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

Ines Thiele12, Daniel R Hyduke3, Benjamin Steeb4, Guy Fankam3, Douglas K Allen5, Susanna Bazzani6, Pep Charusanti3, Feng-Chi Chen7, Ronan MT Fleming18, Chao A Hsiung7, Sigrid CJ De Keersmaecker9, Yu-Chieh Liao7, Kathleen Marchal9, Monica L Mo3, Emre Özdemir10, Anu Raghunathan11, Jennifer L Reed12, Sook-Il Shin11, Sara Sigurbjörnsdóttir13, Jonas Steinmann13, Suresh Sudarsan14, Neil Swainston1516, Inge M Thijs9, Karsten Zengler3, Bernhard O Palsson3, Joshua N Adkins17 and Dirk Bumann4*

Author Affiliations

1 Center for Systems Biology, University of Iceland, Reykjavik, Iceland

2 Faculty of Industrial Engineering, Mechanical Engineering & Computer Science University of Iceland, Reykjavik, Iceland

3 Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA

4 Infection Biology, Biozentrum, University of Basel, Basel, Switzerland

5 USDA-ARS, Plant Genetics Research Unit, Donald Danforth Plant Science Center, St Louis, MO, USA

6 Technical University Braunschweig, Institute for Bioinformatics & Biochemistry, Braunschweig, Germany

7 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan

8 Science Institute, University of Iceland, Reykjavik, Iceland

9 Centre of Microbial and Plant Genetics, Department of Microbial & Molecular Systems, Katholieke Universiteit Leuven, Leuven, Belgium

10 Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne, Swiss Institute of Bioinformatics, Lausanne, Switzerland

11 Department of Infectious Diseases, Mount Sinai School of Medicine, New York City, NY, USA

12 Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA

13 Faculty of Life & Environmental Sciences, University of Iceland, Reykjavik, Iceland

14 Department of Biochemical and Chemical Engineering, Technische Universität Dortmund, Dortmund, Germany

15 School of Computer Science, The University of Manchester, Manchester, UK

16 The Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester, UK

17 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

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BMC Systems Biology 2011, 5:8  doi:10.1186/1752-0509-5-8

Published: 18 January 2011

Additional files

Additional file 1:

Consensus MR. This xlsx file contains the consensus reconstruction and simulation setup/results. - Table S1. Statistics for automated reconciliation of starting reconstructions. - Table S2. Consensus Reconstruction in SBML format. - Table S3a. M9/glc. - Table S3b. LB. - Table S3c. Biomass. - Table S4. Growth benchmark errors. - Table S5a. All Lethal deletion predictions. - Table S5b. Single Deletion/Virulence. - Table S6a. LB Synthetic Lethal. - Table S6b. M9 Synthetic Lethal

Format: XLSX Size: 926KB Download file

Open Data

Additional file 2:

Consensus MR in SBML format. Consensus MR as a computational model in SBML format.

Format: ZIP Size: 149KB Download file

Open Data