COBRAme: A computational framework for genome-scale models of metabolism and gene expression

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

(2017) Ding Ma et al.   Scientific Reports

solveME: fast and reliable solution of nonlinear ME models

(2016) Laurence Yang et al.   BMC BIOINFORMATICS

Multi-omic data integration enables discovery of hidden biological regularities

(2016) Ali Ebrahim et al.   Nature Communications

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Computing the functional proteome: recent progress and future prospects for genome-scale models

(2015) Edward J O’Brien et al.   CURRENT OPINION IN BIOTECHNOLOGY

Do genome-scale models need exact solvers or clearer standards?

(2015) A. Ebrahim et al.   Molecular Systems Biology

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

(2015) Zachary A. King et al.   PLoS Computational Biology

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale

(2014) Joanne K Liu et al.   BMC Systems Biology

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

sybil – Efficient constraint-based modelling in R

(2013) Gabriel Gelius-Dietrich et al.   BMC Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

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

(2013) Rasmus Agren et al.   PLoS Computational Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

(2012) Ines Thiele et al.   PLoS One

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

JSBML: a flexible Java library for working with SBML

(2011) Andreas Dräger et al.   BIOINFORMATICS

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology