Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome

The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges

(2020) Pei Yee Tiew et al.   MYCOPATHOLOGIA

MEMOTE for standardized genome-scale metabolic model testing

(2020) Christian Lieven et al.   NATURE BIOTECHNOLOGY

The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication

(2020) Ygor Parladore Silva et al.   Frontiers in Endocrinology

Role of gut microbiota in type 2 diabetes pathophysiology

(2020) Manoj Gurung et al.   EBioMedicine

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

(2020) Christian Diener et al.   mSystems

Computational Modeling of the Human Microbiome

(2020) Shomeek Chowdhury et al.   Microorganisms

Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

(2020) Mario Matijašić et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome

(2020) Ines Thiele et al.   Molecular Systems Biology

An atlas of human metabolism

(2020) Jonathan L. Robinson et al.   Science Signaling

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions

(2020) Gregory L. Medlock et al.   PLoS Computational Biology

MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome–Host Interactions

(2020) Tahila Andrighetti et al.   Cells

Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions

(2020) Federico Baldini et al.   BMC BIOLOGY

Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models

(2020) Sanjeev Dahal et al.   PROTEOMICS

μBialSim: Constraint-Based Dynamic Simulation of Complex Microbiomes

(2020) Denny Popp et al.   Frontiers in Bioengineering and Biotechnology

Reconstructing organisms in silico: genome-scale models and their emerging applications

(2020) Xin Fang et al.   NATURE REVIEWS MICROBIOLOGY

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

The Era of Big Data: Genome-scale Modelling meets Machine Learning

(2020) Athanasios Antonakoudis et al.   Computational and Structural Biotechnology Journal

Predicting Nash equilibria for microbial metabolic interactions

(2020) Jingyi Cai et al.   BIOINFORMATICS

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

(2019) Laurent Heirendt et al.   Nature Protocols

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

(2019) Almut Heinken et al.   Microbiome

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

(2019) Shinichi Yachida et al.   NATURE MEDICINE

Machine and deep learning meet genome-scale metabolic modeling

(2019) Guido Zampieri et al.   PLoS Computational Biology

Predicting the Longitudinally and Radially Varying Gut Microbiota Composition Using Multi-Scale Microbial Metabolic Modeling

(2019) Chan et al.   Processes

Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome

(2019) Israr Khan et al.   Pathogens

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

(2019) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

BioModels—15 years of sharing computational models in life science

(2019) Rahuman S Malik-Sheriff et al.   NUCLEIC ACIDS RESEARCH

Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities

(2019) Cristal Zuñiga et al.   Nature Microbiology

Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology

(2019) Peter D Karp et al.   BRIEFINGS IN BIOINFORMATICS

Oral microbiota and autism spectrum disorder (ASD)

(2019) Ingar Olsen et al.   Journal of Oral Microbiology

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

The human skin microbiome

(2018) Allyson L. Byrd et al.   NATURE REVIEWS MICROBIOLOGY

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

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

PlantSEED Enables Automated Annotation and Reconstruction of Plant Primary Metabolism with Improved Compartmentalization and Comparative Consistency

(2018) Samuel M. D. Seaver et al.   PLANT JOURNAL

Constraint based modeling of metabolism allows finding metabolic cancer hallmarks and identifying personalized therapeutic windows

(2018) Sergio Bordel   Oncotarget

Alterations of oral microbiota distinguish children with autism spectrum disorders from healthy controls

(2018) Yanan Qiao et al.   Scientific Reports

Role of the gut microbiota in nutrition and health

(2018) Ana M Valdes et al.   BMJ-British Medical Journal

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

(2018) Alyaa M. Abdel-Haleem et al.   PLoS Computational Biology

Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models

(2018) Méziane Aite et al.   PLoS Computational Biology

Role of the gut microbiota in nutrition and health

(2018) Ana M Valdes et al.   BMJ-British Medical Journal

Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling

(2018) Dorines Rosario et al.   Frontiers in Physiology

Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa

(2018) Yan Zhu et al.   GigaScience

Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling

(2018) Manish Kumar et al.   METABOLIC ENGINEERING

Challenges in modeling the human gut microbiome

(2018) Parizad Babaei et al.   NATURE BIOTECHNOLOGY

Reply to "Challenges in modeling the human gut microbiome"

(2018) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

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

(2018) Federico Baldini et al.   BIOINFORMATICS

Automated generation of genome-scale metabolic draft reconstructions based on KEGG

(2018) Emil Karlsen et al.   BMC BIOINFORMATICS

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

(2018) Hao Wang et al.   PLoS Computational Biology

New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract

(2018) Isabel F. Escapa et al.   mSystems

Gut microbiota: Implications in Parkinson's disease

(2017) Arun Parashar et al.   PARKINSONISM & RELATED DISORDERS

A pathology atlas of the human cancer transcriptome

(2017) Mathias Uhlen et al.   SCIENCE

Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions

(2017) Edik M. Blais et al.   Nature Communications

Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition

(2017) Alice Harding et al.   Frontiers in Aging Neuroscience

SteadyCom: Predicting microbial abundances while ensuring community stability

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

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

(2017) Sylvain Prigent et al.   PLoS Computational Biology

BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities

(2017) Eugen Bauer et al.   PLoS Computational Biology

Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

(2017) Matthew B. Biggs et al.   PLoS Computational Biology

Oral Microbiota: Microbial Biomarkers of Metabolic Syndrome Independent of Host Genetic Factors

(2017) Jiyeon Si et al.   Frontiers in Cellular and Infection Microbiology

More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes

(2017) Kees C. H. van der Ark et al.   Microbiome

Discovering missing reactions of metabolic networks by using gene co-expression data

(2017) Zhaleh Hosseini et al.   Scientific Reports

BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods

(2016) Tolutola Oyetunde et al.   BIOINFORMATICS

DEF: an automated dead-end filling approach based on quasi-endosymbiosis

(2016) Lili Liu et al.   BIOINFORMATICS

Microbial interactions: ecology in a molecular perspective

(2016) Raíssa Mesquita Braga et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

The oral microbiome – an update for oral healthcare professionals

(2016) M. Kilian et al.   BRITISH DENTAL JOURNAL

Current Understanding of Dysbiosis in Disease in Human and Animal Models

(2016) Arianna K. DeGruttola et al.   INFLAMMATORY BOWEL DISEASES

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Revised Estimates for the Number of Human and Bacteria Cells in the Body

(2016) Ron Sender et al.   PLOS BIOLOGY

Personalized Cardiovascular Disease Prediction and Treatment—A Review of Existing Strategies and Novel Systems Medicine Tools

(2016) Elias Björnson et al.   Frontiers in Physiology

Metabolic network-guided binning of metagenomic sequence fragments

(2015) Matthew B. Biggs et al.   BIOINFORMATICS

Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

(2015) Saeed Shoaie et al.   Cell Metabolism

Enhanced hexose fermentation by Saccharomyces cerevisiae through integration of stoichiometric modeling and genetic screening

(2015) Josh Quarterman et al.   JOURNAL OF BIOTECHNOLOGY

Multi -omics and metabolic modelling pipelines: Challenges and tools for systems microbiology

(2015) Marco Fondi et al.   MICROBIOLOGICAL RESEARCH

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

(2015) Xuan Zhang et al.   NATURE MEDICINE

MetaNetX/MNXref – reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks

(2015) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

Reconstructing genome-scale metabolic models with merlin

(2015) Oscar Dias 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

fastGapFill: efficient gap filling in metabolic networks

(2014) Ines Thiele et al.   BIOINFORMATICS

Integrating Transcriptomics with Metabolic Modeling Predicts Biomarkers and Drug Targets for Alzheimer's Disease

(2014) Shiri Stempler 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

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

(2014) Esa Pitkänen et al.   PLoS Computational Biology

A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness

(2014) Raphy Zarecki et al.   PLoS Computational Biology

Path2Models: large-scale generation of computational models from biochemical pathway maps

(2013) Finja Büchel et al.   BMC Systems Biology

Microbiological Survey of the Human Gastric Ecosystem Using Culturing and Pyrosequencing Methods

(2013) Susana Delgado et al.   MICROBIAL ECOLOGY

Integration of clinical data with a genome-scale metabolic model of the human adipocyte

(2013) A. Mardinoglu et al.   Molecular Systems Biology

Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory

(2013) José Manuel Otero et al.   PLoS One

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

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

Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence

(2013) Benjamin Steeb et al.   PLoS Pathogens

FAME, the Flux Analysis and Modeling Environment

(2012) Joost Boele et al.   BMC Systems Biology

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

(2012) Erwin G Zoetendal et al.   ISME Journal

Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering

(2012) Chiam Yu Ng et al.   Microbial Cell Factories

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren 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

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

Predicting selective drug targets in cancer through metabolic networks

(2011) O. Folger et al.   Molecular Systems Biology

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

(2011) H. U. Kim et al.   Molecular Systems Biology

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

The skin microbiome

(2011) Elizabeth A. Grice et al.   NATURE REVIEWS MICROBIOLOGY

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

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

(2010) Kai Zhuang et al.   ISME Journal

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

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE

(2009) Hyun Uk Kim et al.   Molecular BioSystems

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

(2008) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY