Publications of the Bacterial genomics group

2012 Ruiz L, Zomer A, O'Connell-Motherway M, van Sinderen D, Margolles A.
Discovering novel bile protection systems in Bifidobacterium breve UCC2003 through functional genomics.
Appl Environ Microbiol, Feb;78(4):1123-1131. Details

2012 Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SA.
Complete Resequencing and Reannotation of the Lactobacillus plantarum WCFS1 Genome.
J Bacteriol, Jan;194(1):195-196. Details

2011 Xiao Y, Francke C, Abee T, Wells-Bennik MH.
Clostridial spore germination versus bacilli: Genome mining and current insights.
Food Microbiology, Apr;28(2):266-274. Details

2011 Van Boeijen IK, Francke C, Moezelaar R, Abee T, Zwietering MH.
Isolation of Highly Heat-Resistant Listeria monocytogenes Variants by Use of a Kinetic Modeling-Based Sampling Scheme.
Appl Environ Microbiol, Apr;77(8):2617-2624. Details

2011 Wels M, Overmars L, Francke C, Kleerebezem M, Siezen RJ.
Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs.
Microb Biotechnol, May;4(3):333-344. Details

2011 Kant R, Blom J, Palva A, Siezen RJ, De Vos WM.
Comparative genomics of Lactobacillus.
Microb Biotechnol, May;4(3):323-332. Details

2011 Schuerch AC, Kremer K, Kiers A, Boeree MJ, Siezen RJ, Soolingen D.
Preferential Deletion Events in the Direct Repeat Locus of Mycobacterium tuberculosis.
J Clin Microbiol, Apr;49(4):1318-1322. Details

2011 Machielsen R, Siezen RJ, van Hijum SA, van Hylckama Vlieg JE.
Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis.
Appl Environ Microbiol, Jan;77(2):555-563. Details

2011 de Been M, Francke C, Siezen RJ, Abee T.
Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases.
Microbiology, Jan;157(Pt 1):3-12. Details

2011 Siezen RJ, Bayjanov JR, Felis GE, van der Sijde MR, Starrenburg M, Molenaar D, Wels M, van Hijum SA, van Hylckama Vlieg JE.
Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.
Microb Biotechnol, May;4(3):383-402. Details

2011 Schuerch AC, Kremer K, Warren RM, Hung NV, Zhao Y, Wan K, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D.
Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype.
Infect Genet Evol, Apr;11(3):587-957. Details

2011 Siezen RJ.
Microbial sunscreens.
Microbial Biotechnology, Jan;4(1):1-7. Details

2011 Boekhorst J, Wilson G, Siezen RJ.
Searching in microbial genomes for encoded small proteins.
Microb Biotechnol, May;4(3):308-313. Details

2011 Winter T, Winter J, Polak M, Kusch K, Mäder U, Sietmann R, Ehlbeck J, van Hijum S, Weltmann KD, Hecker M, Kusch H.
Characterization of the global impact of low temperature gas plasma on vegetative microorganisms.
Proteomics, Sept;11(17):3518-3530. Details

2011 Francke C, Groot Kormelink T, Hagemeijer Y, Overmars L, Sluijter V, Moezelaar R, Siezen RJ.
Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior.
BMC Genomics, Aug 1;12:385. Details

2011 Siezen RJ, Kleerebezem M.
The human gut microbiome: are we our enterotypes?
Microbial Biotechnology, 4(5):550-553. Details

2011 de Jager V, Siezen RJ.
Single-cell genomics: unravelling the genomes of unculturable microorganisms.
Microb. Biotechnology, Jul;4(4):431-437. Details

2011 de Souza GA, Arntzen MØ, Fortuin S, Schürch AC, Målen H, McEvoy CR, van Soolingen D, Thiede B, Warren RM, Wiker HG.
Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database.
Mol Cell Proteomics, Jan;10(1):M110.002527. Details

2011 Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R.
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.
Nucleic Acids Res, 39(Web Server issue):W339-346. Details

2011 O'Connell Motherway M, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, O'Brien F, Flynn K, Casey PG, Munoz JA, Kearney B, Houston AM, O'Mahony C, Higgins DG, Shanahan F, Palva A, de Vos WM, Fitzgerald GF, Ventura M, O'Toole PW, van Sinderen D.
Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.
Proc Natl Acad Sci U S A, 108(27):11217-11222. Details

2011 Pokusaeva K, O'Connell-Motherway M, Zomer A, Macsharry J, Fitzgerald GF, van Sinderen D.
Cellodextrin utilization by bifidobacterium breve UCC2003.
Appl Environ Microbiol, Mar;77(5):1681-1690. Details

2011 Zhurina D, Zomer A, Gleinser M, Brancaccio VF, Auchter M, Waidmann MS, Westermann C, van Sinderen D, Riedel CU.
Complete genome sequence of Bifidobacterium bifidum S17.
J Bacteriol., 193(1):301-302. Details

2011 Schürch AC, Kremer K, Hendriks AC, Freyee B, McEvoy CR, van Crevel R, Boeree MJ, van Helden P, Warren RM, Siezen RJ, van Soolingen D.
SNP/RD Typing of Mycobacterium tuberculosis Beijing Strains Reveals Local and Worldwide Disseminated Clonal Complexes.
PLoS One., 6(12):e28365. Details

2011 Schürch AC, van Soolingen D.
DNA fingerprinting of Mycobacterium tuberculosis: From phage typing to whole-genome sequencing.
Infect Genet Evol., [Epub ahead of print] Details

2011 Rodriguez-Campos S, Schürch AC, Dale J, Lohan AJ, Cunha MV, Botelho A, Cruz KD, Boschiroli ML, Boniotti MB, Pacciarini M, Garcia-Pelayo MC, Romero B, de Juan L, Domínguez L, Gordon SV, van Soolingen D, Loftus B, Berg S, Hewinson RG, Aranaz A, Smith NH.
European 2 - A clonal complex of Mycobacterium bovis dominant in the Iberian Peninsula.
Infect Genet Evol., [Epub ahead of print] Details

2011 Abee T, Wels M, de Been M, den Besten H.
From transcriptional landscapes to the identification of biomarkers for robustness.
Microb Cell Fact, Aug 30;10(Suppl 1):S9. Details

2010 Schürch AC, Kremer K, Kiers A, Daviena O, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D.
The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale.
Infect Genet Evol, Jan;10(1):108-114. Details

2010 Liu M, Bayjanov JR, Renckens B, Nauta A, Siezen RJ.
The proteolytic system of lactic acid bacteria revisited: a genomic comparison.
BMC Genomics, Jan 15;11:36. Details

2010 Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HT, Rademaker JL, Starrneburg MJ, Kleerebezem M, Molenaar D, van Hylckama Vlieg JE.
Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches.
Environmental Microbiology, Mar;12(3):758-773. Details

2010 Gross G, Snel J, Boekhorst J, Smits MA, Kleerebezem M.
Biodiversity of mannose-specific adhesion in Lactobacillus plantarum revisited: strain-specific domain composition of the mannose-adhesin.
Beneficial Microbes, Mar;1(1):61-66. Details

2010 Kleerebezem M, Hols P, Bernard E, Rolain T, Zhou M, Siezen RJ, Bron PA.
The extracellular biology of the lactobacilli.
FEMS Microbiol Rev, Mar;34(2):199-230. Details

2010 Siezen RJ, Wilson G, Todt T.
Genomics update: Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays.
Microbial Biotechnology, Mar;3(2):125-130. Details

2010 Siezen RJ, van Hijum SA.
Genome (re-)annotation and open-source annotation pipelines.
Microbial Biotechnology, 3(4):362-369. Details

2010 Medema MH, Zhou M, van Hijum SA, Gloerich J, Wessels HJ, Siezen RJ, Strous M.
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.
BMC Genomics, May 12;11(1):299. Details

2010 Siezen RJ, Bayjanov J, Renckens B, Wels M, van Hijum SAFT, Molenaar D, van Hylckama Vlieg JET.
Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.
Journal of Bacteriology, May;192(10):2649-2650. Details

2010 Bayjanov JR, Siezen RJ, van Hijum SA.
PanCGHweb: a web tool for genotype calling in pangenome CGH data.
Bioinformatics, May 1;26(9):1256-1257. Details

2010 Mazé A, Boël G, Zúñiga M, Bourand A, Loux V, Yebra MJ, Monedero V, Correia K, Jacques N, Beaufils S, Poncet S, Joyet P, Milohanic E, Casarégola S, Auffray Y, Pérez-Martínez G, Gibrat JF, Zagorec M, Francke C, Hartke A, Deutscher J.
Complete genome sequence of the probiotic Lactobacillus casei strain BL23.
J. Bacteriology, May;192(10):2647-2648. Details

2010 de Vries SP, van Hijum SA, Schueler W, Riesbeck K, Hays JP, Hermans PW, Bootsma HJ.
Genome analysis of Moraxella catarrhalis strain RH4, a human respiratory tract pathogen.
J bacteriology, 192(14):3574-3583. Details

2010 Siezen RJ, Wilson G.
Probiotics genomics.
Microbial Biotechnology, 3:1-9. Details

2010 Medema MH, Zhou M, van Hijum SA, Gloerich J, Wessels HJ, Siezen RJ, Strous M.
A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.
BMC Genomics, May 12;11(1):299. Details

2010 Schürch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D.
High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster.
J Clin Microbiol, Sep;48(9):3403-3406. Details

2010 Brooijmans R, Siezen RJ.
Genomis update: Genomics of microalgae, fuel for the future?
Microbial Biotechnology, 3(5):514-522. Details

2010 Westenberg MA, Roerdink JB, Kuipers OP, van Hijum SA.
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.
Bioinformatics, Nov 15;26(22):2922-2923. Details

2010 Schuerch AC, Siezen RJ.
Genomic tracing of epidemics and disease outbreaks.
Microb Biotechnol, Nov;3(6):628-633. Details

2010 Zhou M, Theunissen D, Wels M, Siezen RJ.
LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria.
BMC Genomics, Nov 23;11:651. Details

2010 Sieuwerts S, Molenaar D, van Hijum SA, Beerthuyzen M, Stevens MJ, Janssen PW, Ingham CJ, de Bok FA, de Vos WM, van Hylckama Vlieg JE.
Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus.
Appl Environ Microbiol, Dec;76(23):7775-7784. Details

2010 de Been M, Tempelaars MH, van Schaik W, Moezelaar R, Siezen RJ, Abee T.
A novel hybrid kinase is essential for regulating the sigma(B)-mediated stress response of Bacillus cereus.
Environ Microbiol, Mar;12(3):730-745. Details

2010 Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HT, Rademaker JL, Starrenburg MJ, Kleerebezem M, Molenaar D, van Hylckama Vlieg JE.
Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches.
Environ Microbiol, Mar;12(3):758-773. Details

2009 Bayjanov J, Wels M, Starrenburg M, van Hylckama Vlieg JET, Siezen RJ, Molenaar D.
PanCGH: a genotype-calling algorithm for pangenome CGH data.
Bioinformatics, Feb 1;25(3):309-314. Details

2009 van Baarlen P, Troost FJ, van Hemert S, van der Meer C, de Vos WM, de Groot PJ, Hooiveld GJ, Brummer RJ, Kleerebezem M.
Differential NF-{kappa}B pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance.
Proc Natl Acad Sci U S A, Feb 17;106(7):2371-2376. Details

2009 Siezen RJ, Wilson G.
Genomics of deep-sea and sub-seafloor microbes.
Microbial Biotechnology, Feb;2(2):157-163. Details

2009 Wels M, Bongers RS, Boekhorst J, Molenaar D, Sturme M, de Vos WM, Siezen RJ, Kleerebezem M.
Large Intergenic Cruciform-like Supermotifs in the Lactobacillus plantarum Genome.
J Bacteriology, May;191(10):3420-3423. Details

2009 Siezen RJ, Wilson G.
Bioleaching genomics.
Microbial Biotechnology, May;2(3):297-303. Details

2009 Patel AK, van Oosterwijk N, Singh VK, Rozeboom HJ, Kalk KH, Siezen RJ, Jagannadham MV, Dijkstra BW.
Crystallization and preliminary X-ray analysis of carnein, a serine protease from Ipomoea carnea.
Acta Crystallogr Sect F Struct Biol Cryst Commun, Apr 1;65(Pt 4):383-385. Details

2009 Liu M, Siezen RJ, Nauta A.
In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing.
Appl Environ Microbiol, Jun;75(12):4120-4129. Details

2009 Beekwilder J, Marcozzi D, Vecchi S, de Vos R, Janssen P, Francke C, van Hylckama Vlieg J, Hall RD.
Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus.
Appl Environ Microbiol, Jun;75(11):3447-3454. Details

2009 van Baarlen P, Siezen RJ.
Genomics of plant-associated microbes.
Microbial Biotechnology, 2(4):406-411. Details

2009 Brooijmans RJW, Pastink MI, Siezen RJ.
Hydrocarbon-degrading bacteria: the oil-spill clean-up crew.
Microbial Biotechnology, 2(6):587-594. Details

2008 Siezen RJ, Starrenburg MJC, Boekhorst J, Renckens B, Molenaar D, van Hylckama Vlieg JET.
Genome-scale genotype-phenotype matching of two Lactococcus lactis plant isolates identifies adaptation mechanisms to the plant niche.
Appl Environ Microbiol, 74(2):424-436. Details

2008 van Baarlen P, van Esse HP, Siezen RJ, Thomma BP.
Challenges in plant cellular pathway reconstruction based on gene expression profiling.
Trends Plant Sci, 13(1):44-50. Details

2008 Francke C, Kerkhove R, Wels M, Siezen RJ.
A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.
BMC Genomics, Mar 27;9:145. Details

2008 Zhou M, Boekhorst J, Francke C, Siezen RJ.
LocateP: genome-scale subcellular-location predictor for bacterial proteins.
BMC Bioinformatics, 9:173. Details

2008 Iritani N, Vennema H, Siebenga JJ, Siezen RJ, Renckens B, Seto Y, Kaida A, Koopmans M.
Genetic analysis of the capsid gene of genotype GII.2 Noroviruses.
J Virol, 82(15):7336-7345. Details

2008 Siezen RJ, Wilson G.
Unpublished but public microbial genomes with biotechnological relevance.
Microbial Biotechnology, 1(3), 202-207. Details

2008 Siezen RJ.
Wine genomics.
Micobial Biotechnology, 1(2):97-103. Details

2008 Liu M, Nauta A, Francke C, Siezen RJ.
Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria.
Appl Environ Microbiology, 74(15):4590-4600. Details

2008 de Been M, Bart MJ, Abee T, Siezen RJ, Francke C.
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.
Environ Microbiol, Oct;10(10):2796-2809. Details

2008 Wels M, Groot Kormelink T, Kleerebezem M, Siezen RJ, Francke C.
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(1):330. Details

2008 Lambert JM, Siezen RJ, de Vos WM, Kleerebezem M.
Improved annotation of conjugated bile acid hydrolase superfamily members in Gram-positive bacteria.
Microbiology, Aug;154(Pt 8):2492-2500. Details

2008 Siezen RJ, Khayatt BI.
Natural products genomics.
Microbial Biotechnology, 1(4):275-282. Details

2008 Siezen RJ, Galardini M.
Genomics of biological wastewater treatment.
Microbial Biotechnology, 1(5):333-340. Details

2008 Siezen RJ, Bachmann H.
Genomics of dairy fermentations.
Microbial Biotechnology, 1(6):435-442 Details

2008 Troost FJ, van Baarlen P, Lindsey P, Kodde A, de Vos WM, Kleerebezem M, Brummer RJ.
Identification of the transcriptional response of human intestinal mucosa to Lacobacillus plantarum WCFS1 in vivo.
BMC Genomics, 9:374. Details

2007 Siezen RJ, Renckens B, Boekhorst J.
Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues.
Proteins: structure, function and bioinformatics, 67(3):681-694. Details

2007 van Baarlen P, van Belkum A, Thomma BP.
Disease induction by human microbial pathogens in plant-model systems: potential, problems and prospects.
Drug Discov Today, Feb;12(3-4):167-173. Details

2007 Siebenga JJ, Vennema H, Renckens B, de Bruin E, van der Veer B, Siezen RJ, Koopmans M.
Epochal Evolution of GGII 4 Norovirus Capsid Proteins from 1995 to 2006.
J Virol, Sep;81(18):9932-9941. Details

2007 Serrano LM, Molenaar D, Wels M, Teusink B, Bron PA, de Vos WM, Smid EJ.
Thioredoxin reductase is a key factor in the oxidative stress response of lactobacillus plantarum WCFS1.
Microb Cell Fact, Aug 28;6:29. Details

2007 Mols M, de Been M, Zwietering M, Moezelaar R, Abee T.
Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics.
Environ Microbiol, Dec;9(12):2933-2944. Details

2007 Sturme MH, Francke C, Siezen RJ, de Vos WM, Kleerebezem M.
Making sense of quorum sensing in lactobacilli: a special focus on Lactobacillus plantarum WCFS1.
Microbiology, Dec;153(Pt 12):3939-3947. Details

2007 van der Meer-van Kraaij C, Siezen RJ, Kramer E, Reinders M, Blokzijl H, van der Meer R, Keijer J.
Dietary modulation and structure prediction of rat mucosal pentraxin (Mptx) protein and loss of function in humans.
Genes Nutrition, Dec;2(3):275-285. Details

2007 van Baarlen P, van Belkum A, Summerbell RC, Crous PW, Thomma BP.
Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps?
FEMS Microbiol Rev, Apr;31(3):239-277. Details

2006 Boekhorst J, Helmer Q, Kleerebezem M, Siezen RJ.
Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria.
Microbiology, Jan;152(Pt 1):273-280. Details

2006 van Hylckama Vlieg J, Rademaker J, Bachmann H, Molenaar D, Kelly W, Siezen RJ.
Natural diversity and adaptive responses of Lactococcus lactis.
Current Opinion in Biotechnology, Apr;17(2):183-190. Details

2006 Notebaart RA, van Enckevort FJH, Francke C, Siezen RJ, Teusink B.
Accelerating the reconstruction of genome-scale metabolic networks.
BMC Bioinformatics, Jun 13;7:296. Details

2006 Siezen RJ, Boekhorst J, Muscariello L, Molenaar D, Renckens B, Kleerebezem M.
Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria.
BMC Genomics, May 24;7:126. Details

2006
Teusink B, Smid E.

Modelling strategies for the industrial exploitation of lactic acid bacteria.
Nat. Rev. Microbiol, Jan;4(1):46-56. Details

2006 de Vries MC, Siezen RJ, Wijman JG, Zhao Y, Kleerebezem M, de Vos WM, Vaughan EE.
Comparative and functional analysis of the rRNA-operons and their tRNA gene complement in different lactic acid bacteria.
System Appl Microbiology, Jul;29(5):358-367. Details

2006 Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen RJ.
Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups.
Nucleic Acids Res, Apr 13;34(7):1947-1958. Details

2006 Liu M, Siezen RJ.
Comparative genomics of flavour-forming pathways in lactic acid bacteria.
Australian Journal of Dairy Technology, 61(2):61-68. Details

2006 de Been M, Francke C, Moezelaar R, Abee T, Siezen RJ.
Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and bacillus anthracis.
Microbiology, Oct;152(Pt 10):3035-3048. Details

2006 Boekhorst J, Wels M, Kleerebezem M, Siezen RJ.
The predicted secretome of Lactobacillus plantarum WCFS1 sheds light om interactions with its environment.
Microbiology, Nov;152(Pt 11):3175-3183. Details

2006 Deutscher J, Francke C, Postma PW.
How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.
Micriobiol Mol Biol Rev, Dec;70(4):939-1031. Details

2006 Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, Smid EJ.
Analysis of growth of lacobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model.
J Biol Chem, Dec 29;281(52):40041-40048. Details

2005 Boekhorst J, de Been MW, Kleerebezem M, Siezen RJ.
Genome-Wide Detection and Analysis of Cell Waal-Bound Proteins with LPxTG-Like Sorting Motifs.
J. Bacteriol, Jul;187(14):4928-4934. Details

2005 Francke C, Siezen RJ, Teusink B.
Reconstructing the metabolic network of a bacterium from its genome.
Trends Microbiol, Nov;13(11):550-558. Details

2005 van Kranenburg R, Golic N, Bongers R, Leer RJ, de Vos WM, Siezen RJ, Kleerebezem M.
Functional Analysis of Three Plasmids from Lactobacillus plantarum.
Appl Environ Microbiol, Mar;71(3):1223-1230. Details

2005 Liu M, van Enckevort FH, Siezen RJ.
Genome update: lactic acid bacteria genome sequencing is booming.
Microbiology, Dec;151(Pt 12):3811-3814. Details

2005 Molenaar D, Bringel F, Schuren FH, de Vos WM, Siezen RJ, Kleerebezem M.
Exploring Lactobacillus Plantarum genome diversity by using microarrays.
J Bacteriol, Sep;187(17):6119-6127. Details

2005 Siezen RJ, Renckens B, van Swam I, Peters S, van Kranenburg R, Kleerebezem M, de Vos WM.
Complete Sequences of Four Plasmids of Lactococcus lactis subsp. cremoris SK11 Reveal Extensive Adaptation to the Dairy Environment.
Appl Environ Microbiol, Dec;71(12):8371-8382. Details

2005 Smid EJ, van Enckevort FJ, Wegkamp A, Boekhorst J, Molenaar D, Hugenholtz J, Siezen RJ, Teusink B.
Metabolic models for rational improvement of lactic acid bacteria as cell factories.
J Appl Microbiol, 98(6):1326-1331. Details

2005 Smid EJ, Molenaar D, Hugenholtz J, de Vos WM, Teusink B.
Functional ingredients production: application of global metabolic models.
Curr Opin Biotechnol, Apr;16(2):190-197. Details

2005 Teusink B, van Enckevort FH, Francke C, Wiersma A, Wegkamp A, Smid EJ, Siezen RJ.
In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments.
Appl Environ Microbiol, Nov;71(11):7253-7262. Details

2004 Abee T, van Schaik W, Siezen RJ.
Impact of genomics on microbial food safety.
Trends in Biotechnol, Dec;22(12):653-660. Details

2004 Boekhorst J, Siezen RJ, Zwahlen MC, Vilanova D, Pridmore RD, Mercenier A, Kleerebezem M, de Vos WM, Brüssow H, Desiere F.
The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content.
Microbiology, Nov;150(Pt 11):3601-3611. Details

2004 Kerkhoven R, Enckevort FHJ van, Boekhorst J, Molenaar D, Siezen RJ.
Visualization for genomics: the Microbial Genome Viewer.
Bioinformatics, Jul 22;20(11):1812-1814. Details

2004 Lopez-Contreras AM, Gabor K, Martens AA, Renckens BA, Claassen PA, Van der Oost J, De Vos WM.
Substrate-induced production and secretion of cellulases by Clostridium acetobutylicum.
Appl Environ Microbiol, Sep;70(9):5238-5243. Details

2004 Siezen RJ, Enckevort FHJ, Kleerebezem M, Teusink B.
Genome data mining of lactic acid bacteria: the impact of bioinformatics.
Curr Opin Biotechnol, Apr;15(2):105-115. Details

2003 Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MW, Stiekema W, Lankhorst RM, Bron PA, Hoffer SM, Groot MN, Kerkhoven R, de Vries M, Ursing B, de Vos WM, Siezen RJ.
Complete genome sequence of Lactobacillus plantarum WCFS1.
Proc Natl Acad Sci USA , Feb 18;100(4):1990-1995. Details

2003 Ventura M, Canchaya C, Kleerebezem M, de Vos WM, Siezen RJ, Brüssow H.
The prophage sequences of Lactobacillus plantarum strain WCFS1.
Virology , Nov 25;316(2):245-255. Details

2002 Fernandez M, Kleerebezem M, Kuipers OP, Siezen RJ, van Kranenburg R.
Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis.
J Bacteriol , Jan;184(1):82-90. Details

2002 Klaenhammer T, Altermann E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou S, Deutscher J, Gasson M, van de Guchte M, Guzzo J, Hartke A, Hawkins T, Hols P, Hutkins R, Kleerebezem M, Kok J, Kuipers O, Lubbers M, Maguin E, McKay L, Mills D, Nauta A, Overbeek R, Pel H, Pridmore D, Saier M, van Sinderen D, Sorokin A, Steele J, O’Sullivan D, de Vos W, Weimer B, Zagorec M, Siezen R.
Discovering lactic acid bacteria by genomics.
Antonie van Leeuwenhoek , Aug;82(1-4):29-58. Details

2002 Kluskens LD, Voorhorst WG, Siezen RJ, Schwerdtfeger RM, Antranikian G, Van Der Oost J, De Vos WM.
Molecular characterization of fervidolysin, a subtilisin-like serine protease from the thermophilic bacterium Fervidobacterium pennivorans.
Extremophiles, Jun;6(3):185-194. Details

2002 van Kranenburg R, Kleerebezem M, van Hylckama Vlieg J, Ursing BM, Smit BA, Ayad E, Smit G, Siezen RJ.
Flavour formation from amino acids by lactic acid bacteria: predictions from genome sequence analysis.
Int. Dairy Journal , 12(2-3), 111-121. Details

2002 Siezen RJ.
Genomics versterkt biotechnologie.
Interview in Zuivelzicht, 94, 16-17.

2001 Gey Van Pittius NC, Gamieldien J, Hide W, Brown GD, Siezen RJ, Beyers AD.
The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C gram-positive bacteria.
Genome Biology, 2(10):RESEARCH0044. Details

2001 Ursing BM, van Enckevort FH, Leunissen JA, Siezen RJ.
EXProt - a database for EXPerimentally verified Protein functions.
In Silico Biol, (1):1-4. Details

2001 de Vos WM, Voorhorst WG, Dijkgraaf M, Kluskens LD, Van der Oost J, Siezen RJ.
Purification, characterization, and molecular modelling of pyrolysin and other extracellular thermostable serine proteases from hyperthermophilic microorganisms.
Methods in Enzymology , 330:383-393. Details

2001 Siezen RJ.
Bioinformatica voorspelt bacterie potentie voor voedingsindustrie.
B for You, 16:14-15.

2000 van Enckevort FH, Pepels PP, Leunissen JA, Martens GJ, Wendelaar Bonga SE, Balm PH.
Oreochromis mossambicus (tilapia) corticotropin-releasing hormone (CRH): cDNA sequence and bioactivity.
J Neuroendocrinol, Feb;12(2):177-186. Details

2000 Fernandez L, Beerthuyzen MM, Brown J, Siezen RJ, Coolbear T, Holland R, Kuipers OP.
Cloning, characterization, controlled overexpression, and inactivation of the major tributyrin esterase gene of Lactococcus lactis.
Appl Environ Microbiol, Apr;66(4):1360-1368. Details

2000 Smit G, Verheul A, van Kranenburg R, Ayad, E, Siezen RJ, Engels WJ.
Cheese flavour development by enzymatic conversions of peptides and amino acids.
Food Research International , 33(3-4):153-160. Details

2000 Smit G, Siezen RJ, Verheul A, Engels WJ.
Control, acceleration and diversification of cheese flavour development by enzymatic conversion of amino acids.
CREAL 98. Paris:Arilait Recherches, ISBN 2-912384-04-4. pp. 60-67.

1999 Siezen RJ.
Multi-domain, cell-envelope proteinases of lactic acid bacteria.
Antonie van Leeuwenhoek , Jul-Nov;76(1-4):139-155. Details

1999 van Kraaij C, de Vos WM, Siezen RJ, Kuipers OP.
Lantibiotics: biosynthesis, mode of action and applications.
Natural Products Report, Oct;16(5):575-587. Details