Related references
Note: Only part of the references are listed.The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Samuel M. D. Seaver et al.
NUCLEIC ACIDS RESEARCH (2021)
The functional repertoire contained within the native microbiota of the model nematode Caenorhabditis elegans
Johannes Zimmermann et al.
ISME JOURNAL (2020)
The MetaCyc database of metabolic pathways and enzymes - a 2019 update
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2020)
Database resources of the National Center for Biotechnology Information
Eric W. Sayers et al.
NUCLEIC ACIDS RESEARCH (2020)
Protein complex prediction: A survey
Javad Zahiri et al.
GENOMICS (2020)
MEMOTE for standardized genome-scale metabolic model testing
Christian Lieven et al.
NATURE BIOTECHNOLOGY (2020)
Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning
Gregory L. Medlock et al.
CELL SYSTEMS (2020)
SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah M. Keating et al.
MOLECULAR SYSTEMS BIOLOGY (2020)
Revealing metabolic mechanisms of interaction in the anaerobic digestion microbiome by flux balance analysis
Arianna Basile et al.
METABOLIC ENGINEERING (2020)
BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis
Lorenz Christian Reimer et al.
NUCLEIC ACIDS RESEARCH (2019)
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion
Sabine Koch et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Improving the accuracy of flux balance analysis through the implementation of carbon availability constraints for intracellular reactions
Maximilian Lularevic et al.
BIOTECHNOLOGY AND BIOENGINEERING (2019)
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential
Mohammad Alanjary et al.
NUCLEIC ACIDS RESEARCH (2019)
Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases
Konrad Aden et al.
GASTROENTEROLOGY (2019)
Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health
Kaitlyn Oliphant et al.
MICROBIOME (2019)
Modelling approaches for studying the microbiome
Manish Kumar et al.
NATURE MICROBIOLOGY (2019)
Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy
Rosina Pryor et al.
CELL (2019)
Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics
Ryan M. Ziels et al.
MSYSTEMS (2019)
Gut microbiota-derived succinate: Friend or foe in human metabolic diseases?
Sonia Fernandez-Veledo et al.
REVIEWS IN ENDOCRINE & METABOLIC DISORDERS (2019)
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
Edoardo Pasolli et al.
CELL (2019)
Gut Dysbiosis With Bacilli Dominance and Accumulation of Fermentation Products Precedes Late-onset Sepsis in Preterm Infants
S. Graspeuntner et al.
CLINICAL INFECTIOUS DISEASES (2019)
New approach for understanding genome variations in KEGG
Minoru Kanehisa et al.
NUCLEIC ACIDS RESEARCH (2019)
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
Jaime Huerta-Cepas et al.
NUCLEIC ACIDS RESEARCH (2019)
BRENDA in 2019: a European ELIXIR core data resource
Lisa Jeske et al.
NUCLEIC ACIDS RESEARCH (2019)
The Pfam protein families database in 2019
Sara El-Gebali et al.
NUCLEIC ACIDS RESEARCH (2019)
Current status and applications of genome-scale metabolic models
Changdai Gu et al.
GENOME BIOLOGY (2019)
A systematic assessment of current genome-scale metabolic reconstruction tools
Sebastian N. Mendoza et al.
GENOME BIOLOGY (2019)
Mucin Cross-Feeding of Infant Bifidobacteria and Eubacterium hallii
Vera Bunesova et al.
MICROBIAL ECOLOGY (2018)
SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis
Bingyao Zhu et al.
NUCLEIC ACIDS RESEARCH (2018)
The MetaCyc database of metabolic pathways and enzymes
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2018)
Constraint-based modeling in microbial food biotechnology
Martin H. Rau et al.
BIOCHEMICAL SOCIETY TRANSACTIONS (2018)
Ecology and evolution of metabolic cross-feeding interactions in bacteria
Glen D'Souza et al.
NATURAL PRODUCT REPORTS (2018)
KBase: The United States Department of Energy Systems Biology Knowledgebase
Adam P. Arkin et al.
NATURE BIOTECHNOLOGY (2018)
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
Daniel Machado et al.
NUCLEIC ACIDS RESEARCH (2018)
Traceability, reproducibility and wiki-exploration for a-la-carte reconstructions of genome-scale metabolic models
Meaziane Aite et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
Methods for automated genome-scale metabolic model reconstruction
Jose P. Faria et al.
BIOCHEMICAL SOCIETY TRANSACTIONS (2018)
Mutant phenotypes for thousands of bacterial genes of unknown function
Morgan N. Price et al.
NATURE (2018)
Automated generation of genome-scale metabolic draft reconstructions based on KEGG
Emil Karlsen et al.
BMC BIOINFORMATICS (2018)
RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor
Hao Wang et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn's disease
Eugen Bauer et al.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS (2018)
Strategies to improve reference databases for soil microbiomes
Jinlyung Choi et al.
ISME JOURNAL (2017)
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Stefania Magnusdottir et al.
NATURE BIOTECHNOLOGY (2017)
UniProt: the universal protein knowledgebase
Alex Bateman et al.
NUCLEIC ACIDS RESEARCH (2017)
metaSPAdes: a new versatile metagenomic assembler
Sergey Nurk et al.
GENOME RESEARCH (2017)
Mathematical modelling of microbes: metabolism, gene expression and growth
Hidde de Jong et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2017)
The evolution of the host microbiome as an ecosystem on a leash
Kevin R. Foster et al.
NATURE (2017)
iML1515, a knowledgebase that computes Escherichia coli traits
Jonathan M. Monk et al.
NATURE BIOTECHNOLOGY (2017)
Shotgun metagenomics, from sampling to analysis
Christopher Quince et al.
NATURE BIOTECHNOLOGY (2017)
Model-based quantification of metabolic interactions from dynamic microbial-community data
Mark Hanemaaijer et al.
PLOS ONE (2017)
Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion
Mariana X. Byndloss et al.
SCIENCE (2017)
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks
Sylvain Prigent et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
Eugen Bauer et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
Peter D. Karp et al.
BRIEFINGS IN BIOINFORMATICS (2016)
Early colonization of functional groups of microbes in the infant gut
Van T. Pham et al.
ENVIRONMENTAL MICROBIOLOGY (2016)
The landscape of microbial phenotypic traits and associated genes
Maria Brbic et al.
NUCLEIC ACIDS RESEARCH (2016)
Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health
David Rios-Covian et al.
FRONTIERS IN MICROBIOLOGY (2016)
Mash: fast genome and metagenome distance estimation using MinHash
Brian D. Ondov et al.
GENOME BIOLOGY (2016)
The Pyromaniac Inside You: Salmonella Metabolism in the Host Gut
Fabian Rivera-Chavez et al.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 69 (2015)
Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides
Audrey Riviere et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simao et al.
BIOINFORMATICS (2015)
Twenty years of bacterial genome sequencing
Nicholas J. Loman et al.
NATURE REVIEWS MICROBIOLOGY (2015)
Essential genome of Pseudomonas aeruginosa in cystic fibrosis sputum
Keith H. Turner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Pathway Analysis: State of the Art
Miguel A. Garcia-Campos et al.
FRONTIERS IN PHYSIOLOGY (2015)
Multivariate and Propensity Score Matching Software with Automated Balance Optimization: TheMatchingPackage forR
Jasjeet S. Sekhon
Journal of Statistical Software (2015)
Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework
Almut Heinken et al.
GUT MICROBES (2015)
FASTGAPFILL: efficient gap filling in metabolic networks
Ines Thiele et al.
BIOINFORMATICS (2014)
Reconciliation of metabolites and biochemical reactions for metabolic networks
Thomas Bernard et al.
BRIEFINGS IN BIOINFORMATICS (2014)
The gut microbiota, bacterial metabolites and colorectal cancer
Petra Louis et al.
NATURE REVIEWS MICROBIOLOGY (2014)
The Transporter Classification Database
Milton H. Saier et al.
NUCLEIC ACIDS RESEARCH (2014)
d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities
All R. Zomorrodi et al.
ACS SYNTHETIC BIOLOGY (2014)
Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
William R. Harcombe et al.
CELL REPORTS (2014)
Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
Matthew N. Benedict et al.
PLOS COMPUTATIONAL BIOLOGY (2014)
A systematic comparison of the MetaCyc and KEGG pathway databases
Tomer Altman et al.
BMC BIOINFORMATICS (2013)
sybil - Efficient constraint-based modelling in R
Gabriel Gelius-Dietrich et al.
BMC SYSTEMS BIOLOGY (2013)
Metabolically re-modeling the drug pipeline
Matthew A. Oberhardt et al.
CURRENT OPINION IN PHARMACOLOGY (2013)
The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis
Patrick M. Smith et al.
SCIENCE (2013)
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM
Jonathan M. Dreyfuss et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum
William R. Harcombe et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation
Jessica R. Sieber et al.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 66 (2012)
Microbial metabolic exchange-the chemotype-to-phenotype link
Vanessa V. Phelan et al.
NATURE CHEMICAL BIOLOGY (2012)
Rhea-a manually curated resource of biochemical reactions
Rafael Alcantara et al.
NUCLEIC ACIDS RESEARCH (2012)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2012)
Mining high-throughput experimental data to link gene and function
Crysten E. Blaby-Haas et al.
TRENDS IN BIOTECHNOLOGY (2011)
Dissecting the in Vivo Metabolic Potential of Two Human Gut Acetogens
Federico E. Rey et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2010)
Omic data from evolved E-coli are consistent with computed optimal growth from genome-scale models
Nathan E. Lewis et al.
MOLECULAR SYSTEMS BIOLOGY (2010)
High-throughput generation, optimization and analysis of genome-scale metabolic models
Christopher S. Henry et al.
NATURE BIOTECHNOLOGY (2010)
A protocol for generating a high-quality genome-scale metabolic reconstruction
Ines Thiele et al.
NATURE PROTOCOLS (2010)
BLAST plus : architecture and applications
Christiam Camacho et al.
BMC BIOINFORMATICS (2009)
Global phenotypic characterization of bacteria
Barry R. Bochner
FEMS MICROBIOLOGY REVIEWS (2009)
LibSBML: an API library for SBML
Benjamin J. Bornstein et al.
BIOINFORMATICS (2008)
Towards systems metabolic engineering of microorganisms for amino acid production
Jin Hwan Park et al.
CURRENT OPINION IN BIOTECHNOLOGY (2008)
Computational approaches to the topology, stability and dynamics of metabolic networks
Ralf Steuer
PHYTOCHEMISTRY (2007)
Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
Robert Schuetz et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
Metabolic modeling of a mutualistic microbial community
Sergey Stolyar et al.
MOLECULAR SYSTEMS BIOLOGY (2007)
Use of constraint-based modeling for the prediction and validation of antimicrobial targets
JD Trawick et al.
BIOCHEMICAL PHARMACOLOGY (2006)
Essential genes of a minimal bacterium
JI Glass et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri
Adam M. Feist et al.
MOLECULAR SYSTEMS BIOLOGY (2006)
Automated generation of heuristics for biological sequence comparison
GS Slater et al.
BMC BIOINFORMATICS (2005)
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
R Overbeek et al.
NUCLEIC ACIDS RESEARCH (2005)
The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks
HG Holzhütter
EUROPEAN JOURNAL OF BIOCHEMISTRY (2004)
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
R Mahadevan et al.
METABOLIC ENGINEERING (2003)
The Pfam protein families database
A Bateman et al.
NUCLEIC ACIDS RESEARCH (2000)
Share Paper
