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Results: 1 to 20 of 194

1.

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.

PMID:
24416282
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24413604
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
23894338
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
23709503
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23637983
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23547764
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23530958
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
23527145
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23469333
[PubMed - as supplied by publisher]
Free PMC Article
10.

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(1):110. [Epub ahead of print]

PMID:
23446317
[PubMed - as supplied by publisher]
Free PMC Article
11.

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.

PMID:
22815439
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
22607086
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
22559291
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
22522891
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
22493200
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
22162765
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
22156394
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
21995294
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
21848611
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
21806785
[PubMed - indexed for MEDLINE]
Free PMC Article

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