Challenges in experimental data integration within genome-scale metabolic models

A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincaré, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in Systems Biology.

[1]  Vinay Satish Kumar,et al.  GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions , 2009, PLoS Comput. Biol..

[2]  Edda Klipp,et al.  SBMLmerge, a system for combining biochemical network models. , 2006, Genome informatics. International Conference on Genome Informatics.

[3]  Eörs Szathmáry,et al.  Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks , 2008, Genome Biology.

[4]  Daniela Calvetti,et al.  Bayesian flux balance analysis applied to a skeletal muscle metabolic model. , 2007, Journal of theoretical biology.

[5]  Eytan Ruppin,et al.  Network-based prediction of metabolic enzymes' subcellular localization , 2009, Bioinform..

[6]  Edda Klipp,et al.  Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data , 2006, Theoretical Biology and Medical Modelling.

[7]  Andreas Wagner,et al.  Genotype networks in metabolic reaction spaces , 2010, BMC Systems Biology.

[8]  D. Fell,et al.  Is maximization of molar yield in metabolic networks favoured by evolution? , 2008, Journal of theoretical biology.

[9]  E. Ruppin,et al.  Predicting metabolic biomarkers of human inborn errors of metabolism , 2009, Molecular systems biology.

[10]  U. Sauer.  High-throughput phenomics: experimental methods for mapping fluxomes. , 2004, Current opinion in biotechnology.

[11]  Reinhart Heinrich,et al.  Structural analysis of expanding metabolic networks. , 2004, Genome informatics. International Conference on Genome Informatics.

[12]  Matthias Heinemann,et al.  Systematic assignment of thermodynamic constraints in metabolic network models , 2006, BMC Bioinformatics.

[13]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[14]  D. Fell,et al.  Challenges to be faced in the reconstruction of metabolic networks from public databases. , 2006, Systems biology.

[15]  Gary D Bader,et al.  The Genetic Landscape of a Cell , 2010, Science.

[16]  Jason A. Papin,et al.  Comparison of network-based pathway analysis methods. , 2004, Trends in biotechnology.

[17]  Oliver Ebenhöh,et al.  Biosynthetic Potentials of Metabolites and Their Hierarchical Organization , 2008, PLoS Comput. Biol..

[18]  Uri Alon,et al.  An Introduction to Systems Biology , 2006 .

[19]  Markus J. Herrgård,et al.  Network-based prediction of human tissue-specific metabolism , 2008, Nature Biotechnology.

[20]  Vinay Satish Kumar,et al.  Optimization based automated curation of metabolic reconstructions , 2007, BMC Bioinformatics.

[21]  Adam M. Feist,et al.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.

[22]  S. Schuster,et al.  Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns. , 2009, Genome research.

[23]  Kiran Raosaheb Patil,et al.  Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes , 2010, PLoS Comput. Biol..

[24]  Eytan Ruppin,et al.  Flux balance analysis accounting for metabolite dilution , 2010, Genome Biology.

[25]  Ali R. Zomorrodi,et al.  Genome-scale gene/reaction essentiality and synthetic lethality analysis , 2009, Molecular systems biology.

[26]  Andreas Kremling,et al.  A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake , 2008, Bioinform..