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CoMeta: classification of metagenomes using k-mers.
Kawulok J, Deorowicz S. Kawulok J, et al. Among authors: deorowicz s. PLoS One. 2015 Apr 17;10(4):e0121453. doi: 10.1371/journal.pone.0121453. eCollection 2015. PLoS One. 2015. PMID: 25884504 Free PMC article.
Compression of DNA sequence reads in FASTQ format.
Deorowicz S, Grabowski S. Deorowicz S, et al. Bioinformatics. 2011 Mar 15;27(6):860-2. doi: 10.1093/bioinformatics/btr014. Epub 2011 Jan 19. Bioinformatics. 2011. PMID: 21252073
Robust relative compression of genomes with random access.
Deorowicz S, Grabowski S. Deorowicz S, et al. Bioinformatics. 2011 Nov 1;27(21):2979-86. doi: 10.1093/bioinformatics/btr505. Epub 2011 Sep 5. Bioinformatics. 2011. PMID: 21896510
CONTACT: sebastian.deorowicz@polsl.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
CONTACT: sebastian.deorowicz@polsl.pl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
miRNEST database: an integrative approach in microRNA search and annotation.
Szcześniak MW, Deorowicz S, Gapski J, Kaczyński Ł, Makalowska I. Szcześniak MW, et al. Among authors: deorowicz s. Nucleic Acids Res. 2012 Jan;40(Database issue):D198-204. doi: 10.1093/nar/gkr1159. Epub 2011 Dec 1. Nucleic Acids Res. 2012. PMID: 22135287 Free PMC article.
Disk-based k-mer counting on a PC.
Deorowicz S, Debudaj-Grabysz A, Grabowski S. Deorowicz S, et al. BMC Bioinformatics. 2013 May 16;14:160. doi: 10.1186/1471-2105-14-160. BMC Bioinformatics. 2013. PMID: 23679007 Free PMC article.
Genome compression: a novel approach for large collections.
Deorowicz S, Danek A, Grabowski S. Deorowicz S, et al. Bioinformatics. 2013 Oct 15;29(20):2572-8. doi: 10.1093/bioinformatics/btt460. Epub 2013 Aug 21. Bioinformatics. 2013. PMID: 23969136
QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.
Gudyś A, Deorowicz S. Gudyś A, et al. Among authors: deorowicz s. PLoS One. 2014 Feb 25;9(2):e88901. doi: 10.1371/journal.pone.0088901. eCollection 2014. PLoS One. 2014. PMID: 24586435 Free PMC article.
DSRC 2--Industry-oriented compression of FASTQ files.
Roguski L, Deorowicz S. Roguski L, et al. Among authors: deorowicz s. Bioinformatics. 2014 Aug 1;30(15):2213-5. doi: 10.1093/bioinformatics/btu208. Epub 2014 Apr 18. Bioinformatics. 2014. PMID: 24747219
CONTACT: sebastian.deorowicz@polsl.pl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
CONTACT: sebastian.deorowicz@polsl.pl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
Indexes of large genome collections on a PC.
Danek A, Deorowicz S, Grabowski S. Danek A, et al. Among authors: deorowicz s. PLoS One. 2014 Oct 7;9(10):e109384. doi: 10.1371/journal.pone.0109384. eCollection 2014. PLoS One. 2014. PMID: 25289699 Free PMC article.
We present MuGI, Multiple Genome Index, which reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s) genomes. ...
We present MuGI, Multiple Genome Index, which reports all occurrences of a given pattern, in exact and approximate matching model, against a …
Disk-based compression of data from genome sequencing.
Grabowski S, Deorowicz S, Roguski Ł. Grabowski S, et al. Among authors: deorowicz s. Bioinformatics. 2015 May 1;31(9):1389-95. doi: 10.1093/bioinformatics/btu844. Epub 2014 Dec 22. Bioinformatics. 2015. PMID: 25536966
CONTACT: sebastian.deorowicz@polsl.pl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
CONTACT: sebastian.deorowicz@polsl.pl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online....
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