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Results: 16

1.

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information.

Boetzer M, Pirovano W.

BMC Bioinformatics. 2014 Jun 20;15:211. doi: 10.1186/1471-2105-15-211.

PMID:
24950923
[PubMed - in process]
Free PMC Article
2.

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.

Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wüster W, Woods AE, Logan JM, Harrison RA, Castoe TA, de Koning AP, Pollock DD, Yandell M, Calderon D, Renjifo C, Currier RB, Salgado D, Pla D, Sanz L, Hyder AS, Ribeiro JM, Arntzen JW, van den Thillart GE, Boetzer M, Pirovano W, Dirks RP, Spaink HP, Duboule D, McGlinn E, Kini RM, Richardson MK.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20651-6. doi: 10.1073/pnas.1314702110. Epub 2013 Dec 2.

PMID:
24297900
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Complete genome sequence analysis of a reassortant strain of bluetongue virus serotype 16 from Italy.

Lorusso A, Costessi A, Pirovano W, Marcacci M, Cammà C, Savini G.

Genome Announc. 2013 Aug 22;1(4). pii: e00622-13. doi: 10.1128/genomeA.00622-13.

PMID:
23969049
[PubMed]
Free PMC Article
4.

SNP genotyping for detecting the 'rare allele phenomenon' in hybrid zones.

Lammers Y, Kremer D, Brakefield PM, Groenenberg DS, Pirovano W, Schilthuizen M.

Mol Ecol Resour. 2013 Mar;13(2):237-42. doi: 10.1111/1755-0998.12044. Epub 2012 Dec 14.

PMID:
23241161
[PubMed - indexed for MEDLINE]
5.

First draft genome sequence of the Japanese eel, Anguilla japonica.

Henkel CV, Dirks RP, de Wijze DL, Minegishi Y, Aoyama J, Jansen HJ, Turner B, Knudsen B, Bundgaard M, Hvam KL, Boetzer M, Pirovano W, Weltzien FA, Dufour S, Tsukamoto K, Spaink HP, van den Thillart GE.

Gene. 2012 Dec 15;511(2):195-201. doi: 10.1016/j.gene.2012.09.064. Epub 2012 Sep 29.

PMID:
23026207
[PubMed - indexed for MEDLINE]
Free Article
6.

Toward almost closed genomes with GapFiller.

Boetzer M, Pirovano W.

Genome Biol. 2012 Jun 25;13(6):R56. doi: 10.1186/gb-2012-13-6-r56.

PMID:
22731987
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing.

Groenenberg DS, Pirovano W, Gittenberger E, Schilthuizen M.

BMC Genomics. 2012 Mar 26;13:114. doi: 10.1186/1471-2164-13-114.

PMID:
22448618
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Scaffolding pre-assembled contigs using SSPACE.

Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W.

Bioinformatics. 2011 Feb 15;27(4):578-9. doi: 10.1093/bioinformatics/btq683. Epub 2010 Dec 12.

PMID:
21149342
[PubMed - indexed for MEDLINE]
Free Article
9.

Protein secondary structure prediction.

Pirovano W, Heringa J.

Methods Mol Biol. 2010;609:327-48. doi: 10.1007/978-1-60327-241-4_19. Review.

PMID:
20221928
[PubMed - indexed for MEDLINE]
10.

CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations.

van Houte BP, Binsl TW, Hettling H, Pirovano W, Heringa J.

BMC Genomics. 2009 Aug 26;10:401. doi: 10.1186/1471-2164-10-401.

PMID:
19709427
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The meaning of alignment: lessons from structural diversity.

Pirovano W, Feenstra KA, Heringa J.

BMC Bioinformatics. 2008 Dec 23;9:556. doi: 10.1186/1471-2105-9-556.

PMID:
19105835
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Multiple sequence alignment.

Pirovano W, Heringa J.

Methods Mol Biol. 2008;452:143-61. doi: 10.1007/978-1-60327-159-2_7. Review.

PMID:
18566763
[PubMed - indexed for MEDLINE]
13.

PRALINETM: a strategy for improved multiple alignment of transmembrane proteins.

Pirovano W, Feenstra KA, Heringa J.

Bioinformatics. 2008 Feb 15;24(4):492-7. doi: 10.1093/bioinformatics/btm636. Epub 2008 Jan 2.

PMID:
18174178
[PubMed - indexed for MEDLINE]
Free Article
14.

Correlated substitution analysis and the prediction of amino acid structural contacts.

Horner DS, Pirovano W, Pesole G.

Brief Bioinform. 2008 Jan;9(1):46-56. Epub 2007 Nov 13. Review.

PMID:
18000015
[PubMed - indexed for MEDLINE]
Free Article
15.

Sequence harmony: detecting functional specificity from alignments.

Feenstra KA, Pirovano W, Krab K, Heringa J.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W495-8. Epub 2007 Jun 21.

PMID:
17584793
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Sequence comparison by sequence harmony identifies subtype-specific functional sites.

Pirovano W, Feenstra KA, Heringa J.

Nucleic Acids Res. 2006;34(22):6540-8. Epub 2006 Nov 27.

PMID:
17130172
[PubMed - indexed for MEDLINE]
Free PMC Article

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