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Lactobacillus plantarum Strains Can Enhance Human Mucosal and Systemic Immunity and Prevent Non-steroidal Anti-inflammatory Drug Induced Reduction in T Regulatory Cells.

de Vos P, Mujagic Z, de Haan BJ, Siezen RJ, Bron PA, Meijerink M, Wells JM, Masclee AAM, Boekschoten MV, Faas MM, Troost FJ.

Front Immunol. 2017 Aug 23;8:1000. doi: 10.3389/fimmu.2017.01000. eCollection 2017.


Draft Genome Sequences of 24 Lactococcus lactis Strains.

Backus L, Wels M, Boekhorst J, Dijkstra AR, Beerthuyzen M, Kelly WJ, Siezen RJ, van Hijum SA, Bachmann H.

Genome Announc. 2017 Mar 30;5(13). pii: e01737-16. doi: 10.1128/genomeA.01737-16.


Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains.

Wels M, Backus L, Boekhorst J, Dijkstra A, Beerthuyzen M, Siezen RJ, Bachmann H, van Hijum SA.

Genome Announc. 2017 Mar 16;5(11). pii: e01739-16. doi: 10.1128/genomeA.01739-16.


Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5.

Urshev Z, Hajo K, Lenoci L, Bron PA, Dijkstra A, Alkema W, Wels M, Siezen RJ, Minkova S, van Hijum SA.

Genome Announc. 2016 Oct 6;4(5). pii: e01090-16. doi: 10.1128/genomeA.01090-16.


Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity.

Warda AK, Siezen RJ, Boekhorst J, Wells-Bennik MH, de Jong A, Kuipers OP, Nierop Groot MN, Abee T.

PLoS One. 2016 Jun 7;11(6):e0156796. doi: 10.1371/journal.pone.0156796. eCollection 2016.


Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland.

Wels M, Serrano LM, Eibrink BJ, Backus L, Bongers RS, Vriesendorp B, Siezen RJ, van Hijum SA, Meijer WC.

Genome Announc. 2015 Nov 25;3(6). pii: e01377-15. doi: 10.1128/genomeA.01377-15.


A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites.

Overmars L, Siezen RJ, Francke C.

PLoS One. 2015 Jul 23;10(7):e0133691. doi: 10.1371/journal.pone.0133691. eCollection 2015.


CiVi: circular genome visualization with unique features to analyze sequence elements.

Overmars L, van Hijum SA, Siezen RJ, Francke C.

Bioinformatics. 2015 Sep 1;31(17):2867-9. doi: 10.1093/bioinformatics/btv249. Epub 2015 Apr 24.


Draft Genome Sequence of Lactobacillus plantarum CMPG5300, a Human Vaginal Isolate.

Malik S, Siezen RJ, Renckens B, Vaneechoutte M, Vanderleyden J, Lebeer S.

Genome Announc. 2014 Nov 13;2(6). pii: e01149-14. doi: 10.1128/genomeA.01149-14.


Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering".

Liu M, Bienfait B, Sacher O, Gasteiger J, Siezen RJ, Nauta A, Geurts JM.

PLoS One. 2014 Jan 8;9(1):e84769. doi: 10.1371/journal.pone.0084769. eCollection 2014.


Safety of the surrogate microorganism Enterococcus faecium NRRL B-2354 for use in thermal process validation.

Kopit LM, Kim EB, Siezen RJ, Harris LJ, Marco ML.

Appl Environ Microbiol. 2014 Mar;80(6):1899-909. doi: 10.1128/AEM.03859-13. Epub 2014 Jan 10.


Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, Boekhorst J, van Hylckama Vlieg JE, Siezen RJ.

PLoS One. 2013 Jul 19;8(7):e68731. doi: 10.1371/journal.pone.0068731. Print 2013.


The highly autoaggregative and adhesive phenotype of the vaginal Lactobacillus plantarum strain CMPG5300 is sortase dependent.

Malik S, Petrova MI, Claes IJ, Verhoeven TL, Busschaert P, Vaneechoutte M, Lievens B, Lambrichts I, Siezen RJ, Balzarini J, Vanderleyden J, Lebeer S.

Appl Environ Microbiol. 2013 Aug;79(15):4576-85. doi: 10.1128/AEM.00926-13. Epub 2013 May 24.


Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models.

Khayatt BI, Overmars L, Siezen RJ, Francke C.

PLoS One. 2013 Apr 18;8(4):e62136. doi: 10.1371/journal.pone.0062136. Print 2013.


MGcV: the microbial genomic context viewer for comparative genome analysis.

Overmars L, Kerkhoven R, Siezen RJ, Francke C.

BMC Genomics. 2013 Apr 1;14:209. doi: 10.1186/1471-2164-14-209.


Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.

Bayjanov JR, Starrenburg MJ, van der Sijde MR, Siezen RJ, van Hijum SA.

BMC Microbiol. 2013 Mar 26;13:68. doi: 10.1186/1471-2180-13-68.


Genome sequence of Lactobacillus pentosus KCA1: vaginal isolate from a healthy premenopausal woman.

Anukam KC, Macklaim JM, Gloor GB, Reid G, Boekhorst J, Renckens B, van Hijum SA, Siezen RJ.

PLoS One. 2013;8(3):e59239. doi: 10.1371/journal.pone.0059239. Epub 2013 Mar 19.


Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment.

Caspers MP, Boekhorst J, Abee T, Siezen RJ, Kort R.

Genome Announc. 2013 Jan;1(1). pii: e00010-13. doi: 10.1128/genomeA.00010-13. Epub 2013 Feb 28.


Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data.

Bryant JM, Schürch AC, van Deutekom H, Harris SR, de Beer JL, de Jager V, Kremer K, van Hijum SA, Siezen RJ, Borgdorff M, Bentley SD, Parkhill J, van Soolingen D.

BMC Infect Dis. 2013 Feb 27;13:110. doi: 10.1186/1471-2334-13-110.


Complete genome sequence of Geobacillus thermoglucosidans TNO-09.020, a thermophilic sporeformer associated with a dairy-processing environment.

Zhao Y, Caspers MP, Abee T, Siezen RJ, Kort R.

J Bacteriol. 2012 Aug;194(15):4118. doi: 10.1128/JB.00318-12.


Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli.

Groot Kormelink T, Koenders E, Hagemeijer Y, Overmars L, Siezen RJ, de Vos WM, Francke C.

BMC Genomics. 2012 May 18;13:191. doi: 10.1186/1471-2164-13-191.


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.

BMC Genomics. 2012 May 4;13:170. doi: 10.1186/1471-2164-13-170.


Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria.

Liu M, Prakash C, Nauta A, Siezen RJ, Francke C.

J Bacteriol. 2012 Jul;194(13):3522-33. doi: 10.1128/JB.06816-11. Epub 2012 Apr 20.


Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730).

Axelsson L, Rud I, Naterstad K, Blom H, Renckens B, Boekhorst J, Kleerebezem M, van Hijum S, Siezen RJ.

J Bacteriol. 2012 May;194(9):2391-2. doi: 10.1128/JB.00141-12.


SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes.

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.

PLoS One. 2011;6(12):e28365. doi: 10.1371/journal.pone.0028365. Epub 2011 Dec 5.


Complete resequencing and reannotation of the Lactobacillus plantarum WCFS1 genome.

Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SA.

J Bacteriol. 2012 Jan;194(1):195-6. doi: 10.1128/JB.06275-11.


Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer.

Siezen RJ, van Hylckama Vlieg JE.

Microb Cell Fact. 2011 Aug 30;10 Suppl 1:S3. doi: 10.1186/1475-2859-10-S1-S3. Epub 2011 Aug 30. Review.


The human gut microbiome: are we our enterotypes?

Siezen RJ, Kleerebezem M.

Microb Biotechnol. 2011 Sep;4(5):550-3. doi: 10.1111/j.1751-7915.2011.00290.x. No abstract available.


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.

BMC Genomics. 2011 Aug 1;12:385. doi: 10.1186/1471-2164-12-385.


Single-cell genomics: unravelling the genomes of unculturable microorganisms.

de Jager V, Siezen RJ.

Microb Biotechnol. 2011 Jul;4(4):431-7. doi: 10.1111/j.1751-7915.2011.00271.x. No abstract available.


Searching in microbial genomes for encoded small proteins.

Boekhorst J, Wilson G, Siezen RJ.

Microb Biotechnol. 2011 May;4(3):308-13. doi: 10.1111/j.1751-7915.2011.00261.x. No abstract available.


Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs.

Wels M, Overmars L, Francke C, Kleerebezem M, Siezen RJ.

Microb Biotechnol. 2011 May;4(3):333-44. doi: 10.1111/j.1751-7915.2010.00217.x. Epub 2010 Oct 26.


Comparative genomics of Lactobacillus.

Kant R, Blom J, Palva A, Siezen RJ, de Vos WM.

Microb Biotechnol. 2011 May;4(3):323-32. doi: 10.1111/j.1751-7915.2010.00215.x. Epub 2010 Oct 21.


Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.

Siezen RJ, Bayjanov JR, Felis GE, van der Sijde MR, Starrenburg M, Molenaar D, Wels M, van Hijum SA, van Hylckama Vlieg JE.

Microb Biotechnol. 2011 May;4(3):383-402. doi: 10.1111/j.1751-7915.2011.00247.x. Epub 2011 Feb 21.


Preferential deletion events in the direct repeat locus of Mycobacterium tuberculosis.

Schürch AC, Kremer K, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D.

J Clin Microbiol. 2011 Apr;49(4):1318-22. doi: 10.1128/JCM.01848-10. Epub 2011 Feb 16.


Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype.

Schürch AC, Kremer K, Warren RM, Hung NV, Zhao Y, Wan K, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D.

Infect Genet Evol. 2011 Apr;11(3):587-97. doi: 10.1016/j.meegid.2011.01.009. Epub 2011 Jan 28.


Microbial sunscreens.

Siezen RJ.

Microb Biotechnol. 2011 Jan;4(1):1-7. doi: 10.1111/j.1751-7915.2010.00241.x. No abstract available.


Genomic tracing of epidemics and disease outbreaks.

Schürch AC, Siezen RJ.

Microb Biotechnol. 2010 Nov;3(6):628-33. doi: 10.1111/j.1751-7915.2010.00224.x. No abstract available.


Genomics of microalgae, fuel for the future?

Brooijmans RJ, Siezen RJ.

Microb Biotechnol. 2010 Sep;3(5):514-22. doi: 10.1111/j.1751-7915.2010.00204.x. No abstract available.


Genome (re-)annotation and open-source annotation pipelines.

Siezen RJ, van Hijum SA.

Microb Biotechnol. 2010 Jul;3(4):362-9. doi: 10.1111/j.1751-7915.2010.00191.x. No abstract available.


Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays.

Siezen RJ, Wilson G, Todt T.

Microb Biotechnol. 2010 Mar;3(2):125-30. doi: 10.1111/j.1751-7915.2010.00166.x. No abstract available.


Probiotics genomics.

Siezen RJ, Wilson G.

Microb Biotechnol. 2010 Jan;3(1):1-9. doi: 10.1111/j.1751-7915.2009.00159.x. No abstract available.


Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis.

Machielsen R, Siezen RJ, van Hijum SA, van Hylckama Vlieg JE.

Appl Environ Microbiol. 2011 Jan;77(2):555-63. doi: 10.1128/AEM.02283-10. Epub 2010 Nov 29.


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.

BMC Genomics. 2010 Nov 23;11:651. doi: 10.1186/1471-2164-11-651.


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.

Microbiology. 2011 Jan;157(Pt 1):3-12. doi: 10.1099/mic.0.045740-0. Epub 2010 Nov 4. Review.


High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster.

Schürch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D.

J Clin Microbiol. 2010 Sep;48(9):3403-6. doi: 10.1128/JCM.00370-10. Epub 2010 Jun 30.


A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.

Medema MH, Zhou M, van Hijum SA, Gloerich J, Wessels HJ, Siezen RJ, Strous M.

BMC Genomics. 2010 May 12;11:299. doi: 10.1186/1471-2164-11-299.


Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.

Siezen RJ, Bayjanov J, Renckens B, Wels M, van Hijum SA, Molenaar D, van Hylckama Vlieg JE.

J Bacteriol. 2010 May;192(10):2649-50. doi: 10.1128/JB.00276-10. Epub 2010 Mar 26.


PanCGHweb: a web tool for genotype calling in pangenome CGH data.

Bayjanov JR, Siezen RJ, van Hijum SA.

Bioinformatics. 2010 May 1;26(9):1256-7. doi: 10.1093/bioinformatics/btq103. Epub 2010 Mar 10.


The extracellular biology of the lactobacilli.

Kleerebezem M, Hols P, Bernard E, Rolain T, Zhou M, Siezen RJ, Bron PA.

FEMS Microbiol Rev. 2010 Mar;34(2):199-230. doi: 10.1111/j.1574-6976.2010.00208.x. Epub 2010 Jan 19. Review.

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