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Reconstructing the metabolic network of a bacterium from its genome.
Francke C, Siezen RJ, Teusink B. Francke C, et al. Among authors: siezen rj. Trends Microbiol. 2005 Nov;13(11):550-8. doi: 10.1016/j.tim.2005.09.001. Epub 2005 Sep 19. Trends Microbiol. 2005. PMID: 16169729 Review.
Challenges in plant cellular pathway reconstruction based on gene expression profiling.
van Baarlen P, van Esse HP, Siezen RJ, Thomma BP. van Baarlen P, et al. Among authors: siezen rj. Trends Plant Sci. 2008 Jan;13(1):44-50. doi: 10.1016/j.tplants.2007.11.003. Epub 2007 Dec 21. Trends Plant Sci. 2008. PMID: 18155635 Review.
Co-regulation of metabolic genes is better explained by flux coupling than by network distance.
Notebaart RA, Teusink B, Siezen RJ, Papp B. Notebaart RA, et al. Among authors: siezen rj. PLoS Comput Biol. 2008 Jan;4(1):e26. doi: 10.1371/journal.pcbi.0040026. PLoS Comput Biol. 2008. PMID: 18225949 Free PMC article.
CiVi: circular genome visualization with unique features to analyze sequence elements.
Overmars L, van Hijum SA, Siezen RJ, Francke C. Overmars L, et al. Among authors: siezen rj. Bioinformatics. 2015 Sep 1;31(17):2867-9. doi: 10.1093/bioinformatics/btv249. Epub 2015 Apr 24. Bioinformatics. 2015. PMID: 25910699
Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior.
Francke C, Groot Kormelink T, Hagemeijer Y, Overmars L, Sluijter V, Moezelaar R, Siezen RJ. Francke C, et al. Among authors: siezen rj. BMC Genomics. 2011 Aug 1;12:385. doi: 10.1186/1471-2164-12-385. BMC Genomics. 2011. PMID: 21806785 Free PMC article.
Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases.
de Been M, Francke C, Siezen RJ, Abee T. de Been M, et al. Among authors: siezen rj. Microbiology (Reading). 2011 Jan;157(Pt 1):3-12. doi: 10.1099/mic.0.045740-0. Epub 2010 Nov 4. Microbiology (Reading). 2011. PMID: 21051490 Review.
Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues.
Siezen RJ, Renckens B, Boekhorst J. Siezen RJ, et al. Proteins. 2007 May 15;67(3):681-94. doi: 10.1002/prot.21290. Proteins. 2007. PMID: 17348030
MGcV: the microbial genomic context viewer for comparative genome analysis.
Overmars L, Kerkhoven R, Siezen RJ, Francke C. Overmars L, et al. Among authors: siezen rj. BMC Genomics. 2013 Apr 1;14:209. doi: 10.1186/1471-2164-14-209. BMC Genomics. 2013. PMID: 23547764 Free PMC article.
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
Bayjanov JR, Molenaar D, Tzeneva V, Siezen RJ, van Hijum SA. Bayjanov JR, et al. Among authors: siezen rj. BMC Genomics. 2012 May 4;13:170. doi: 10.1186/1471-2164-13-170. BMC Genomics. 2012. PMID: 22559291 Free PMC article.
LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria.
Zhou M, Theunissen D, Wels M, Siezen RJ. Zhou M, et al. Among authors: siezen rj. BMC Genomics. 2010 Nov 23;11:651. doi: 10.1186/1471-2164-11-651. BMC Genomics. 2010. PMID: 21092245 Free PMC article.
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