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Results: 1 to 20 of 28

1.

Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem.

Van den Bogert B, Boekhorst J, Herrmann R, Smid EJ, Zoetendal EG, Kleerebezem M.

PLoS One. 2013 Dec 30;8(12):e83418. doi: 10.1371/journal.pone.0083418. eCollection 2013.

PMID:
24386196
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Draft Genome Sequence of Enterococcus sp. Strain HSIEG1, Isolated from the Human Small Intestine.

van den Bogert B, Boekhorst J, Smid EJ, Zoetendal EG, Kleerebezem M.

Genome Announc. 2013 Dec 12;1(6). pii: e01013-13. doi: 10.1128/genomeA.01013-13.

PMID:
24336366
[PubMed]
Free PMC Article
3.

Draft Genome Sequence of Veillonella parvula HSIVP1, Isolated from the Human Small Intestine.

van den Bogert B, Boekhorst J, Smid EJ, Zoetendal EG, Kleerebezem M.

Genome Announc. 2013 Dec 5;1(6). pii: e00977-13. doi: 10.1128/genomeA.00977-13.

PMID:
24309734
[PubMed]
Free PMC Article
4.

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets.

Leimena MM, Ramiro-Garcia J, Davids M, van den Bogert B, Smidt H, Smid EJ, Boekhorst J, Zoetendal EG, Schaap PJ, Kleerebezem M.

BMC Genomics. 2013 Aug 2;14:530. doi: 10.1186/1471-2164-14-530.

PMID:
23915218
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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
6.

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
7.

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
8.

Microbiome dynamics of human epidermis following skin barrier disruption.

Zeeuwen PL, Boekhorst J, van den Bogaard EH, de Koning HD, van de Kerkhof PM, Saulnier DM, van Swam II, van Hijum SA, Kleerebezem M, Schalkwijk J, Timmerman HM.

Genome Biol. 2012 Nov 15;13(11):R101. doi: 10.1186/gb-2012-13-11-r101.

PMID:
23153041
[PubMed - in process]
Free PMC Article
9.

Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?

Touw WG, Bayjanov JR, Overmars L, Backus L, Boekhorst J, Wels M, van Hijum SA.

Brief Bioinform. 2013 May;14(3):315-26. doi: 10.1093/bib/bbs034. Epub 2012 Jul 10.

PMID:
22786785
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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
11.

Database independent proteomics analysis of the ostrich and human proteome.

Altelaar AF, Navarro D, Boekhorst J, van Breukelen B, Snel B, Mohammed S, Heck AJ.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):407-12. doi: 10.1073/pnas.1108399108. Epub 2011 Dec 22.

PMID:
22198768
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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
13.

Evaluating experimental bias and completeness in comparative phosphoproteomics analysis.

Boekhorst J, Boersema PJ, Tops BB, van Breukelen B, Heck AJ, Snel B.

PLoS One. 2011;6(8):e23276. doi: 10.1371/journal.pone.0023276. Epub 2011 Aug 10.

PMID:
21853102
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
21518296
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Tyrosine phosphorylation profiling in FGF-2 stimulated human embryonic stem cells.

Ding VM, Boersema PJ, Foong LY, Preisinger C, Koh G, Natarajan S, Lee DY, Boekhorst J, Snel B, Lemeer S, Heck AJ, Choo A.

PLoS One. 2011 Mar 17;6(3):e17538. doi: 10.1371/journal.pone.0017538.

PMID:
21437283
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Comparative genomics of prevaccination and modern Bordetella pertussis strains.

Bart MJ, van Gent M, van der Heide HG, Boekhorst J, Hermans P, Parkhill J, Mooi FR.

BMC Genomics. 2010 Nov 11;11:627. doi: 10.1186/1471-2164-11-627.

PMID:
21070624
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed.

Booijink CC, Boekhorst J, Zoetendal EG, Smidt H, Kleerebezem M, de Vos WM.

Appl Environ Microbiol. 2010 Aug;76(16):5533-40. doi: 10.1128/AEM.00502-10. Epub 2010 Jun 18.

PMID:
20562280
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Pyrosequencing-based comparative genome analysis of the nosocomial pathogen Enterococcus faecium and identification of a large transferable pathogenicity island.

van Schaik W, Top J, Riley DR, Boekhorst J, Vrijenhoek JE, Schapendonk CM, Hendrickx AP, Nijman IJ, Bonten MJ, Tettelin H, Willems RJ.

BMC Genomics. 2010 Apr 14;11:239. doi: 10.1186/1471-2164-11-239.

PMID:
20398277
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Enrichment of homologs in insignificant BLAST hits by co-complex network alignment.

Fokkens L, Botelho SM, Boekhorst J, Snel B.

BMC Bioinformatics. 2010 Feb 12;11:86. doi: 10.1186/1471-2105-11-86.

PMID:
20152020
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

In-depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immunoaffinity purification and stable isotope dimethyl labeling.

Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ.

Mol Cell Proteomics. 2010 Jan;9(1):84-99. doi: 10.1074/mcp.M900291-MCP200. Epub 2009 Sep 21.

PMID:
19770167
[PubMed - indexed for MEDLINE]
Free PMC Article

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