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Items: 30

1.

Author Correction: FQSqueezer: k-mer-based compression of sequencing data.

Deorowicz S.

Sci Rep. 2020 Feb 21;10(1):3460. doi: 10.1038/s41598-020-60472-x.

2.

FQSqueezer: k-mer-based compression of sequencing data.

Deorowicz S.

Sci Rep. 2020 Jan 17;10(1):578. doi: 10.1038/s41598-020-57452-6. Erratum in: Sci Rep. 2020 Feb 21;10(1):3460.

3.

Environmental metagenome classification for constructing a microbiome fingerprint.

Kawulok J, Kawulok M, Deorowicz S.

Biol Direct. 2019 Nov 13;14(1):20. doi: 10.1186/s13062-019-0251-z.

4.

GTShark: genotype compression in large projects.

Deorowicz S, Danek A.

Bioinformatics. 2019 Nov 1;35(22):4791-4793. doi: 10.1093/bioinformatics/btz508.

PMID:
31225861
5.

Whisper: read sorting allows robust mapping of DNA sequencing data.

Deorowicz S, Debudaj-Grabysz A, Gudyś A, Grabowski S.

Bioinformatics. 2019 Jun 1;35(12):2043-2050. doi: 10.1093/bioinformatics/bty927.

PMID:
30407485
6.

CoMSA: compression of protein multiple sequence alignment files.

Deorowicz S, Walczyszyn J, Debudaj-Grabysz A.

Bioinformatics. 2019 Jan 15;35(2):227-234. doi: 10.1093/bioinformatics/bty619.

PMID:
30010777
7.

Kmer-db: instant evolutionary distance estimation.

Deorowicz S, Gudys A, Dlugosz M, Kokot M, Danek A.

Bioinformatics. 2019 Jan 1;35(1):133-136. doi: 10.1093/bioinformatics/bty610.

PMID:
29986074
8.

FaStore: a space-saving solution for raw sequencing data.

Roguski L, Ochoa I, Hernaez M, Deorowicz S.

Bioinformatics. 2018 Aug 15;34(16):2748-2756. doi: 10.1093/bioinformatics/bty205.

PMID:
29617939
9.

GTC: how to maintain huge genotype collections in a compressed form.

Danek A, Deorowicz S.

Bioinformatics. 2018 Jun 1;34(11):1834-1840. doi: 10.1093/bioinformatics/bty023.

PMID:
29351600
10.

KMC 3: counting and manipulating k-mer statistics.

Kokot M, Dlugosz M, Deorowicz S.

Bioinformatics. 2017 Sep 1;33(17):2759-2761. doi: 10.1093/bioinformatics/btx304.

PMID:
28472236
11.

QuickProbs 2: Towards rapid construction of high-quality alignments of large protein families.

Gudyś A, Deorowicz S.

Sci Rep. 2017 Jan 31;7:41553. doi: 10.1038/srep41553.

12.

RECKONER: read error corrector based on KMC.

Dlugosz M, Deorowicz S.

Bioinformatics. 2017 Apr 1;33(7):1086-1089. doi: 10.1093/bioinformatics/btw746.

PMID:
28062451
13.

FAMSA: Fast and accurate multiple sequence alignment of huge protein families.

Deorowicz S, Debudaj-Grabysz A, Gudyś A.

Sci Rep. 2016 Sep 27;6:33964. doi: 10.1038/srep33964.

14.

Comment on: 'ERGC: an efficient referential genome compression algorithm'.

Deorowicz S, Grabowski S, Ochoa I, Hernaez M, Weissman T.

Bioinformatics. 2016 Apr 1;32(7):1115-7. doi: 10.1093/bioinformatics/btv704. Epub 2015 Nov 28.

15.

Inter-population Differences in Retrogene Loss and Expression in Humans.

Kabza M, Kubiak MR, Danek A, Rosikiewicz W, Deorowicz S, Polański A, Makałowska I.

PLoS Genet. 2015 Oct 16;11(10):e1005579. doi: 10.1371/journal.pgen.1005579. eCollection 2015 Oct.

16.

Indexing Arbitrary-Length k-Mers in Sequencing Reads.

Kowalski T, Grabowski S, Deorowicz S.

PLoS One. 2015 Jul 16;10(7):e0133198. doi: 10.1371/journal.pone.0133198. eCollection 2015.

17.

GDC 2: Compression of large collections of genomes.

Deorowicz S, Danek A, Niemiec M.

Sci Rep. 2015 Jun 25;5:11565. doi: 10.1038/srep11565.

18.

Correction: Indexes of Large Genome Collections on a PC.

Danek A, Deorowicz S, Grabowski S.

PLoS One. 2015 May 8;10(5):e0128172. doi: 10.1371/journal.pone.0128172. eCollection 2015. No abstract available.

19.

CoMeta: classification of metagenomes using k-mers.

Kawulok J, Deorowicz S.

PLoS One. 2015 Apr 17;10(4):e0121453. doi: 10.1371/journal.pone.0121453. eCollection 2015.

20.

KMC 2: fast and resource-frugal k-mer counting.

Deorowicz S, Kokot M, Grabowski S, Debudaj-Grabysz A.

Bioinformatics. 2015 May 15;31(10):1569-76. doi: 10.1093/bioinformatics/btv022. Epub 2015 Jan 20.

PMID:
25609798
21.

Disk-based compression of data from genome sequencing.

Grabowski S, Deorowicz S, Roguski Ł.

Bioinformatics. 2015 May 1;31(9):1389-95. doi: 10.1093/bioinformatics/btu844. Epub 2014 Dec 22.

PMID:
25536966
22.

Indexes of large genome collections on a PC.

Danek A, Deorowicz S, Grabowski S.

PLoS One. 2014 Oct 7;9(10):e109384. doi: 10.1371/journal.pone.0109384. eCollection 2014. Erratum in: PLoS One. 2015;10(5):e0128172.

23.

DSRC 2--Industry-oriented compression of FASTQ files.

Roguski L, Deorowicz S.

Bioinformatics. 2014 Aug 1;30(15):2213-5. doi: 10.1093/bioinformatics/btu208. Epub 2014 Apr 18.

PMID:
24747219
24.

QuickProbs--a fast multiple sequence alignment algorithm designed for graphics processors.

Gudyś A, Deorowicz S.

PLoS One. 2014 Feb 25;9(2):e88901. doi: 10.1371/journal.pone.0088901. eCollection 2014. Erratum in: PLoS One. 2014;9(7):e103051.

25.

Data compression for sequencing data.

Deorowicz S, Grabowski S.

Algorithms Mol Biol. 2013 Nov 18;8(1):25. doi: 10.1186/1748-7188-8-25.

26.

Genome compression: a novel approach for large collections.

Deorowicz S, Danek A, Grabowski S.

Bioinformatics. 2013 Oct 15;29(20):2572-8. doi: 10.1093/bioinformatics/btt460. Epub 2013 Aug 21.

PMID:
23969136
27.

Disk-based k-mer counting on a PC.

Deorowicz S, Debudaj-Grabysz A, Grabowski S.

BMC Bioinformatics. 2013 May 16;14:160. doi: 10.1186/1471-2105-14-160.

28.

miRNEST database: an integrative approach in microRNA search and annotation.

Szcześniak MW, Deorowicz S, Gapski J, Kaczyński Ł, Makalowska I.

Nucleic Acids Res. 2012 Jan;40(Database issue):D198-204. doi: 10.1093/nar/gkr1159. Epub 2011 Dec 1.

29.

Robust relative compression of genomes with random access.

Deorowicz S, Grabowski S.

Bioinformatics. 2011 Nov 1;27(21):2979-86. doi: 10.1093/bioinformatics/btr505. Epub 2011 Sep 5.

PMID:
21896510
30.

Compression of DNA sequence reads in FASTQ format.

Deorowicz S, Grabowski S.

Bioinformatics. 2011 Mar 15;27(6):860-2. doi: 10.1093/bioinformatics/btr014. Epub 2011 Jan 19.

PMID:
21252073

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