Publications: Foundations of Quantitative Viral Ecology

Title	Year	Journal
Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing	2022	Ecology Letters
Time-Scales Modulate Optimal Lysis-Lysogeny Decision Switches and Near-Term Phage Reproduction	2022	Virus Evolution
Infect while the iron is scarce: nutrient-explicit phage-bacteria games	2021	Theoretical Ecology
A Primer for Microbiome Time-Series Analysis	2020	Frontiers in Genetics
When to be Temperate: On the Fitness Benefits of Lysis vs. Lysogeny	2020	Virus Evolution
Large sample spaces do not imply biological systems are ‘fine-tuned’	2020	Journal of Theoretical Biology
Viral invasion fitness across a continuum from lysis to latency	2019	Virus Evolution
Quantitative Infection Dynamics of Cafeteria Roenbergensis Virus	2018	Viruses
Information sharing for a coordination game in fluctuating environments	2018	Journal of Theoretical Biology
Lysis, lysogeny and virus–microbe ratios	2017	Nature
Viral ecology comes of age	2017	Environmental Microbiology Reports
Disentangling niche competition from grazing mortality in phytoplankton dilution experiments	2017	PloS One
Conflicting attachment and the growth of bipartite networks	2016	Physical Review E
Multiple regimes of robust patterns between network structure and biodiversity	2015	Scientific Reports
Reconstructing weighted networks from dynamics	2015	Physical Review E
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space	2014	Nature
The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection	2014	Journal of Theoretical Biology
Extracting connectivity from dynamics of networks with uniform bidirectional coupling	2013	Physical Review E
A guide to sensitivity analysis of quantitative models of gene expression dynamics	2013	Methods
Mechanisms of multi-strain coexistence in host–phage systems with nested infection networks	2013	Journal of Theoretical Biology
Phage–bacteria infection networks	2013	Trends in Microbiology
Distinguishing between indirect and direct modes of transmission using epidemiological time series	2013	The American Naturalist
Testing the metabolic theory of ecology	2012	Ecology Letters
Hierarchical Ordering of Reticular Networks	2012	PloS One
A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data	2012	Journal of Mathematical Biology
To lyse or not to lyse: transient-mediated stochastic fate determination in cells infected by bacteriophages	2011	PLoS Computational Biology
Quantifying enzymatic lysis: estimating the combined effects of chemistry, physiology and physics	2010	Physical Biology
Bacterivorous grazers facilitate organic matter decomposition: a stoichiometric modeling approach	2009	FEMS Microbiology Ecology
Unsupervised statistical clustering of environmental shotgun sequences	2009	BMC Bioinformatics
Collective decision making in bacterial viruses	2008	Biophysical Journal

The Weitz Group