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Reconstructing the metabolic network of a bacterium from its genome.
Francke C, Siezen RJ, Teusink B. Francke C, et al. 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.
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: francke c. Bioinformatics. 2015 Sep 1;31(17):2867-9. doi: 10.1093/bioinformatics/btv249. Epub 2015 Apr 24. Bioinformatics. 2015. PMID: 25910699
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: francke c. 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.
Genome context and protein sequence analyses of 118 RsbK homologues revealed extreme variability in N-terminal sensory as well as C-terminal regulatory domains and suggested that RsbK-type kinases are subject to complex fine-tuning systems, including sensitization and dese …
Genome context and protein sequence analyses of 118 RsbK homologues revealed extreme variability in N-terminal sensory as well as C-t …
LocateP: genome-scale subcellular-location predictor for bacterial proteins.
Zhou M, Boekhorst J, Francke C, Siezen RJ. Zhou M, et al. Among authors: francke c. BMC Bioinformatics. 2008 Mar 27;9:173. doi: 10.1186/1471-2105-9-173. BMC Bioinformatics. 2008. PMID: 18371216 Free PMC article.
It distinguishes 7 different SCLs within Gram-positive bacteria: intracellular, multi-transmembrane, N-terminally membrane anchored, C-terminally membrane anchored, lipid-anchored, LPxTG-type cell-wall anchored, and secreted/released proteins. ...
It distinguishes 7 different SCLs within Gram-positive bacteria: intracellular, multi-transmembrane, N-terminally membrane anchored, C
Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria.
Liu M, Nauta A, Francke C, Siezen RJ. Liu M, et al. Among authors: francke c. Appl Environ Microbiol. 2008 Aug;74(15):4590-600. doi: 10.1128/AEM.00150-08. Epub 2008 Jun 6. Appl Environ Microbiol. 2008. PMID: 18539796 Free PMC article. Review. No abstract available.
Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus.
Beekwilder J, Marcozzi D, Vecchi S, de Vos R, Janssen P, Francke C, van Hylckama Vlieg J, Hall RD. Beekwilder J, et al. Among authors: francke c. Appl Environ Microbiol. 2009 Jun;75(11):3447-54. doi: 10.1128/AEM.02675-08. Epub 2009 Apr 3. Appl Environ Microbiol. 2009. PMID: 19346347 Free PMC article.
The identification of response regulator-specific binding sites reveals new roles of two-component systems in Bacillus cereus and closely related low-GC Gram-positives.
de Been M, Bart MJ, Abee T, Siezen RJ, Francke C. de Been M, et al. Among authors: francke c. Environ Microbiol. 2008 Oct;10(10):2796-809. doi: 10.1111/j.1462-2920.2008.01700.x. Epub 2008 Jul 25. Environ Microbiol. 2008. PMID: 18662309
New biological roles could be attributed to various TCSs, including roles in cytochrome c biogenesis (HssRS), transport of carbohydrates, peptides and/or amino acids (YkoGH, LytSR), and resistance to toxic ions (LiaSR), antimicrobial peptides (BceRS) and beta-lactam antibi …
New biological roles could be attributed to various TCSs, including roles in cytochrome c biogenesis (HssRS), transport of carbohydra …
Making sense of quorum sensing in lactobacilli: a special focus on Lactobacillus plantarum WCFS1.
Sturme MHJ, Francke C, Siezen RJ, de Vos WM, Kleerebezem M. Sturme MHJ, et al. Among authors: francke c. Microbiology (Reading). 2007 Dec;153(Pt 12):3939-3947. doi: 10.1099/mic.0.2007/012831-0. Microbiology (Reading). 2007. PMID: 18048908 Review.
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.
Francke C, Kerkhoven R, Wels M, Siezen RJ. Francke C, et al. BMC Genomics. 2008 Mar 27;9:145. doi: 10.1186/1471-2164-9-145. BMC Genomics. 2008. PMID: 18371204 Free PMC article.
Clostridial spore germination versus bacilli: genome mining and current insights.
Xiao Y, Francke C, Abee T, Wells-Bennik MH. Xiao Y, et al. Among authors: francke c. Food Microbiol. 2011 Apr;28(2):266-74. doi: 10.1016/j.fm.2010.03.016. Epub 2010 Apr 1. Food Microbiol. 2011. PMID: 21315983
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