Export 68 results:
A touch of sleep: biophysical model of contact-mediated dormancy of archaea by viruses. Proceedings of the Royal Society of London B: Biological Sciences. 283. 2016.
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer. BMC Genomics. 17:930.. 2016.
Inferring phage–bacteria infection networks from time-series data. Royal Society Open Science. 3:160654.. 2016.
An oscillating tragedy of the commons in replicator dynamics with game-environment feedback. Proceedings of the National Academy of Sciences.. 2016.
BiMat: a MATLAB package to facilitate the analysis of bipartite networks. Methods in Ecology and Evolution. 7:127-132.. 2016.
Conflicting attachment and the growth of bipartite networks. Physical Review E. 93. 2016.
Re-examination of the relationship between marine virus and microbial cell abundances. Nature Microbiology. 1:15024.. 2016.
Stochasticity and the limits to confidence when estimating of Ebola and other emerging infectious diseases. Journal of Theoretical Biology. 408:145-154.. 2016.
Epidemic Spread Over Networks with Agent Awareness and Social Distancing. 53rd Annual Allerton Conference on Communication, Control, and Computing. :51-57.. 2015.
Modeling post-death transmission of Ebola: challenges for inference and opportunities for control. Scientific Reports. 5:8751.. 2015.
Multiple regimes of robust patterns between network structure and biodiversity. Scientific Reports. 5:17856.. 2015.
Quantitative Viral Ecology: Dynamics of Viruses and Their Microbial Hosts. Monographs in Population Biology, Princeton University Press, Princeton, NJ.. 2015.
The elemental composition of virus particles: implications for marine biogeochemical cycles. Nature Reviews Microbiology. 12:519-528.. 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.. 2014.
CRISPR-induced distributed immunity in microbial populations. PLoS One. 9:e101710.. 2014.
Estimates of leaf vein density are scale dependent. Plant Physiology. 164:173-180.. 2014.
The Fiber Walk: A Model of Tip-Driven Growth with Lateral Expansion. PLoS One. 9:e85585.. 2014.
Suppression of expression between adjacent genes within heterologous modules in yeast. G3: Genes, Genomes and Genetics. 4:109-116.. 2014.
Costs and benefits of reticulate leaf venation. BMC Plant Biology. 14:234.. 2014.
Image-based high-throughput field phenotyping of crop roots. Plant Physiology. 166:470-486.. 2014.
Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. 513:242-245.. 2014.
Coevolution can reverse predator-prey cycles. Proceedings of the National Academy of Sciences USA. 111:7486-7491.. 2014.
ClearedLeavesDB: an online database of cleared plant leaf images. Plant Methods. 10:8.. 2014.
A Guide to Sensitivity Analysis of Quantitative Models of Gene Expression Dynamics. Methods. 62:109-120.. 2013.
Distinguishing between indirect and direct modes of transmission using epidemiological time series. American Naturalist. 181:E43-E52.. 2013.
Genotypic recognition and spatial responses by rice roots. Proceedings of the National Academy of Sciences USA. 110:2670-2675.. 2013.
3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. Proceedings of the National Academy of Sciences USA. 110:E1695-E1704.. 2013.
CRISPR-Cas Systems to Probe Ecological Diversity and Host–Viral Interactions. CRISPR-Cas Systems. 9:221-250.. 2013.
Critical cell wall hole size for lysis in Gram-positive bacteria. Journal of the Royal Society Interface. 10:20120892.. 2013.
Dynamics of Shigellosis Epidemics: Estimating Individual-Level Transmission and Reporting Rates From National Epidemiologic Data Sets . American Journal of Epidemiology. 178:1319-1326.. 2013.
Mechanisms of Multi-strain Coexistence in Host-Phage Systems with Nested Infection Networks. Journal of Theoretical Biology. 332:65-77.. 2013.
Phage-bacteria infection networks. Trends in Microbiology. 21:82-91.. 2013.
Scaling and structure of dicotyledonous leaf venation networks. Ecology Letters. 15:87-95.. 2012.
Ocean Viruses and Their Dynamical Effects on Microbial Communities and Biogeochemical Cycles. F1000 Biology Reports. 4:17.. 2012.
Hierarchical ordering of reticular networks. PLoS One. 7(6):e36715.. 2012.
A neutral theory of genome evolution and the frequency distribution of genes. BMC Genomics. 13:196.. 2012.
Allometric covariation: a hallmark behavior of plants and leaves. New Phytologist. 192(4):882-889.. 2012.
Multi-scale Model of CRISPR-induced Coevolutionary Dynamics: Diversification at the Interface of Lamarck and Darwin. Evolution. 66(7):2015-2029.. 2012.
A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data. Journal of Mathematical Biology. 64:697-711.. 2012.
GiA Roots: Software for the High Throughput Analysis of Plant Root System Architecture. BMC Plant Biology. 12:116.. 2012.
Testing the metabolic theory of ecology. Ecology Letters.. 2012.
Genomic fluidity: an integrative view of gene diversity within microbial populations. BMC Genomics. 12:32.. 2011.
To lyse or not to lyse: transient-mediated stochastic fate determination in cells infected by bacteriophages. PLoS Computational Biology. 7:e1002006.. 2011.
LEAF GUI: segmenting and analyzing the structure of leaf veins and areoles. Plant Physiology. 155:236-245.. 2011.
Statistical structure of host-phage interactions. Proceedings of the National Academy of Sciences. 108:E288-E297.. 2011.
Quantifying enzymatic lysis: estimating the combined effects of chemistry, physiology, and physics. Physical Biology. 7:046002.. 2010.
Fluctuation domains in adaptive evolution. Theoretical Population Biology. 77:6-13.. 2010.
Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiology. 152:1148-1157.. 2010.
Bifurcation analysis of gene regulatory circuits subject to copy number variation. SIAM Journal on Applied Dynamical Systems. 9:799-826.. 2010.
A discrepancy between Michaelis-Menten based nutrient uptake model predictions and nitrogen to phosphorus stoichiometry in the surface ocean. Limnology and Oceanography. 55:997-1008.. 2010.
An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure. Ecology Letters. 13:1073-1084.. 2010.
Zero-sum allocational strategies determine the allometry of specific leaf area. American Journal of Botany. 97. 2010.
Bacterivorous grazers facilitate organic matter decomposition: a stoichiometric modeling approach. FEMS Microbiology Ecology. 69:170-179.. 2009.
Evaluating scaling models in biology using hierarchical Bayesian approaches. Ecology Letters. 12:641-651.. 2009.
Collective decision making in bacterial viruses. Biophysical Journal. 95:2673-2680.. 2008.
Small-scale copy number variation and large-scale changes in gene expression. Proceedings of the National Academy of Sciences USA. 105:16659-16664.. 2008.
Alternative stable states in host-phage dynamics. Theoretical Ecology. 1:DOI10.1007/s12080-007-0001-1.. 2008.
Evolutionary ecology of bacterial viruses. 3:171-178.. 2008.
A neutral metapopulation model of biodiversity in river networks. Journal of Theoretical Biology. 245:351-363.. 2007.
The evolution of dispersal in reserve networks. American Naturalist. 170:59-78.. 2007.
Evolution, interactions, and biological networks. PLoS Biology. 5:10-12.. 2007.