Emergent Biosynthetic Capacity in Simple Microbial Communities

Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

(2013) Sharon Greenblum et al.   CURRENT OPINION IN BIOTECHNOLOGY

Agricultural soils, pesticides and microbial diversity

(2013) Carsten Suhr Jacobsen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Restoration of the gut microbial habitat as a disease therapy

(2013) David A Relman   NATURE BIOTECHNOLOGY

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

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

Metabolic Proximity in the Order of Colonization of a Microbial Community

(2013) Varun Mazumdar 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

Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass

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

Understanding the interactions between bacteria in the human gut through metabolic modeling

(2013) Saeed Shoaie et al.   Scientific Reports

Artificial stool transplantation: progress towards a safer, more effective and acceptable alternative

(2013) Emma Allen-Vercoe et al.   Expert Review of Gastroenterology & Hepatology

Strong inter-population cooperation leads to partner intermixing in microbial communities

(2013) Babak Momeni et al.   eLife

Stool substitute transplant therapy for the eradication of Clostridium difficile infection: ‘RePOOPulating’ the gut

(2013) Elaine O Petrof et al.   Microbiome

MicrobesFlux: a web platform for drafting metabolic models from the KEGG database

(2012) Xueyang Feng et al.   BMC Systems Biology

Computational systems biology and in silico modeling of the human microbiome

(2012) E. Borenstein   BRIEFINGS IN BIOINFORMATICS

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Temporal Expression-based Analysis of Metabolism

(2012) Sara B. Collins et al.   PLoS Computational Biology

Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1

(2012) Xueyang Feng et al.   PLoS Computational Biology

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice

(2012) Trevor D. Lawley et al.   PLoS Pathogens

Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer

(2011) Joy D. Van Nostrand et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures

(2011) Timothy J. Hanly et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

(2011) Eleftheria Tzamali et al.   BMC Systems Biology

Influence of C4-dicarboxylic acid transporters on succinate production

(2011) Joeri J. Beauprez et al.   GREEN CHEMISTRY

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

Prospects for systems biology and modeling of the gut microbiome

(2011) Fredrik H. Karlsson et al.   TRENDS IN BIOTECHNOLOGY

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

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

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks

(2010) Eytan Ruppin et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2010) Kai Zhuang et al.   ISME Journal

Temporal Patterns in Glycolate-Utilizing Bacterial Community Composition Correlate with Phytoplankton Population Dynamics in Humic Lakes

(2010) Sara F. Paver et al.   MICROBIAL ECOLOGY

Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute et al.   Molecular Systems Biology

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

BRENDA, the enzyme information system in 2011

(2010) M. Scheer et al.   NUCLEIC ACIDS RESEARCH

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

(2010) Jesse R. Zaneveld et al.   NUCLEIC ACIDS RESEARCH

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

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Constraint-Based Model of Shewanella oneidensis MR-1 Metabolism: A Tool for Data Analysis and Hypothesis Generation

(2010) Grigoriy E. Pinchuk et al.   PLoS Computational Biology

Role of urea in microbial metabolism in aquatic systems: a biochemical and molecular review

(2009) CM Solomon et al.   AQUATIC MICROBIAL ECOLOGY

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

(2009) Caroline B. Milne et al.   Biotechnology Journal

Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction

(2009) Anu Raghunathan et al.   BMC Systems Biology

Syntrophy in anaerobic global carbon cycles

(2009) Michael J McInerney et al.   CURRENT OPINION IN BIOTECHNOLOGY

Obesity and the human microbiome

(2009) Ruth E Ley   CURRENT OPINION IN GASTROENTEROLOGY

Synthesis of Methyl Halides from Biomass Using Engineered Microbes

(2009) Travis S. Bayer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

Electron transfer in syntrophic communities of anaerobic bacteria and archaea

(2009) Alfons J. M. Stams et al.   NATURE REVIEWS MICROBIOLOGY

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

Bacterial Toxin–Antitoxin Systems: More Than Selfish Entities?

(2009) Laurence Van Melderen et al.   PLoS Genetics

Metabolic-network-driven analysis of bacterial ecological strategies

(2009) Shiri Freilich et al.   GENOME BIOLOGY

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

(2009) Christopher S Henry et al.   GENOME BIOLOGY

Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities

(2008) Ainslie E.F. Little et al.   Annual Review of Microbiology

An Invitation to the Marriage of Metagenomics and Metabolomics

(2008) Peter J. Turnbaugh et al.   CELL

Complementary cooperation between two syntrophic bacteria in pesticide degradation

(2008) Chie Katsuyama et al.   JOURNAL OF THEORETICAL BIOLOGY

The evolution of modularity in bacterial metabolic networks

(2008) A. Kreimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY

Ecology and genomics of Bacillus subtilis

(2008) Ashlee M. Earl et al.   TRENDS IN MICROBIOLOGY

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology

Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains ofEscherichia coli C that produce succinate and malate

(2007) Kaemwich Jantama et al.   BIOTECHNOLOGY AND BIOENGINEERING