Minimizing the number of optimizations for efficient community dynamic flux balance analysis

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth

(2019) Antonella Succurro et al.   mSystems

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

(2019) Sabine Koch et al.   PLoS Computational Biology

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

(2019) Benedict Borer et al.   PLoS Computational Biology

Metabolite-mediated modelling of microbial community dynamics captures emergent behaviour more effectively than species–species modelling

(2019) J. D. Brunner et al.   Journal of the Royal Society Interface

Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions

(2019) Mohammad Mazharul Islam et al.   Frontiers in Microbiology

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems

(2018) Akshit Goyal et al.   PHYSICAL REVIEW LETTERS

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

(2018) Colton J. Lloyd et al.   PLoS Computational Biology

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions

(2018) Xihui Xu et al.   ISME Journal

Microbiota-driven interleukin-17-producing cells and eosinophils synergize to accelerate multiple myeloma progression

(2018) Arianna Calcinotto et al.   Nature Communications

Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers

(2018) Vanessa L. Hale et al.   Genome Medicine

Metabolic Trade-Offs Promote Diversity in a Model Ecosystem

(2017) Anna Posfai et al.   PHYSICAL REVIEW LETTERS

Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

(2017) Jaeyun Sung et al.   Nature Communications

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

(2017) Babak Momeni et al.   eLife

Community structure follows simple assembly rules in microbial microcosms

(2017) Jonathan Friedman et al.   Nature Ecology & Evolution

MMinte: an application for predicting metabolic interactions among the microbial species in a community

(2016) Helena Mendes-Soares et al.   BMC BIOINFORMATICS

Tumour-associated and non-tumour-associated microbiota in colorectal cancer

(2016) Burkhardt Flemer et al.   GUT

Constraint-based stoichiometric modelling from single organisms to microbial communities

(2016) Willi Gottstein et al.   Journal of the Royal Society Interface

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

(2016) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Calibration and analysis of genome-based models for microbial ecology

(2015) Stilianos Louca et al.   eLife

Individualized medicine and the microbiome in reproductive tract

(2015) Andrea G. Braundmeier et al.   Frontiers in Physiology

DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis

(2014) Jose A Gomez et al.   BMC BIOINFORMATICS

Dynamic flux balance analysis for synthetic microbial communities

(2014) Michael A. Henson et al.   IET Systems Biology

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

DRUM: A New Framework for Metabolic Modeling under Non-Balanced Growth. Application to the Carbon Metabolism of Unicellular Microalgae

(2014) Caroline Baroukh et al.   PLoS One

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

(2014) Ali R. Zomorrodi et al.   ACS Synthetic Biology

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

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

Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

(2014) Hyun-Seob Song et al.   Processes

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

The design of long-term effective uranium bioremediation strategy using a community metabolic model

(2012) K. Zhuang et al.   BIOTECHNOLOGY AND BIOENGINEERING

A reliable simulator for dynamic flux balance analysis

(2012) K. Höffner et al.   BIOTECHNOLOGY AND BIOENGINEERING

Development of microbial cell factories for bio-refinery through synthetic bioengineering

(2012) Akihiko Kondo et al.   JOURNAL OF BIOTECHNOLOGY

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

The fundamental theorem of linear programming: extensions and applications

(2010) F. Tardella   OPTIMIZATION