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An artificial intelligence approach fit for tRNA gene studies in the era of big sequence data.

Iwasaki Y, Abe T, Wada K, Wada Y, Ikemura T.

Genes Genet Syst. 2017 Sep 12;92(1):43-54. doi: 10.1266/ggs.16-00068. Epub 2017 Mar 24.


Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count.

Wada Y, Wada K, Iwasaki Y, Kanaya S, Ikemura T.

Sci Rep. 2016 Nov 3;6:36197. doi: 10.1038/srep36197.


Development of self-compressing BLSOM for comprehensive analysis of big sequence data.

Kikuchi A, Ikemura T, Abe T.

Biomed Res Int. 2015;2015:506052. doi: 10.1155/2015/506052. Epub 2015 Oct 1.


CG-containing oligonucleotides and transcription factor-binding motifs are enriched in human pericentric regions.

Wada Y, Iwasaki Y, Abe T, Wada K, Tooyama I, Ikemura T.

Genes Genet Syst. 2015;90(1):43-53. doi: 10.1266/ggs.90.43.


tRNADB-CE: tRNA gene database well-timed in the era of big sequence data.

Abe T, Inokuchi H, Yamada Y, Muto A, Iwasaki Y, Ikemura T.

Front Genet. 2014 May 1;5:114. doi: 10.3389/fgene.2014.00114. eCollection 2014. Review.


A novel bioinformatics method for efficient knowledge discovery by BLSOM from big genomic sequence data.

Bai Y, Iwasaki Y, Kanaya S, Zhao Y, Ikemura T.

Biomed Res Int. 2014;2014:765648. doi: 10.1155/2014/765648. Epub 2014 Apr 3.


Evolutionary changes in vertebrate genome signatures with special focus on coelacanth.

Iwasaki Y, Abe T, Okada N, Wada K, Wada Y, Ikemura T.

DNA Res. 2014 Oct;21(5):459-67. doi: 10.1093/dnares/dsu012. Epub 2014 May 6.


Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

Abe T, Hamano Y, Ikemura T.

Biomed Res Int. 2014;2014:985706. doi: 10.1155/2014/985706. Epub 2014 Mar 11.


8-oxoguanine causes spontaneous de novo germline mutations in mice.

Ohno M, Sakumi K, Fukumura R, Furuichi M, Iwasaki Y, Hokama M, Ikemura T, Tsuzuki T, Gondo Y, Nakabeppu Y.

Sci Rep. 2014 Apr 15;4:4689. doi: 10.1038/srep04689.


Notable clustering of transcription-factor-binding motifs in human pericentric regions and its biological significance.

Iwasaki Y, Wada K, Wada Y, Abe T, Ikemura T.

Chromosome Res. 2013 Aug;21(5):461-74. doi: 10.1007/s10577-013-9371-y. Epub 2013 Jul 30.


Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database.

Ikeda S, Abe T, Nakamura Y, Kibinge N, Hirai Morita A, Nakatani A, Ono N, Ikemura T, Nakamura K, Altaf-Ul-Amin M, Kanaya S.

Plant Cell Physiol. 2013 May;54(5):711-27. doi: 10.1093/pcp/pct041. Epub 2013 Mar 18.


A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks.

Nakao R, Abe T, Nijhof AM, Yamamoto S, Jongejan F, Ikemura T, Sugimoto C.

ISME J. 2013 May;7(5):1003-15. doi: 10.1038/ismej.2012.171. Epub 2013 Jan 10. Erratum in: ISME J. 2014 Aug;8(8):1752.


Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

Sakai H, Lee SS, Tanaka T, Numa H, Kim J, Kawahara Y, Wakimoto H, Yang CC, Iwamoto M, Abe T, Yamada Y, Muto A, Inokuchi H, Ikemura T, Matsumoto T, Sasaki T, Itoh T.

Plant Cell Physiol. 2013 Feb;54(2):e6. doi: 10.1093/pcp/pcs183. Epub 2013 Jan 7.


Replication timing in a single human chromosome 11 transferred into the Chinese hamster ovary (CHO) cell line.

Watanabe Y, Kazuki Y, Oshimura M, Ikemura T, Maekawa M.

Gene. 2012 Nov 15;510(1):1-6. doi: 10.1016/j.gene.2012.08.045. Epub 2012 Sep 3.


Prediction of directional changes of influenza A virus genome sequences with emphasis on pandemic H1N1/09 as a model case.

Iwasaki Y, Abe T, Wada K, Itoh M, Ikemura T.

DNA Res. 2011 Apr;18(2):125-36. doi: 10.1093/dnares/dsr005. Epub 2011 Mar 28.


tRNADB-CE 2011: tRNA gene database curated manually by experts.

Abe T, Ikemura T, Sugahara J, Kanai A, Ohara Y, Uehara H, Kinouchi M, Kanaya S, Yamada Y, Muto A, Inokuchi H.

Nucleic Acids Res. 2011 Jan;39(Database issue):D210-3. doi: 10.1093/nar/gkq1007. Epub 2010 Nov 11.


A novel bioinformatics strategy for function prediction of poorly-characterized protein genes obtained from metagenome analyses.

Abe T, Kanaya S, Uehara H, Ikemura T.

DNA Res. 2009 Oct;16(5):287-97. doi: 10.1093/dnares/dsp018. Epub 2009 Oct 3.

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