A gap-filling algorithm for prediction of metabolic interactions in microbial communities

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

(2021) Ilija Dukovski et al.   Nature Protocols

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

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

VFFVA: dynamic load balancing enables large-scale flux variability analysis

(2020) Marouen Ben Guebila   BMC BIOINFORMATICS

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

(2020) Samuel M D Seaver et al.   NUCLEIC ACIDS RESEARCH

Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli

(2020) Magdalena San Roman et al.   PLoS Computational Biology

An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community

(2019) Po-Hsiang Wang et al.   ISME Journal

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Taxonomic Weighting Improves the Accuracy of a Gap-Filling Algorithm for Metabolic Models

(2019) Wai Kit Ong et al.   BIOINFORMATICS

The MetaCyc database of metabolic pathways and enzymes - a 2019 update

(2019) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

(2019) N. T. Devika et al.   Scientific Reports

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

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

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Searching for the Bacterial Effector: The Example of the Multi-Skilled Commensal Bacterium Faecalibacterium prausnitzii

(2018) Rebeca Martín et al.   Frontiers in Microbiology

Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications

(2018) Kok Siong Ang et al.   CURRENT GENOMICS

Metabolism in dense microbial colonies: 13C metabolic flux analysis of E. coli grown on agar identifies two distinct cell populations with acetate cross-feeding

(2018) Eric Wolfsberg et al.   METABOLIC ENGINEERING

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

(2018) Federico Baldini et al.   BIOINFORMATICS

Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics

(2017) Mireia Lopez-Siles et al.   ISME Journal

SteadyCom: Predicting microbial abundances while ensuring community stability

(2017) Siu Hung Joshua Chan et al.   PLoS Computational Biology

The Human Microbiota in Health and Disease

(2017) Baohong Wang et al.   Engineering

Bifidobacterial inulin-type fructan degradation capacity determines cross-feeding interactions between bifidobacteria and Faecalibacterium prausnitzii

(2016) Frédéric Moens et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction

(2016) Christopher S. Henry et al.   JOURNAL OF CELLULAR PHYSIOLOGY

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation

(2016) Bat-Erdene Jugder et al.   Frontiers in Microbiology

Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut

(2016) Audrey Rivière et al.   Frontiers in Microbiology

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

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

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

Gut Microbiome

(2015) Gail A. Cresci et al.   NUTRITION IN CLINICAL PRACTICE

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

(2014) Ibrahim E El-Semman et al.   BMC Systems Biology

Bioaugmentation with Distinct Dehalobacter Strains Achieves Chloroform Detoxification in Microcosms

(2014) Shandra D. Justicia-Leon et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

(2014) A. Heinken et al.   JOURNAL OF BACTERIOLOGY

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

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

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

(2014) Matthew N. Benedict et al.   PLoS Computational Biology

Microbial degradation of chloroform

(2012) M. Cappelletti et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer

(2012) Weiguang Chen et al.   PLoS One

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

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

MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks

(2012) Edward Vitkin et al.   GENOME BIOLOGY

GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

(2012) Radhakrishnan Mahadevan et al.   Computational and Structural Biotechnology Journal

Dichloromethane Fermentation by a Dehalobacter sp. in an Enrichment Culture Derived from Pristine River Sediment

(2011) Shandra D. Justicia-Leon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth

(2011) Mireia Lopez-Siles et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Carbohydrate metabolism in Bifidobacteria

(2011) Karina Pokusaeva et al.   Genes and Nutrition

Cross-feeding between bifidobacteria and butyrate-producing colon bacteria explains bifdobacterial competitiveness, butyrate production, and gas production

(2011) Luc De Vuyst et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Fermentation in the Human Large Intestine

(2011) George T. Macfarlane et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

Chloroform respiration to dichloromethane by a Dehalobacter population

(2010) Ariel Grostern et al.   ENVIRONMENTAL MICROBIOLOGY

Dysbiosis of fecal microbiota in Crohnʼs disease patients as revealed by a custom phylogenetic microarray

(2010) Seungha Kang et al.   INFLAMMATORY BOWEL DISEASES

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

(2010) Kai Zhuang et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

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

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

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

(2010) Ines Thiele et al.   Nature Protocols

Characterization of a Dehalobacter Coculture That Dechlorinates 1,2-Dichloroethane to Ethene and Identification of the Putative Reductive Dehalogenase Gene

(2009) A. Grostern et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

What is microbial community ecology?

(2009) Allan Konopka   ISME Journal

GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions

(2009) Vinay Satish Kumar et al.   PLoS Computational Biology

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE