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

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in-silico evaluation of their potentials

(2012) Luis Caspeta et al.   BMC Systems Biology

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

(2012) Naomi Habib et al.   Molecular Systems Biology

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

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism

(2011) Markus Heinonen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Predicting selective drug targets in cancer through metabolic networks

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

eQuilibrator--the biochemical thermodynamics calculator

(2011) A. Flamholz et al.   NUCLEIC ACIDS RESEARCH

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

Computational methods for metabolic reconstruction

(2010) Esa Pitkänen et al.   CURRENT OPINION IN BIOTECHNOLOGY

Reconstruction annotation jamborees: a community approach to systems biology

(2010) Ines Thiele et al.   Molecular Systems Biology

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network

(2010) Germán Plata et al.   Molecular Systems Biology

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

Network-based prediction of metabolic enzymes' subcellular localization

(2009) S. Mintz-Oron et al.   BIOINFORMATICS

A fungal phylogeny based on 82 complete genomes using the composition vector method

(2009) Hao Wang et al.   BMC EVOLUTIONARY BIOLOGY

Inferring branching pathways in genome-scale metabolic networks

(2009) Esa Pitkänen et al.   BMC Systems Biology

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Comparative Genome-Scale Metabolic Reconstruction and Flux Balance Analysis of Multiple Staphylococcus aureus Genomes Identify Novel Antimicrobial Drug Targets

(2009) D.-S. Lee et al.   JOURNAL OF BACTERIOLOGY

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

(2009) Patrick F. Suthers et al.   PLoS Computational Biology

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

(2008) Ari Rantanen et al.   BMC BIOINFORMATICS

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

The 2008 update of the Aspergillus nidulans genome annotation: A community effort

(2008) Jennifer Russo Wortman et al.   FUNGAL GENETICS AND BIOLOGY

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function

(2008) Marco Punta et al.   PLoS Computational Biology

Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

(2008) Evan S Snitkin et al.   GENOME BIOLOGY