Genome assembly and annotation of passerine Salmonella Typhimurium
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ABSTRACT:
PROVIDER: PRJEB11556 | ENA |
REPOSITORIES: ENA
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Project description:Thiele2011 - Genome-scale metabolic network
of Salmonella Typhimurium (STM_v1_0)
This model is described in the article:
A community effort towards a
knowledge-base and mathematical model of the human pathogen
Salmonella Typhimurium LT2.
Thiele I, Hyduke DR, Steeb B, Fankam
G, Allen DK, Bazzani S, Charusanti P, Chen FC, Fleming RM, Hsiung
CA, De Keersmaecker SC, Liao YC, Marchal K, Mo ML, Özdemir
E, Raghunathan A, Reed JL, Shin SI, Sigurbjörnsdóttir
S, Steinmann J, Sudarsan S, Swainston N, Thijs IM, Zengler K,
Palsson BO, Adkins JN, Bumann D.
BMC Syst Biol 2011; 5: 8
Abstract:
BACKGROUND: Metabolic reconstructions (MRs) are common
denominators in systems biology and represent biochemical,
genetic, and genomic (BiGG) knowledge-bases for target
organisms by capturing currently available information in a
consistent, structured manner. Salmonella enterica subspecies I
serovar Typhimurium is a human pathogen, causes various
diseases and its increasing antibiotic resistance poses a
public health problem. RESULTS: Here, we describe a
community-driven effort, in which more than 20 experts in S.
Typhimurium biology and systems biology collaborated to
reconcile and expand the S. Typhimurium BiGG knowledge-base.
The consensus MR was obtained starting from two independently
developed MRs for S. Typhimurium. Key results of this
reconstruction jamboree include i) development and
implementation of a community-based workflow for MR annotation
and reconciliation; ii) incorporation of thermodynamic
information; and iii) use of the consensus MR to identify
potential multi-target drug therapy approaches. CONCLUSION:
Taken together, with the growing number of parallel MRs a
structured, community-driven approach will be necessary to
maximize quality while increasing adoption of MRs in
experimental design and interpretation.
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