A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …
biology tool for modeling cellular physiology and growth. Extensions of this approach are …
[HTML][HTML] KBase: the United States department of energy systems biology knowledgebase
…, MW Sneddon, ML Henderson, WJ Riehl… - Nature …, 2018 - nature.com
Although similar integrative tools exist (Supplementary Note 2), no other open platform
shares all KBase’s features, which include the following:(i) comprehensive support for data …
shares all KBase’s features, which include the following:(i) comprehensive support for data …
[PDF][PDF] Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics
WR Harcombe, WJ Riehl, I Dukovski, BR Granger… - Cell reports, 2014 - cell.com
The interspecies exchange of metabolites plays a key role in the spatiotemporal dynamics
of microbial communities. This raises the question of whether ecosystem-level behavior of …
of microbial communities. This raises the question of whether ecosystem-level behavior of …
Metagenome-assembled genome extraction and analysis from microbiomes using KBase
Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but
obtaining their genomes directly from the environment, using shotgun sequencing, has only …
obtaining their genomes directly from the environment, using shotgun sequencing, has only …
The DOE systems biology knowledgebase (KBase)
…, S Canon, MW Sneddon, ML Henderson, WJ Riehl… - BioRxiv, 2016 - biorxiv.org
The US Department of Energy Systems Biology Knowledgebase (KBase) is an open-source
software and data platform designed to meet the grand challenge of systems biology — …
software and data platform designed to meet the grand challenge of systems biology — …
A bacterial sensor taxonomy across earth ecosystems for machine learning applications
…, MP Joachimiak, SP Jungbluth, Z Yang, WJ Riehl… - Msystems, 2024 - Am Soc Microbiol
Microbial communities have evolved to colonize all ecosystems of the planet, from the deep
sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate …
sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate …
[HTML][HTML] Signatures of arithmetic simplicity in metabolic network architecture
WJ Riehl, PL Krapivsky, S Redner… - PLoS Computational …, 2010 - journals.plos.org
Metabolic networks perform some of the most fundamental functions in living cells, including
energy transduction and building block biosynthesis. While these are the best characterized …
energy transduction and building block biosynthesis. While these are the best characterized …
Optimal metabolic regulation using a constraint-based model
WJ Riehl, D Segrè - Genome Informatics, 2008 - jstage.jst.go.jp
Regulation of metabolic enzymes plays a crucial role in the maintenance of metabolic
homeostasis, and in the capacity of living systems to undergo physiological adaptation under …
homeostasis, and in the capacity of living systems to undergo physiological adaptation under …
Genome extraction from shotgun metagenome sequence data
Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but
obtaining their genomes directly from the environment, using shotgun sequencing, has only …
obtaining their genomes directly from the environment, using shotgun sequencing, has only …
Moab Desert Crust-Sample 4E
Uncultivated Bacteria and Archaea comprise the vast majority of species on Earth, but
obtaining their genomes directly from the environment, using shotgun sequencing, has only …
obtaining their genomes directly from the environment, using shotgun sequencing, has only …