Knowledge representation in metabolic pathway databases

Construction and completion of flux balance models from pathway databases

(2012) Mario Latendresse et al.   BIOINFORMATICS

The virtual liver: a multidisciplinary, multilevel challenge for systems biology

(2012) Hermann-Georg Holzhütter et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis

(2012) Leonid Chindelevitch et al.   GENOME BIOLOGY

A survey of metabolic databases emphasizing the MetaCyc family

(2011) Peter D. Karp et al.   ARCHIVES OF TOXICOLOGY

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

(2011) Luca Beltrame et al.   BIOINFORMATICS

Critical assessment of human metabolic pathway databases: a stepping stone for future integration

(2011) Miranda D Stobbe et al.   BMC Systems Biology

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Compartmentalization of the Edinburgh Human Metabolic Network

(2010) Tong Hao et al.   BMC BIOINFORMATICS

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

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

(2010) Karin Radrich et al.   BMC Systems Biology

The BioPAX community standard for pathway data sharing

(2010) Emek Demir 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

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

Chemical Entities of Biological Interest: an update

(2009) Paula de Matos et al.   NUCLEIC ACIDS RESEARCH

An Introduction to Metabolic Networks and Their Structural Analysis

(2008) V. Lacroix et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2008) Markus J Herrgård et al.   NATURE BIOTECHNOLOGY

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network

(2008) Alexey V Antonov et al.   GENOME BIOLOGY