Research graph
References from Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools. Local targets link to admitted publications; unresolved targets remain external evidence.
The vocabulary of microbiome research: a proposal
10.1186/s40168-015-0094-5 · 2015 · External reference
10.1038/s41575-019-0157-3
10.1038/s41575-019-0157-3 · External reference
10.1038/s41575-018-0061-2
10.1038/s41575-018-0061-2 · External reference
10.1016/j.cell.2016.05.041
10.1016/j.cell.2016.05.041 · External reference
10.1016/j.cub.2019.04.017
10.1016/j.cub.2019.04.017 · External reference
10.1007/s00394-017-1445-8
10.1007/s00394-017-1445-8 · External reference
10.1016/j.coph.2019.07.005
10.1016/j.coph.2019.07.005 · External reference
The role of gut microbiota in obesity, diabetes mellitus, and effect of metformin: new insights into old diseases
10.1016/j.coph.2019.03.011 · 2019 · External reference
10.1016/j.csbj.2020.06.028
10.1016/j.csbj.2020.06.028 · External reference
10.1038/s41564-019-0491-9
10.1038/s41564-019-0491-9 · External reference
Modeling metabolic interactions in a consortium of the infant gut microbiome
10.3389/fmicb.2017.02507 · 2017 · External reference
10.1111/j.1574-6941.2011.01085.x
10.1111/j.1574-6941.2011.01085.x · External reference
Determination of potential metabolic pathways of human intestinal bacteria by modeling growth kinetics from cross-feeding dynamics
10.1016/j.foodres.2016.02.004 · 2016 · External reference
Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
10.1038/s41598-018-23931-0 · 2018 · External reference
10.1136/gutjnl-2015-309618
10.1136/gutjnl-2015-309618 · External reference
10.1126/science.aac4812
10.1126/science.aac4812 · External reference
10.1371/journal.pone.0207072
10.1371/journal.pone.0207072 · External reference
ACBM: an integrated agent and constraint based modeling framework for simulation of microbial communities
10.1038/s41598-020-65659-w · 2020 · External reference
10.1016/j.coisb.2017.12.004
10.1016/j.coisb.2017.12.004 · External reference
10.1371/journal.pone.0148386
10.1371/journal.pone.0148386 · External reference
10.1016/j.cmet.2015.07.001
10.1016/j.cmet.2015.07.001 · External reference
10.1016/j.celrep.2014.03.070
10.1016/j.celrep.2014.03.070 · External reference
Metabolic modeling of human gut microbiota on a genome scale: an overview
2019 · External reference
Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)
10.1371/journal.pcbi.1007127 · 2019 · External reference
Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems
10.1038/s41598-019-53188-0 · 2019 · External reference
10.1038/nbt.1672
10.1038/nbt.1672 · External reference
10.1371/journal.pcbi.1006541
10.1371/journal.pcbi.1006541 · External reference
10.1186/s13059-019-1730-3
10.1186/s13059-019-1730-3 · External reference
Optimization based automated curation of metabolic reconstructions
10.1186/1471-2105-8-212 · 2007 · External reference
OptFill, a tool for infeasible cycle-free gapfilling of stoichiometric metabolic models
10.1016/j.isci.2019.100783 · 2020 · External reference
10.1093/nar/gky537
10.1093/nar/gky537 · External reference
BiGG Models: a platform for integrating, standardizing and sharing genome-scale models
10.1093/nar/gkv1049 · 2016 · External reference
10.1038/nbt.3703
10.1038/nbt.3703 · External reference
10.1186/s40168-019-0689-3
10.1186/s40168-019-0689-3 · External reference
10.1128/msystems.00606-19
10.1128/msystems.00606-19 · External reference
Large-scale metabolic interaction network of the mouse and human gut microbiota
10.1038/s41597-020-0516-5 · 2020 · External reference
10.1128/jb.180.19.5109-5116.1998
10.1128/jb.180.19.5109-5116.1998 · External reference
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110
10.1128/aem.60.10.3724-3731.1994 · 1994 · External reference
Contextualized genome-scale model unveils high-order metabolic effects of the specific growth rate and oxygenation level in recombinant Pichia pastoris
10.1016/j.mec.2019.e00103 · 2019 · External reference
Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii
10.1186/1752-0509-3-4 · 2009 · External reference
A comprehensive genome-scale reconstruction of Escherichia coli metabolism–2011
10.1038/msb.2011.65 · 2011 · External reference
10.1371/journal.pone.0064567
10.1371/journal.pone.0064567 · External reference
10.7554/elife.08208
10.7554/elife.08208 · External reference
10.1038/ismej.2010.117
10.1038/ismej.2010.117 · External reference
Metabolic network modeling of microbial interactions in natural and engineered environmental systems
10.3389/fmicb.2016.00673 · 2016 · External reference
10.1371/journal.pcbi.1005539
10.1371/journal.pcbi.1005539 · External reference
10.1371/journal.pcbi.1002363
10.1371/journal.pcbi.1002363 · External reference
10.1021/sb4001307
10.1021/sb4001307 · External reference
μBialSim: constraint-based dynamic simulation of complex microbiomes
10.3389/fbioe.2020.00574 · 2020 · External reference
10.1016/s0006-3495(02)73903-9
10.1016/s0006-3495(02)73903-9 · External reference
10.1016/j.biotechadv.2017.09.005
10.1016/j.biotechadv.2017.09.005 · External reference
Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy
10.1186/s13068-016-0441-1 · 2016 · External reference
10.7717/peerj.3443
10.7717/peerj.3443 · External reference
10.1097/00041433-200202000-00002
10.1097/00041433-200202000-00002 · External reference
10.1371/journal.pcbi.1005544
10.1371/journal.pcbi.1005544 · External reference
10.1053/j.gastro.2014.07.020
10.1053/j.gastro.2014.07.020 · External reference
10.1038/ismej.2011.161
10.1038/ismej.2011.161 · External reference
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities
10.1093/bioinformatics/bty941 · 2018 · External reference
10.1016/j.celrep.2019.04.001
10.1016/j.celrep.2019.04.001 · External reference
Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis
10.1093/femsle/fnv176 · 2015 · External reference
10.1016/j.csbj.2020.03.019 · Admitted local publication
Release of dissolved organic nitrogen by marine diazotrophic cyanobacteria, trichodesmium spp
10.1128/aem.60.11.3996-4000.1994 · 1994 · External reference
Unveiling genomic diversity among members of the species <em>Bifidobacterium pseudolongum</em>, a widely distributed gut commensal of the animal kingdom
10.1128/aem.03065-18 · 2019 · External reference
10.1038/nrmicro2832
10.1038/nrmicro2832 · External reference
10.1038/nature18848
10.1038/nature18848 · External reference
Predicting the longitudinally and radially varying gut microbiota composition using multi-scale microbial metabolic modeling
2019 · External reference
A multi-scale model of the whole human body based on dynamic parsimonious flux balance analysis
10.1016/j.ifacol.2016.07.319 · 2016 · External reference
Engineering microbial consortia to enhance biomining and bioremediation
10.3389/fmicb.2012.00203 · 2012 · External reference
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia
10.1093/bioinformatics/bty588 · 2018 · External reference
Species deletions from microbiome consortia reveal key metabolic interactions between gut microbes
10.1128/msystems.00185-19 · 2019 · External reference
Expanding metabolic capabilities using novel pathway designs: computational tools and case studies
10.1002/biot.201800734 · 2019 · External reference