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Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans.
Morita K, Saito Y, Sato K, Oka K, Hotta K, Sakakibara Y. Morita K, et al. Nucleic Acids Res. 2009 Feb;37(3):999-1009. doi: 10.1093/nar/gkn1054. Epub 2009 Jan 7. Nucleic Acids Res. 2009. PMID: 19129214 Free PMC article.
CENTROIDFOLD: a web server for RNA secondary structure prediction.
Sato K, Hamada M, Asai K, Mituyama T. Sato K, et al. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W277-80. doi: 10.1093/nar/gkp367. Epub 2009 May 12. Nucleic Acids Res. 2009. PMID: 19435882 Free PMC article.
Improvement of structure conservation index with centroid estimators.
Okada Y, Sato K, Sakakibara Y. Okada Y, et al. Pac Symp Biocomput. 2010:88-97. doi: 10.1142/9789814295291_0011. Pac Symp Biocomput. 2010. PMID: 19908361
Robust and accurate prediction of noncoding RNAs from aligned sequences.
Saito Y, Sato K, Sakakibara Y. Saito Y, et al. BMC Bioinformatics. 2010 Oct 15;11 Suppl 7(Suppl 7):S3. doi: 10.1186/1471-2105-11-S7-S3. BMC Bioinformatics. 2010. PMID: 21106125 Free PMC article.
COPICAT: a software system for predicting interactions between proteins and chemical compounds.
Sakakibara Y, Hachiya T, Uchida M, Nagamine N, Sugawara Y, Yokota M, Nakamura M, Popendorf K, Komori T, Sato K. Sakakibara Y, et al. Bioinformatics. 2012 Mar 1;28(5):745-6. doi: 10.1093/bioinformatics/bts031. Epub 2012 Jan 17. Bioinformatics. 2012. PMID: 22257668
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.
Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y. Sato K, et al. Bioinformatics. 2012 Dec 15;28(24):3218-24. doi: 10.1093/bioinformatics/bts612. Epub 2012 Oct 11. Bioinformatics. 2012. PMID: 23060618
An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds.
Nakamura M, Hachiya T, Saito Y, Sato K, Sakakibara Y. Nakamura M, et al. BMC Bioinformatics. 2012;13 Suppl 17(Suppl 17):S8. doi: 10.1186/1471-2105-13-S17-S8. Epub 2012 Dec 13. BMC Bioinformatics. 2012. PMID: 23282285 Free PMC article.
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