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Items: 9

1.

Relative Suffix Trees.

Farruggia A, Gagie T, Navarro G, Puglisi SJ, Sirén J.

Comput J. 2018 May;61(5):773-788. doi: 10.1093/comjnl/bxx108. Epub 2017 Nov 21.

2.

Document retrieval on repetitive string collections.

Gagie T, Hartikainen A, Karhu K, Kärkkäinen J, Navarro G, Puglisi SJ, Sirén J.

Inf Retr Boston. 2017;20(3):253-291. doi: 10.1007/s10791-017-9297-7. Epub 2017 Apr 1.

3.

emMAW: computing minimal absent words in external memory.

Héliou A, Pissis SP, Puglisi SJ.

Bioinformatics. 2017 Sep 1;33(17):2746-2749. doi: 10.1093/bioinformatics/btx209.

PMID:
28407038
4.

Succinct colored de Bruijn graphs.

Muggli MD, Bowe A, Noyes NR, Morley PS, Belk KE, Raymond R, Gagie T, Puglisi SJ, Boucher C.

Bioinformatics. 2017 Oct 15;33(20):3181-3187. doi: 10.1093/bioinformatics/btx067.

5.

Misassembly detection using paired-end sequence reads and optical mapping data.

Muggli MD, Puglisi SJ, Ronen R, Boucher C.

Bioinformatics. 2015 Jun 15;31(12):i80-8. doi: 10.1093/bioinformatics/btv262.

6.

Searching and Indexing Genomic Databases via Kernelization.

Gagie T, Puglisi SJ.

Front Bioeng Biotechnol. 2015 Feb 9;3:12. doi: 10.3389/fbioe.2015.00012. eCollection 2015. Review.

7.

Hybrid indexes for repetitive datasets.

Ferrada H, Gagie T, Hirvola T, Puglisi SJ.

Philos Trans A Math Phys Eng Sci. 2014 Apr 21;372(2016):20130137. doi: 10.1098/rsta.2013.0137. Print 2014 May 28.

PMID:
24751871
8.

SHREC: a short-read error correction method.

Schröder J, Schröder H, Puglisi SJ, Sinha R, Schmidt B.

Bioinformatics. 2009 Sep 1;25(17):2157-63. doi: 10.1093/bioinformatics/btp379. Epub 2009 Jun 19.

PMID:
19542152
9.

A fast hybrid short read fragment assembly algorithm.

Schmidt B, Sinha R, Beresford-Smith B, Puglisi SJ.

Bioinformatics. 2009 Sep 1;25(17):2279-80. doi: 10.1093/bioinformatics/btp374. Epub 2009 Jun 17.

PMID:
19535537

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