Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0

Spatially-resolved metabolic cooperativity within dense bacterial colonies

(2015) John A Cole et al.   BMC Systems Biology

Modeling cancer metabolism on a genome scale

(2015) K. Yizhak et al.   Molecular Systems Biology

Calibration and analysis of genome-based models for microbial ecology

(2015) Stilianos Louca et al.   eLife

MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data

(2014) Paul A. Jensen et al.   BIOINFORMATICS

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies

(2013) Zhenjun Hu et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Clostridium difficile Is an Autotrophic Bacterial Pathogen

(2013) Michael Köpke et al.   PLoS One

The COMBREX Project: Design, Methodology, and Initial Results

(2013) Brian P. Anton et al.   PLOS BIOLOGY

GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization

(2012) Y.-C. Liao et al.   BIOINFORMATICS

Paint4Net: COBRA Toolbox extension for visualization of stoichiometric models of metabolism

(2012) Andrejs Kostromins et al.   BIOSYSTEMS

FAME, the Flux Analysis and Modeling Environment

(2012) Joost Boele et al.   BMC Systems Biology

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

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

Rapid Reaction Kinetics of Proline Dehydrogenase in the Multifunctional Proline Utilization A Protein

(2011) Michael A. Moxley et al.   BIOCHEMISTRY

JSBML: a flexible Java library for working with SBML

(2011) Andreas Dräger et al.   BIOINFORMATICS

Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

(2011) Jacek Sroka et al.   BMC BIOINFORMATICS

Web-Based Metabolic Network Visualization with a Zooming User Interface

(2011) Mario Latendresse et al.   BMC BIOINFORMATICS

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

(2011) Aarash Bordbar et al.   BMC Systems Biology

Ecosystems biology of microbial metabolism

(2011) Niels Klitgord et al.   CURRENT OPINION IN BIOTECHNOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks

(2010) A. Gevorgyan et al.   BIOINFORMATICS

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

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

FBA-SimVis: interactive visualization of constraint-based metabolic models

(2009) E. Grafahrend-Belau et al.   BIOINFORMATICS

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

(2009) Anu Raghunathan et al.   BMC Systems Biology

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology

(2009) Zhenjun Hu et al.   NUCLEIC ACIDS RESEARCH

VisANT: an integrative framework for networks in systems biology

(2008) Z. Hu et al.   BRIEFINGS IN BIOINFORMATICS

The Microbial Engines That Drive Earth's Biogeochemical Cycles

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