Towards multidimensional genome annotation

By Jennie L. Reed, Iman Famili, Ines Thiele, Bernhard O. Palsson. Nature reviews genetics, 2006

383 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/67520ac289048668c52c7519bfc0981e6b2e8335

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Citations in the corpus

Network visualization and analysis of gene expression data using BioLayout Express3D (2009, background): “More recently, enormous amounts of data pertaining to the activity of genes and proteins and their interactions in the cell have been generated by a number of high-throughput techniques, including yeast two-hybrid assays, mass spectrometry, RNA interference and gene expression analysis 1 .”
Systems medicine: the future of medical genomics and healthcare (2009, neutral): “[106-110].”
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions (2010, methodology): “This has spurred the development of an ever increasing number of reconstructions [16-22].”
Applications of genome-scale metabolic reconstructions (2009, methodology): “reconstructions”
Genome-scale models of bacterial metabolism: reconstruction and applications (2008, methodology): “The systematic and automated reconstruction of genome-scale models from genomes and additional high-throughput data may seem like a natural extension of genome annotation (Reed et al ., 2006a), but remains beyond the reach of current methods.”
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 (2007, neutral): “that relate biological functions, such as metabolic reactions, to the genome through the use of the gene-protein-reaction formalis”
Reconstruction of Biochemical Networks in Microbial Organisms (2008, background): “The conceptual basis for the reconstruction process has been outline”
The Edinburgh human metabolic network reconstruction and its functional analysis (2007, background): “A preliminary metabolic network can be computationally reconstructed easily from the gene annotation information (Ma and Zeng, 2003; Romero et al, 2005; Reed et al, 2006 ).”
A protocol for generating a high-quality genome-scale metabolic reconstruction (2010, background): “These network reconstructions, and in silico models, are created in a bottom– up manner based on genomic and bibliomic data and thus represent a biochemical, genetic and genomic (BiGG) knowledge base for the target organism 9 .”
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models (2015, background): “A further advantage of mathematical structure is that the accuracy of GEMs increases continuously through comparison with experimental data (15).”
The model organism as a system: integrating 'omics' data sets (2006, methodology): “This technique begins with developing a network reconstruction on the basis of annotated genome sequence, known biochemistry and other high-throughput resources, such as proteomics, localizomics and phenomics dat”
Context-Specific Metabolic Networks Are Consistent with Experiments (2008, background): “Commonly, genome-scale metabolic networks are reconstructed to contain all known metabolic genes and reactions in a particular organism [1].”
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods (2012, background): “A genome provides the genetic basis for the metabolic network of an organism, and genome annotation defines the relationships between genes, enzymes and the reactions that they catalyse 14 (FIG.”
Hypergraphs and Cellular Networks (2009, background): “This completes the description of a stoichiometric network, which is in practice often conveniently described by a stoichiometric matrix (Figure 1C): The columns correspond to the reactions, i.e., hyperarcs, and the rows to the nodes, i.e., metabolites with their stoichiometric coefficients [15].”