Model-based quantification of metabolic interactions from dynamic microbial-community data

Networks of energetic and metabolic interactions define dynamics in microbial communities

(2015) Mallory Embree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

(2015) Mark Hanemaaijer et al.   Frontiers in Microbiology

A Data Integration and Visualization Resource for the Metabolic Network of Synechocystis sp. PCC 6803

(2014) T. R. Maarleveld et al.   PLANT PHYSIOLOGY

The environmental controls that govern the end product of bacterial nitrate respiration

(2014) B. Kraft et al.   SCIENCE

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Inhibitory activity of reuterin, nisin, lysozyme and nitrite against vegetative cells and spores of dairy-related Clostridium species

(2013) Marta Ávila et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Ecosystems biology of microbial metabolism

(2011) Niels Klitgord et al.   CURRENT OPINION IN BIOTECHNOLOGY

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

(2011) J. Zhou et al.   mBio

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

(2010) K. Yizhak et al.   BIOINFORMATICS

Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures

(2010) Timothy J. Hanly et al.   BIOTECHNOLOGY AND BIOENGINEERING

Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing

(2010) Fahimeh Salimi et al.   Biotechnology Journal

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

(2010) Kai Zhuang et al.   ISME Journal

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Development of Real-Time PCR Primer and Probe Sets for Detecting Degenerated and Non-degenerated Forms of the Butanol-Producing Bacterium Clostridium acetobutylicum ATCC 824

(2009) Sun-Mi Lee et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Initial community evenness favours functionality under selective stress

(2009) Lieven Wittebolle et al.   NATURE

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

(2008) Joungmin Lee et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome-scale model forClostridium acetobutylicum: Part I. Metabolic network resolution and analysis

(2008) Ryan S. Senger et al.   BIOTECHNOLOGY AND BIOENGINEERING

Community-based degradation of 4-chorosalicylate tracked on the single cell level

(2008) Sonja Pawelczyk et al.   JOURNAL OF MICROBIOLOGICAL METHODS