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BMC systems biology (3)
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Thiele, Ines (3)
[ 1 ] Univ Amsterdam, Acad Med Ctr, Bioinformat Lab, NL-1100 DE Amsterdam, Netherlands [ 2 ] Univ Amsterdam, Swammerdam Inst Life Sci, NL-1098 XH Amsterdam, Netherlands [ 3 ] Univ Luxembourg, Luxembourg Ctr Syst Biomed, L-4362 Esch Sur Alzette, Luxembourg [ 4 ] Univ Med Ctr Groningen, Genom Coordinat Ctr, NL-9700 RB Groningen, Netherlands [ 5 ] Univ Groningen, NL-9700 RB Groningen, Netherlands [ 6 ] Netherlands Bioinformat Ctr, NL-6525 GA Nijmegen, Netherlands [ 7 ] Univ Amsterdam, Netherlands Consortium Syst Biol, NL-1090 GE Amsterdam, Netherlands (1)[ 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, Louvain, 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 (1)Addresses: [Show the Organization-Enhanced name(s)] [ 1 ] Univ Iceland, Ctr Syst Biol, IS-101 Reykjavik, Iceland [Show the Organization-Enhanced name(s)] [ 2 ] Univ Iceland, Fac Ind Engn Mech Engn & Comp Sci, IS-101 Reykjavik, Iceland (1)Adkins, Joshua N (1)View MoreTypes
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Consensus and conflict cards for metabolic pathway databases.

Stobbe, Miranda D; Swertz, Morris A; Thiele, Ines; Rengaw, Trebor; van Kampen, Antoine H C; Moerland, Perry D (BioMed Central, 2013)
The metabolic network of H. sapiens and many other organisms is described in multiple pathway databases. The level of agreement between these descriptions, however, has proven to be low. We can use these different descriptions to our advantage by identifying conflicting information and combining their knowledge into a single, more accurate, and more complete description. This task is, however, far from trivial.
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A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.

Thiele, Ines; Hyduke, Daniel R; Steeb, Benjamin; Fankam, Guy; Allen, Douglas K; Bazzani, Susanna; Charusanti, Pep; Chen, Feng-Chi; Fleming, Ronan M T; Hsiung, Chao A; et al. (BioMed Central Ltd, 2011)
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.
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The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.

Rolfsson, Ottar; Palsson, Bernhard Ø; Thiele, Ines (BioMed Central Ltd, 2011)
Metabolic network reconstructions formalize our knowledge of metabolism. Gaps in these networks pinpoint regions of metabolism where biological components and functions are "missing." At the same time, a major challenge in the post genomic era involves characterisation of missing biological components to complete genome annotation.
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