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LETTER: Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model
- Natalie C. Duarte,
- Markus J. Herrgård,
- and Bernhard Ø. Palsson
Genome Res. July 2004 14: 1298-1309; Published in Advance June 14, 2004, doi:10.1101/gr.2250904
...assembly is preferred because it allows for the inclusion of disparate data sources, such as annotations, gene expression experiments, enzymatic assays, and physiological data, rather than exclusively genomic data ( Covert et al. 2001 ). Genome-scale metabolic networks have been manually reconstructed...
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Methods: Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions
- Anthony P. Burgard,
- Evgeni V. Nikolaev,
- Christophe H. Schilling,
- and Costas D. Maranas
Genome Res. February 2004 14: 301-312; Published in Advance January 12, 2004, doi:10.1101/gr.1926504
...metabolic networks. The framework is demonstrated on genome-scale metabolic reconstructions of Helicobacter pylori, Escherichia coli , and Saccharomyces cerevisiae . The analysis allows one to determine whether any two metabolic fluxes, v 1 and v 2 , are (1) directionally coupled, if a non...
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LETTER: Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae
- Markus J. Herrgård,
- Baek-Seok Lee,
- Vasiliy Portnoy,
- and Bernhard Ø. Palsson
Genome Res. May 2006 16: 627-635; Published in Advance April 10, 2006, doi:10.1101/gr.4083206
...to discover novel regulatory mechanisms in Saccharomyces cerevisiae. We have reconstructed the nutrient-controlled transcriptional regulatory network controlling metabolism in S. cerevisiae consisting of 55 transcription factors regulating 750 metabolic genes, based on information in the primary literature...
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LETTER: Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures
- Markus J. Herrgård,
- Markus W. Covert,
- and Bernhard ø. Palsson
Genome Res. November 2003 13: 2423-2434; Published in Advance January 1, 2003, doi:10.1101/gr.1330003
...Diego, La Jolla, California 92093-0412, USA Abstract The availability of genome-scale gene expression data sets has initiated the development of methods that use this data to infer transcriptional regulatory networks. Alternatively, such regulatory network structures can be reconstructed...
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LETTER: Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism
- Irina Borodina,
- Preben Krabben,
- and Jens Nielsen
Genome Res. June 2005 15: 820-829; doi:10.1101/gr.3364705
.... ↵ Förster, J., Famili, I., Fu, P., Palsson, B.Ø., and Nielsen, J. 2003a . Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13 : 244 -253. ↵ Förster, J., Famili, I., Palsson, B.Ø., and Nielsen, J. 2003b . Large-scale evaluation of in silico gene deletions...
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Method: Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
- Yiming Kang,
- Nikhil R. Patel,
- Christian Shively,
- Pamela Samantha Recio,
- Xuhua Chen,
- Bernd J. Wranik,
- Griffin Kim,
- R. Scott McIsaac,
- Robi Mitra,
- and Michael R. Brent
Genome Res. March 2020 30: 459-471; Published in Advance February 14, 2020, doi:10.1101/gr.259655.119
...on binding and perturbation-response data, and show that it improves convergence. It also enables comparison of binding data to perturbation-response data that have been processed by network inference algorithms, which further improves convergence. The combination of dual threshold optimization and network...
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Method: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
- Emily R. Miraldi,
- Maria Pokrovskii,
- Aaron Watters,
- Dayanne M. Castro,
- Nicholas De Veaux,
- Jason A. Hall,
- June-Yong Lee,
- Maria Ciofani,
- Aviv Madar,
- Nick Carriero,
- Dan R. Littman,
- and Richard Bonneau
Genome Res. March 2019 29: 449-463; Published in Advance January 29, 2019, doi:10.1101/gr.238253.118
...humans and animal models.Advances in -scale measurement and mathematical modeling herald opportunities for high-quality reconstruction of transcriptional regulatory networks (TRNs). TRNs describe the control of gene expression patterns by transcription factors (TFs) (Hecker et al. 2009; Chai et al. 2014...
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METHODS: Comparative Analysis of Multiple Genome-Scale Data Sets
- Margaret Werner-Washburne,
- Brian Wylie,
- Kevin Boyack,
- Edwina Fuge,
- Judith Galbraith,
- Jose Weber,
- and George Davidson
Genome Res. October 1, 2002 12: 1564-1573; doi:10.1101/gr.225402
...both data sets is that the complete set of interacting proteins creates a network over the entire expression topography (Fig. 5 A,B; see supplemental data). At this level of analysis, differences in the structure of the data can be detected only at the margins. When the protein interactions...
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LETTER: Metabolic functions of duplicate genes in Saccharomyces cerevisiae
- Lars Kuepfer,
- Uwe Sauer,
- and Lars M. Blank
Genome Res. October 2005 15: 1421-1430; doi:10.1101/gr.3992505
.... ↵ Förster, J., Famili, I., Fu, P., Palsson, B.O., and Nielsen, J. 2003a . Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13 : 244 -253. ↵ Förster, J., Famili, I., Palsson, B.O., and Nielsen, J. 2003b . Large-scale evaluation of in silico gene deletions...
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Methods: Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
- Christoph Kaleta,
- Luís Filipe de Figueiredo,
- and Stefan Schuster
Genome Res. October 2009 19: 1872-1883; Published in Advance June 18, 2009, doi:10.1101/gr.090639.108
...Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns Christoph Kaleta 1 , 2 , 3 , Luís Filipe de Figueiredo 1 and Stefan Schuster 1 1 Department of Bioinformatics...

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