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Items: 15

1.

Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile.

Melton ED, Sorokin DY, Overmars L, Lapidus AL, Pillay M, Ivanova N, Del Rio TG, Kyrpides NC, Woyke T, Muyzer G.

Stand Genomic Sci. 2017 Sep 21;12:57. doi: 10.1186/s40793-017-0268-9. eCollection 2017.

2.

Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes.

Berben T, Overmars L, Sorokin DY, Muyzer G.

Front Microbiol. 2017 Feb 28;8:254. doi: 10.3389/fmicb.2017.00254. eCollection 2017.

3.

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio.

Ahn AC, Meier-Kolthoff JP, Overmars L, Richter M, Woyke T, Sorokin DY, Muyzer G.

PLoS One. 2017 Mar 10;12(3):e0173517. doi: 10.1371/journal.pone.0173517. eCollection 2017.

4.

Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.

Melton ED, Sorokin DY, Overmars L, Chertkov O, Clum A, Pillay M, Ivanova N, Shapiro N, Kyrpides NC, Woyke T, Lapidus AL, Muyzer G.

Stand Genomic Sci. 2016 Sep 8;11(1):67. doi: 10.1186/s40793-016-0184-4. eCollection 2016.

5.

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.

6.

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.

PMID:
25910699
7.

Microbial diversity and biogeochemical cycling in soda lakes.

Sorokin DY, Berben T, Melton ED, Overmars L, Vavourakis CD, Muyzer G.

Extremophiles. 2014 Sep;18(5):791-809. doi: 10.1007/s00792-014-0670-9. Epub 2014 Aug 26. Review.

8.

Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction.

Ederveen TH, Overmars L, van Hijum SA.

PLoS One. 2013 May 10;8(5):e63523. doi: 10.1371/journal.pone.0063523. Print 2013.

9.

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.

10.

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.

11.

Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum.

Bron PA, Wels M, Bongers RS, van Bokhorst-van de Veen H, Wiersma A, Overmars L, Marco ML, Kleerebezem M.

PLoS One. 2012;7(7):e38720. doi: 10.1371/journal.pone.0038720. Epub 2012 Jul 3.

12.

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.

13.

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.

14.

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.

15.

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.

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