WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction

By R. Overbeek, Neil Larsen, G. Pusch, M. D'Souza, Evgeni Selkov Jr., Nikos Kyrpides, M. Fonstein, N. Maltsev. Nucleic Acids Res., 2000

413 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4482509f32f566947373616c00685cdfc36f6c55

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Citations in the corpus

Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum (2001, methodology): “acetobutylicum in conjunction with the KEGG (37) and WIT (55)”
The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks (2003, neutral): “Organism-specific metabolic networks can be reconstructed from genome information using databases such as KEGG, WIT and Ecocyc (Ogata et al., 1999; Overbeek et al., 2000; Wittig and De Beuckelaer, 2001; Karp et al., 2002).”
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes (2005, methodology): “The WIT database (36) has not been available on the web for more than 1 year, and appears to have been succeeded by the PUMA2 system (see http://compbio.”
GenDB--an open source genome annotation system for prokaryote genomes. (2003, background): “), BioScout (Genequiz, Lion AG), WIT (4) and the open source system Artemis (5).”
OptStrain: a computational framework for redesign of microbial production systems. (2004, background): “At the same time, individual reactions are deposited in databases such as KEGG, EMP, MetaCyc, UM-BBD, and many more (Selkov Jr. et al. 1998; Overbeek et al. 2000; Karp et al. 2002; Ellis et al. 2003; Kanehisa et al. 2004; Krieger et al. 2004), forming encompassing and growing collections of the biot”
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms (2003, methodology): “Several methods and metabolic databases are available to reconstruct an organism specific metabolic network from genome information, such as KEGG (http://www.genome.ad.jp/kegg), WIT (wit.mcs.anl.gov/WIT) and EcoCyc (biocyc.org/ecocyc/) (Ogata et al., 1999; Overbeek et al., 2000; Karp et al., 2002).”
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world (2008, background): “Additional functional information can be obtained through genome-context analysis approaches that are, also, steeped in genome comparison and rely on conservation of arrays of functionally linked genes (55,56) (see below).”
The Proteomics Protocols Handbook (2005, background): “It is interesting to note that although the addition of thiourea to this mixture increases both the number and quality of proteins that are detected, these additional proteins are water-soluble proteins, not membrane proteins (56,57).”