Publications3

Title	Year	Journal	Tools
Overcoming the law of the hidden cyberinfrastructures	2017	Trends in Plant Science
Disentangling niche competition from grazing mortality in phytoplankton dilution experiments	2017	PloS One	Github Repository
Inferring phage–bacteria infection networks from time-series data	2016	Royal Society Open Science
An oscillating tragedy of the commons in replicator dynamics with game-environment feedback	2016	PNAS
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer	2016	BMC Genomics
Re-examination of the relationship between marine virus and microbial cell abundances	2016	Nature Microbiology	Github Repository
Stochasticity and the limits to confidence when estimating R0 of Ebola and other emerging infectious diseases	2016	Journal of Theoretical Biology	Github Repository
A touch of sleep: biophysical model of contact-mediated dormancy of archaea by viruses	2016	Proceedings of the Royal Society B: Biological Sciences
Conflicting attachment and the growth of bipartite networks	2016	Physical Review E	Github Repository
Multiple regimes of robust patterns between network structure and biodiversity	2015	Scientific Reports	Github Repository
Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics	2015	Plant Methods	Github Repository
Reconstructing weighted networks from dynamics	2015	Physical Review E
A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes	2015	The ISME Journal
Modeling post-death transmission of Ebola: challenges for inference and opportunities for control	2015	Scientific Reports	Github Respository
Costs and benefits of reticulate leaf venation	2014	BMC Plant Biology
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space	2014	Nature
The elemental composition of virus particles: implications for marine biogeochemical cycles	2014	Nature Reviews Microbiology
CRISPR-induced distributed immunity in microbial populations	2014	PloS One
Coevolution can reverse predator–prey cycles	2014	PNAS
ClearedLeavesDB: an online database of cleared plant leaf images	2014	Plant Methods
The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection	2014	Journal of Theoretical Biology
Let my people go (home) to Spain: a genealogical model of Jewish identities since 1492	2014	PloS One
The fiber walk: a model of tip-driven growth with lateral expansion	2014	PloS One
Estimates of leaf vein density are scale dependent	2014	Plant Physiology
Suppression of expression between adjacent genes within heterologous modules in yeast	2014	G3: Genes, Genomes, Genetics
Extracting connectivity from dynamics of networks with uniform bidirectional coupling	2013	Physical Review E
Dynamics of shigellosis epidemics: estimating individual-level transmission and reporting rates from national epidemiologic data sets	2013	American Journal of Epidemiology
3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture	2013	PNAS
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

The Weitz Group