English version

Publicaties van C. Francke

  • Overmars L, Kerkhoven R, Siezen RJ, Francke C. 2013. MGcV: the Microbial Genomic context Viewer for comparative genome analysis. BMC Genomics 14:209 PMID:23547764.
  • Khayatt BI, Overmars L, Siezen RJ, Francke C. 2013. Classification of the Adenylation and Acyl-Transferase Activity of NRPS and PKS Systems Using Ensembles of Substrate Specific Hidden Markov Models. PLoS ONE 8:e62136.
  • van Brakel RBJ, Fiers MWEJ, Francke C, Westenberg MA, van de Wetering H. 2013. COMBat: Visualizing co-occurrence of annotation terms. BioVis 2013: 17-24
    Francke C. 10.07.2012. COGEM Onderzoeksrapport: The potential of applying bioinformatics approaches in the risk assessment of genes that lack a function annotation. CGM 2012-03.
  • Groot Kormelink T, Koenders E, Hagemeijer Y, Overmars L, Siezen RJ, de Vos WM, Francke C. 2012. Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli. BMC Genomics 13: 191 PMID:22607086.
  • Liu M, Prakash C, Nauta A, Siezen RJ, Francke C. 2012. Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria. J Bacteriol. 194: 3522 PMID:22522891.
  • Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SAFT. 2012. Complete resequencing and reannotation of the Lb. plantarum WCFS1 genome.
    J. Bacteriol. 194: 195 PMID:22156394.
  • Francke C, Groot Kormelink T, Hagemeijer Y, Overmars L, Sluijter V, Moezelaar R, Siezen RJ. 2011. Comparative analyses imply that the enigmatic Sigma factor 54 is a central controller of the bacterial exterior. BMC Genomics 12: 385 PMID:21806785.
  • Wels M, Overmars L, Francke C, Kleerebezem M, Siezen RJ. 2011. Reconstruction of the regulatory network of Lb plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs. Microb. Biotechnol. 4: 333 PMID: 21375715.
  • Van Boeijen IK, Francke C, Moezelaar R, Abee T, Zwietering MH. 2011. Isolation of highly heat-resistant Listeria monocytogenes variants by use of a kinetic modeling-based sampling scheme. Appl. Environ. Microbiol. 77:2617-24. PMID: 21357432.
  • Xiao Y, Francke C, Abee T, Wells-Bennik MH. 2011. Clostridial spore germination versus bacilli: genome mining and current insights. Food Microbiol. 28: 266 PMID: 21315983.
  • de Been M, Francke C, Siezen RJ, Abee T. 2011. Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases. Microbiology 157: 3 PMID: 21051490.
  • Mazť A, BoŽl G, ZķŮiga M, Bourand A, Loux V, Yebra MJ, Monedero V, Correia K, Jacques N, Beaufils S, Poncet S, Joyet P, Milohanic E, Casarťgola S, Auffray Y, Pťrez-MartŪnez G, Gibrat JF, Zagorec M, Francke C, Hartke A, Deutscher J. 2010. Complete genome sequence of the probiotic Lactobacillus casei strain BL23. J. Bacteriol. 192: 2647 PMID: 20348264.
  • Beekwilder J, Marcozzi D, Vecchi S, de Vos R, Janssen P, Francke C, van Hylckama Vlieg J, Hall RD. 2009. Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus. Appl. Environ. Microbiol. 75: 3447 PMID: 19346347.
  • Francke C*, Kerkhoven R*, Wels M, Siezen RJ. 2008. A generic approach to identify TF-specific operator motifs; Inferences for LacI-family mediated regulation in Lb. plantarum WCFS1. BMC Genomics 9: 145 PMID:18371204.
  • de Been M, Bart MJ, Abee T, Siezen RJ, Francke C. 2008. The identification of response regulator-specific binding sites reveals new roles of TC systems in B. cereus and closely related low-GC Gram-positives. Env. Microbiol. 10: 2796 PMID:18662309.
  • Wels M, Groot Kormelink T, Kleerebezem M, Siezen RJ, Francke C. 2008. An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters. BMC Genomics 9: 330 PMID:18625071.
  • Liu M, Nauta A, Francke C, Siezen RJ. 2008. Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria. Appl. Environ. Microbiol. 74: 4590 PMID:18539796.
  • Zhou M, Boekhorst J, Francke C, Siezen RJ. 2008. LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics 9: 173 PMID:18371216.
  • Sturme MH, Francke C, Siezen RJ, de Vos WM, Kleerebezem M. 2007. Making sense of quorum sensing in lactobacilli: a special focus on Lactobacillus plantarum WCFS1. Microbiology 153: 3939 PMID: 18048908.
  • Deutscher J*, Francke C*, Postma PW*. 2006. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol. Mol. Biol. Rev. 70: 939 Erratum in: MMBR 2008 72: 555 PMID: 17158705.
  • de Been M, Francke C, Moezelaar R, Abee T, Siezen RJ. 2006. Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis. Microbiology 152: 3035 PMID: 17005984.
  • Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen RJ. 2006. Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res. 34: 1947 Erratum in: NAR 2006 34: 2844 PMID: 16614445.
  • Notebaart RA, van Enckevort FH, Francke C, Siezen RJ, Teusink B. 2006. Accelerating the reconstruction of genome-scale metabolic networks. BMC Bioinformatics 7: 296 PMID:16772023.
  • Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, Smid EJ. 2006. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J. Biol. Chem. 281: 40041 PMID: 17062565.
  • Rossell S, van der Weijden CC, Lindenbergh A, van Tuijl A, Francke C, Bakker BM, Westerhoff HV. 2006. Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U S A. 103: 2166 PMID: 16467155.
  • Francke C, Siezen RJ, Teusink B. 2005. Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol. 13: 550 PMID:16169729.
  • Teusink B*, van Enckevort FH*, Francke C*, Wiersma A, Wegkamp A, Smid EJ, Siezen RJ. 2005. In silico reconstruction of the metabolic pathways of Lb. plantarum: comparing predictions of nutrient requirements with those from growth experiments. Appl Env. Microbiol. 71: 7253 PMID:16269766.