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

被引：108

作者：

Thiele, Ines ^{[2
,3
]}

Hyduke, Daniel R. ^{[4
]}

Steeb, Benjamin ^{[1
]}

Fankam, Guy ^{[4
]}

Allen, Douglas K. ^{[5
]}

Bazzani, Susanna ^{[6
]}

Charusanti, Pep ^{[4
]}

Chen, Feng-Chi ^{[7
]}

Fleming, Ronan M. T. ^{[2
,8
]}

Hsiung, Chao A. ^{[7
]}

De Keersmaecker, Sigrid C. J. ^{[9
]}

Liao, Yu-Chieh ^{[7
]}

Marchal, Kathleen ^{[9
]}

Mo, Monica L. ^{[4
]}

Oezdemir, Emre ^{[10
]}

Raghunathan, Anu ^{[11
]}

Reed, Jennifer L. ^{[12
]}

Shin, Sook-Il ^{[11
]}

Sigurbjornsdottir, Sara ^{[13
]}

Steinmann, Jonas ^{[13
]}

Sudarsan, Suresh ^{[14
]}

Swainston, Neil ^{[15
,16
]}

Thijs, Inge M. ^{[9
]}

Zengler, Karsten ^{[4
]}

Palsson, Bernhard O. ^{[4
]}

Adkins, Joshua N. ^{[17
]}

Bumann, Dirk ^{[1
]}

机构：

[1] Univ Basel, Biozentrum, Basel, Switzerland

[2] Univ Iceland, Ctr Syst Biol, Reykjavik, Iceland

[3] Univ Iceland, Fac Ind Engn Mech Engn & Comp Sci, Reykjavik, Iceland

[4] Univ Calif San Diego, Dept Bioengn, La Jolla, CA 92093 USA

[5] USDA ARS, Plant Genet Res Unit, Donald Danforth Plant Sci Ctr, St Louis, MO USA

[6] Tech Univ Carolo Wilhelmina Braunschweig, Inst Bioinformat & Biochem, Braunschweig, Germany

[7] Natl Hlth Res Inst, Div Biostat & Bioinformat, Inst Populat Hlth Sci, Zhunan, Taiwan

[8] Univ Iceland, Inst Sci, IS-107 Reykjavik, Iceland

[9] Katholieke Univ Leuven, Ctr Microbial & Plant Genet, Dept Microbial & Mol Syst, Leuven, Belgium

[10] Ecole Polytech Fed Lausanne, Lab Computat Syst Biotechnol, Swiss Inst Bioinformat, Lausanne, Switzerland

[11] Mt Sinai Sch Med, Dept Infect Dis, New York, NY USA

[12] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI USA

[13] Univ Iceland, Fac Life & Environm Sci, Reykjavik, Iceland

[14] Tech Univ Dortmund, Dept Biochem & Chem Engn, Dortmund, Germany

[15] Univ Manchester, Sch Comp Sci, Manchester, Lancs, England

[16] Univ Manchester, Manchester Ctr Integrat Syst Biol, Manchester Interdisciplinary Bioctr, Manchester, Lancs, England

[17] Pacific NW Natl Lab, Div Biol Sci, Richland, WA 99352 USA

来源：

BMC SYSTEMS BIOLOGY | 2011年 / 5卷

关键词：

ESCHERICHIA-COLI; RECONSTRUCTION; ANNOTATION; METABOLISM; NETWORKS; GENOMES; PROTEIN;

D O I：

10.1186/1752-0509-5-8

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：9

共 46 条

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