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| Daniel Segrè | Ilija Dukovsky | Jing Zhang | |
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| Hui Shi | Melisa Osborne | Michael Silverstein | Helen Scott |
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| Mrugakshi Chidrawar |
Research Team
Dr. Daniel Segrè leads the Boston University research group working with the m-CAFEs SFA. Learn more about the Segrè Lab.
m-CAFEs Publications
Bernstein, D.B.; S. Sulheim, E. Almaas, D. Segrè (2021) Addressing uncertainty in genome-scale metabolic model reconstruction and analysis, Genome Biology (2021) 22, 64. [doi]:10.1186/s13059-021-02289-z OSTI:1812364
Dukovski, I.; D. Bajić, J.M. Chacón, M. Quintin, J.C.C. Vila, S. Sulheim, A.R. Pacheco, D.B. Bernstein, W.J. Riehl, K.S. Korolev, A. Sanchez, W.R. Harcombe, D. Segrè (2021), A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS), Nature Protocols. https://arxiv.org/abs/2009.01734
Jo, C., Bernstein, D. B., Vaisman, N., Frydman, H. M., & Segrè, D. (2021). A co-culture microplate for real-time measurement of microbial interactions. bioRxiv. [doi]:10.1101/2021.01.07.425753
Kishore, D., Birzu, G., Hu, Z., DeLisi, C., Korolev, K. S., & Segrè, D. (2020). Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation. bioRxiv. [doi]:10.1101/2020.09.23.309781
Pacheco, A. R., Osborne, M. L., & Segrè, D. (2021). Non-additive microbial community responses to environmental complexity. Nature Communications, 12(1), 2365. [doi]:10.1038/s41467-021-22426-3 PMID: 33888697, PMCID: PMC8062479 OSTI:1812365. News article highlight.
Pacheco, A. R., & Segrè, D. (2021). An evolutionary algorithm for designing microbial communities via environmental modification. Journal of the Royal Society Interface. [doi]:10.1098/rsif.2021.0348
Resources
Computation Of Microbial Ecosystems in Time and Space (COMETS)
Open-source code available on GitHub, distributed under GNU General Public License Version 3
The documentation is also available on GitHub and is structured as a tutorial
The MATLAB toolbox is available, distributed under the GNU General PublicLicense Version 3
The COMETS Python toolbox is available, distributed under the GNU General Public License Version 3
The COMETS Protocols GitHub repository contains all input files and Jupyter notebooks from which one can reproduce the results presented in the paper. The data are distributed under the Creative Commons CC0 1.0 Universal license.
