Biology 2011
Quantifying enzymatic lysis: estimating the combined effects of chemistry, physiology and physics Physical Biology 2010
Unsupervised statistical clustering of environmental shotgun sequences BMC Bioinformatics 2009
Bacterivorous grazers facilitate organic matter decomposition: a stoichiometric modeling approach FEMS Microbiology Ecology 2009
Small-scale copy number variation and large-scale changes in gene expression PNAS 2008
Collective decision making in bacterial viruses Biophysical Journal 2008
Size and scaling of predator-prey dynamics Ecology Letters 2006
A null model of morphospace occupation The American Naturalist 2005
Scale-dependence of resource-biodiversity relationships Journal of Theoretical Biology 2003
Packing-limited growth of irregular objects Physical Review E 2003
Explaining mortality rate plateaus PNAS 2001
Re-examination of the “3/4” law of metabolism Journal of Theoretical Biology 2001