BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

JSBML 1.0: providing a smorgasbord of options to encode systems biology models: Table 1.

(2015) Nicolas Rodriguez et al.   BIOINFORMATICS

Next-generation genome-scale models for metabolic engineering

(2015) Zachary A King et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

Implications of Big Data for cell biology

(2015) Kara Dolinski et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain

(2015) Anand K. Gavai et al.   PLoS One

The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data

(2014) Ronald Margolis et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease

(2014) Janan T. Eppig et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2014) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

(2014) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Gene: a gene-centered information resource at NCBI

(2014) Garth R. Brown et al.   NUCLEIC ACIDS RESEARCH

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

(2013) M. Ganter et al.   BIOINFORMATICS

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

Saccharomycesgenome database provides new regulation data

(2013) Maria C. Costanzo et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt 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

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The evolution of genome-scale models of cancer metabolism

(2013) Nathan E. Lewis et al.   Frontiers in Physiology

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

(2012) Akhil Kumar et al.   BMC BIOINFORMATICS

Analysis of omics data with genome-scale models of metabolism

(2012) Daniel R. Hyduke et al.   Molecular BioSystems

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

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

HMDB 3.0—The Human Metabolome Database in 2013

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

Controlled vocabularies and semantics in systems biology

(2011) M. Courtot et al.   Molecular Systems Biology

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

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

(2011) N. Juty et al.   NUCLEIC ACIDS RESEARCH

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Reconstruction of biochemical networks in microorganisms

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