Enhancing Microbiome Research through Genome-Scale Metabolic Modeling

Understanding the host-microbe interactions using metabolic modeling

(2021) Jack Jansma et al.   Microbiome

CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention

(2021) Jun Geng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

(2021) Linnea Österberg et al.   PLoS Computational Biology

Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster

(2021) Nana Y. D. Ankrah et al.   mSystems

Target classification in the 14th round of the critical assessment of protein structure prediction ( CASP14 )

(2021) Lisa N. Kinch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

(2021) Ilija Dukovski et al.   Nature Protocols

Automatic construction of metabolic models with enzyme constraints

(2020) Pavlos Stephanos Bekiaris et al.   BMC BIOINFORMATICS

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning

(2020) Gregory L. Medlock et al.   Cell Systems

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

(2020) Christian Diener et al.   mSystems

Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium

(2020) George C. diCenzo et al.   Nature Communications

Credible practice of modeling and simulation in healthcare: ten rules from a multidisciplinary perspective

(2020) Ahmet Erdemir et al.   Journal of Translational Medicine

Reconstructing organisms in silico: genome-scale models and their emerging applications

(2020) Xin Fang et al.   NATURE REVIEWS MICROBIOLOGY

Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production

(2020) Snorre Sulheim et al.   iScience

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

(2019) Alan R. Pacheco et al.   Nature Communications

Systems Biology of Plant-Microbiome Interactions

(2019) Patricia A. Rodriguez et al.   Molecular Plant

Modelling approaches for studying the microbiome

(2019) Manish Kumar et al.   Nature Microbiology

Automated generation of bacterial resource allocation models

(2019) Ana Bulović et al.   METABOLIC ENGINEERING

Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies

(2019) Cecilia Noecker et al.   mSystems

Emerging whole-cell modeling principles and methods

(2018) Arthur P Goldberg et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Towards predicting the environmental metabolome from metagenomics with a mechanistic model

(2018) Daniel R. Garza et al.   Nature Microbiology

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

(2018) Eugen Bauer et al.   mSystems

Seven Billion Microcosms: Evolution within Human Microbiomes

(2018) Tami D. Lieberman   mSystems

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Systems analysis of intracellular pH vulnerabilities for cancer therapy

(2018) Erez Persi et al.   Nature Communications

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota

(2018) Gregory L. Medlock et al.   Cell Systems

On the deformability of an empirical fitness landscape by microbial evolution

(2018) Djordje Bajić et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

(2017) Eugen Bauer et al.   PLoS Computational Biology

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

(2017) Matthew B. Biggs et al.   PLoS Computational Biology

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Computing the functional proteome: recent progress and future prospects for genome-scale models

(2015) Edward J O’Brien et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metabolic network modeling of microbial communities

(2015) Matthew B. Biggs et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Data-driven integration of genome-scale regulatory and metabolic network models

(2015) Saheed Imam et al.   Frontiers in Microbiology

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

Cell design in bacteria as a convex optimization problem

(2011) Anne Goelzer et al.   AUTOMATICA

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis

(2010) Sriram Chandrasekaran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA