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

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

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

(2019) Laurent Heirendt et al.   Nature Protocols

The gut microbiota regulates white adipose tissue inflammation and obesity via a family of microRNAs

(2019) Anthony T. Virtue et al.   Science Translational Medicine

Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae

(2019) Jing Yuan et al.   Cell Metabolism

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

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

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

GABA-modulating bacteria of the human gut microbiota

(2018) Philip Strandwitz et al.   Nature Microbiology

Alcohol, microbiome, life style influence alcohol and non-alcoholic organ damage

(2017) Manuela G. Neuman et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY

A wellness study of 108 individuals using personal, dense, dynamic data clouds

(2017) Nathan D Price et al.   NATURE BIOTECHNOLOGY

Predictive model identifies key network regulators of cardiomyocyte mechano-signaling

(2017) Philip M. Tan et al.   PLoS Computational Biology

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

(2017) Sjoerd Opdam et al.   Cell Systems

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease

(2016) Timothy R. Sampson et al.   CELL

Conditions for duality between fluxes and concentrations in biochemical networks

(2016) Ronan M.T. Fleming et al.   JOURNAL OF THEORETICAL BIOLOGY

Recon 2.2: from reconstruction to model of human metabolism

(2016) Neil Swainston et al.   Metabolomics

Diet–microbiota interactions as moderators of human metabolism

(2016) Justin L. Sonnenburg et al.   NATURE

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

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

(2016) Maike K. Aurich et al.   Frontiers in Physiology

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Basal Metabolic Rate of Adolescent Modern Pentathlon Athletes: Agreement between Indirect Calorimetry and Predictive Equations and the Correlation with Body Parameters

(2015) Luiz Lannes Loureiro et al.   PLoS One

Minireview: Gut Microbiota: The Neglected Endocrine Organ

(2014) Gerard Clarke et al.   MOLECULAR ENDOCRINOLOGY

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

BioModels: ten-year anniversary

(2014) Vijayalakshmi Chelliah et al.   NUCLEIC ACIDS RESEARCH

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

(2014) Swagatika Sahoo et al.   Frontiers in Physiology

Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells

(2013) Swagatika Sahoo et al.   HUMAN MOLECULAR GENETICS

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

A vision and strategy for the virtual physiological human: 2012 update

(2013) P. Hunter et al.   Interface Focus

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Multiscale Modeling and Data Integration in the Virtual Physiological Rat Project

(2012) Daniel A. Beard et al.   ANNALS OF BIOMEDICAL ENGINEERING

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: A connection between endogenous alcohol and NASH

(2012) Lixin Zhu et al.   HEPATOLOGY

A framework for human microbiome research

(2012)   NATURE

Mammalian heart renewal by pre-existing cardiomyocytes

(2012) Samuel E. Senyo et al.   NATURE

HMDB 3.0—The Human Metabolome Database in 2013

(2012) David S. Wishart et al.   NUCLEIC ACIDS RESEARCH

Integrating Cellular Metabolism into a Multiscale Whole-Body Model

(2012) Markus Krauss et al.   PLoS Computational Biology

iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states

(2011) Aarash Bordbar et al.   BMC Systems Biology

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

(2011) Aarash Bordbar et al.   BMC Systems Biology

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

(2011) Ottar Rolfsson et al.   BMC Systems Biology

The Microbiome and Butyrate Regulate Energy Metabolism and Autophagy in the Mammalian Colon

(2011) Dallas R. Donohoe et al.   Cell Metabolism

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

A Computational Systems Biology Software Platform for Multiscale Modeling and Simulation: Integrating Whole-Body Physiology, Disease Biology, and Molecular Reaction Networks

(2011) Thomas Eissing   Frontiers in Physiology

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

(2010) K. Yizhak et al.   BIOINFORMATICS

Functional Characterization of Alternate Optimal Solutions of Escherichia coli's Transcriptional and Translational Machinery

(2010) Ines Thiele et al.   BIOPHYSICAL JOURNAL

Computationally efficient flux variability analysis

(2010) Steinn Gudmundsson et al.   BMC BIOINFORMATICS

The physiological regulation of glucose flux into muscle in vivo

(2010) D. H. Wasserman et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology

(2010) Christoph Gille et al.   Molecular Systems Biology

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen 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

Grand challenges in systems physiology

(2010) Hiroaki Kitano   Frontiers in Physiology

Proteomic analysis of human bile and potential applications for cancer diagnosis

(2009) Annarita Farina et al.   Expert Review of Proteomics

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Human Organ/Tissue Growth Algorithms that Include Obese Individuals and Black/White Population Organ Weight Similarities from Autopsy Data

(2009) John F. Young et al.   JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH-PART A-CURRENT ISSUES

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Comparison of Carbon Nutrition for Pathogenic and Commensal Escherichia coli Strains in the Mouse Intestine

(2008) A. J. Fabich et al.   INFECTION AND IMMUNITY

Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes

(2008) Sandrine P Claus et al.   Molecular Systems Biology

KEGG Atlas mapping for global analysis of metabolic pathways

(2008) S. Okuda et al.   NUCLEIC ACIDS RESEARCH