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Tiling Nussinov's RNA folding loop nest with a space-time approach.
BMC Bioinformatics. 2019 Apr 24;20(1):208. doi: 10.1186/s12859-019-2785-6.
BMC Bioinformatics. 2019.
PMID: 31014228
Free PMC article.
Tuning iteration space slicing based tiled multi-core code implementing Nussinov's RNA folding.
Palkowski M, Bielecki W.
Palkowski M, et al. Among authors: bielecki w.
BMC Bioinformatics. 2018 Jan 15;19(1):12. doi: 10.1186/s12859-018-2008-6.
BMC Bioinformatics. 2018.
PMID: 29334891
Free PMC article.
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Parallel Tiled Codes Implementing the Smith-Waterman Alignment Algorithm for Two and Three Sequences.
Palkowski M, Bielecki W.
Palkowski M, et al. Among authors: bielecki w.
J Comput Biol. 2018 Oct;25(10):1106-1119. doi: 10.1089/cmb.2018.0006. Epub 2018 Jul 11.
J Comput Biol. 2018.
PMID: 29993269
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Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing.
Palkowski M, Bielecki W.
Palkowski M, et al. Among authors: bielecki w.
BMC Bioinformatics. 2017 Jun 2;18(1):290. doi: 10.1186/s12859-017-1707-8.
BMC Bioinformatics. 2017.
PMID: 28578661
Free PMC article.
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