Areas of Interest
The Jones Lab studies microbiome assembly and microbiome spatial structure with a combination of statistical modeling and confocal fluorescence microscopy. Our lab images the spatial distribution of fluorescently labeled bacterial strains in the fruit fly gut at single-cell resolution. We also work with empirical datasets collected by experimentalist collaborators that study fruit flies, duckweed, and activated sludge bioreactors. Our research is motivated by the prospect of improving microbiome-based medical therapies like fecal microbiota transplantation. The Jones Lab employs techniques from statistical physics, mathematical modeling, biophysics, and complex systems science to understand and predict these awesome microbial ecosystems.
Published Works
2013 - Analysis and simulation of the three-component model of HIV dynamics
E Jones, P Roemer, M Raghupathi, S Pankavich
SIAM Undergraduate Research Online 7, 89-106
2018 - Microbiome interactions shape host fitness
AL Gould, V Zhang, L Lamberti, EW Jones, B Obadia, N Korasidis, ...
Proceedings of the National Academy of Sciences, 201809349
2018 - A modified SEIR model for the spread of Ebola in Western Africa and metrics for resource allocation
P Diaz, P Constantine, K Kalmbach, E Jones, S Pankavich
Applied Mathematics and Computation 324, 141-155
2018 - In silico analysis of antibiotic-induced Clostridium difficile infection: Remediation techniques and biological adaptations
EW Jones, JM Carlson
PLoS computational biology 14 (2), e1006001
2019 - Steady-state reduction of generalized Lotka-Volterra systems in the microbiome
EW Jones, JM Carlson
Physical Review E 99 (3), 032403
2020 - Navigation and control of outcomes in a generalized Lotka-Volterra model of the microbiome
EW Jones, P Shankin-Clarke, JM Carlson
Advances in Nonlinear Biological Systems: Modeling and Optimal Control 11 …
2020 - Control of ecological outcomes through deliberate parameter changes in a model of the gut microbiome
Z Wang, EW Jones, JM Mueller, JM Carlson
Physical Review E 101 (5), 052402
2020 - Simplification and control of microbial ecosystems in theory and experiment
EW Jones
UC Santa Barbara
2021 - Aging-induced fragility of the immune system
E Jones, J Sheng, J Carlson, S Wang
Journal of Theoretical Biology 510, 110473
2022 - Stochastic microbiome assembly depends on context
EW Jones, JM Carlson, DA Sivak, WB Ludington
Proceedings of the National Academy of Sciences 119 (7), e2115877119
2023 - A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota
R Dodge, EW Jones, H Zhu, B Obadia, DJ Martinez, C Wang, ...
Nature Communications 14 (1), 1557
2023 - First-passage-time statistics of growing microbial populations carry an imprint of initial conditions
EW Jones, J Derrick, RM Nisbet, WB Ludington, DA Sivak
Scientific Reports 13 (1), 21340