Computational Tools and Models
Computation Of Microbial Ecosystems in Time and Space (COMETS)
COMETS on GitHub. Learn more about the software and the Segrè Lab at Boston University.
Metabolite, Annotation and Gene Integration (MAGI)
MAGI is a tool to quickly find and score consensus between metabolite identifications and gene annotations.
Experimental Complexity
Scripts for analyzing multispecies microbial community yields and taxonomic composition as functions of environmental complexity.
Evolutionary Algorithms
Scripts to run evolutionary search algorithms for microbial community design.
OpenMSI
Web-based visualization, analysis and management of mass spectrometry imaging data.
Metatlas
Metabolite Atlas is a Python-based workflow for efficient and accurate analysis of mass spectrometry datasets.
Biorack
Various data analysis tools for metabolomic and other information.
Experimental Data in Databases
Web of Microbes (WoM)
WoM (also on KBase) is a repository of experimental assertions on how organisms transform their environments through the increase and decrease of metabolites.
ggKbase
ggKBase is a knowledgebase system where omics data can be interpreted, integrated and linked to other databases and services. Learn more.
Fitness Browser
Fitness Browser is a repository of bacterial fitness experiments. Learn more.
Other Experimental Data
Protein cost minimization promotes the emergence of coenzyme redundancy: [doi]:10.1073/pnas.2110787119. Supplementary data.
Species- and site-specific genome editing in complex bacterial communities: [doi]:10.1038/s41564-021-01014-7. NCBI data. Supplementary data.
A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria: [doi]:10.3389/fmicb.2022.855331. JGI Genome Portal. Supplementary data.
A reproducible and tunable synthetic soil microbial community provides new insights into microbial ecology: [doi]:10.1101/2022.05.19.492707. Supplementary data.
Computational design and construction of an Escherichia Ecoli strain engineered to produce a non-standard amino acid: [doi]: 10.1101/2022.04.02.486821. Supplementary data.
RNA-targeting CRISPR-Cas13 Provides Broad-spectrum Phage Immunity: [doi]: 10.1101/2022.03.25.485874. Supplementary data.
Microbial Community Field Surveys Reveal Abundant Pseudomonas Population in Sorghum Rhizosphere Composed of Many Closely Related Phylotypes: [doi]:10.3389/fmicb.2021.598180. NCBI repository/repositories and accession number(s): SRP130758, SRP130755, SRP130757, SRP130767, SRP130775, SRP135653, SRP165130, PRJNA692505.
Root morphology and exudate availability are shaped by particle size and chemistry in Brachypodium distachyon: [doi]:10.1002/pld3.207. JGI Genome Portal.
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis: [doi]: 10.1186/s13059-021-02289-z. Supplementary data.
Microbial community field surveys reveal abundant pseudomonas population in sorghum rhizosphere composed of many closely related phylotypes: [doi]: 10.3389/fmicb.2021.598180. Supplementary data.
A metabolic modeling platform for the Computation Of Microbial Ecosystems in Time and Space (COMETS): [doi]: 10.1038/s41596-021-00593-3. Supplementary data.
Microfabrication of a Chamber for High-Resolution, In Situ Imaging of the Whole Root for Plant–Microbe Interactions: [doi]: 10.3390/ijms22157880. Supplementary data.
Non-additive microbial community responses to environmental complexity: [doi]: 10.1038/s41467-021-22426-3. Supplementary data.
An evolutionary algorithm for designing microbial communities via environmental modification: [doi]: 10.1098/rsif.2021.0348. Supplementary data.
Spray-induced gene silencing for disease control is dependent on the efficiency of pathogen RNA uptake: [doi]: 10.1111/pbi.13589. Supplementary data.
Root morphology and exudate availability are shaped by particle size and chemistry in Brachypodium distachyon: [doi]: 10.1002/pld3.207. Supplementary data.
CRAGE-Duet Facilitates Modular Assembly of Biological Systems for Studying Plant-Microbe Interactions: [doi]: 10.1021/acssynbio.0c00280. Supplementary data.
Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass: [doi]: 10.1111/nph.15662. Supplementary data.
Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly: [doi]:10.1038/s41564-018-0129-3. Global Natural Products Social Molecular Networking accession number(s): MSV000081804, MSV000081808, MSV000081810. Supplementary data.
