Nishimura O - Search Results

1

Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization.

Yamaguchi K, Uno Y, Kadota M, Nishimura O, Nozu R, Murakumo K, Matsumoto R, Sato K, Kuraku S. Yamaguchi K, et al. Among authors: nishimura o. Genome Res. 2023 Sep;33(9):1527-1540. doi: 10.1101/gr.276840.122. Epub 2023 Aug 17. Genome Res. 2023. PMID: 37591668 Free PMC article.

2

Intra-genomic GC heterogeneity in sauropsids: evolutionary insights from cDNA mapping and GC(3) profiling in snake.

Matsubara K, Kuraku S, Tarui H, Nishimura O, Nishida C, Agata K, Kumazawa Y, Matsuda Y. Matsubara K, et al. Among authors: nishimura o. BMC Genomics. 2012 Nov 9;13:604. doi: 10.1186/1471-2164-13-604. BMC Genomics. 2012. PMID: 23140509 Free PMC article.

3

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.

Kuraku S, Zmasek CM, Nishimura O, Katoh K. Kuraku S, et al. Among authors: nishimura o. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W22-8. doi: 10.1093/nar/gkt389. Epub 2013 May 15. Nucleic Acids Res. 2013. PMID: 23677614 Free PMC article.

4

Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing.

Tatsumi K, Nishimura O, Itomi K, Tanegashima C, Kuraku S. Tatsumi K, et al. Among authors: nishimura o. Biotechniques. 2015 May 1;58(5):253-7. doi: 10.2144/000114288. eCollection 2015 May. Biotechniques. 2015. PMID: 25967904 Free article.

5

CTCF binding landscape in jawless fish with reference to Hox cluster evolution.

Kadota M, Hara Y, Tanaka K, Takagi W, Tanegashima C, Nishimura O, Kuraku S. Kadota M, et al. Among authors: nishimura o. Sci Rep. 2017 Jul 10;7(1):4957. doi: 10.1038/s41598-017-04506-x. Sci Rep. 2017. PMID: 28694486 Free PMC article.

6

gVolante for standardizing completeness assessment of genome and transcriptome assemblies.

Nishimura O, Hara Y, Kuraku S. Nishimura O, et al. Bioinformatics. 2017 Nov 15;33(22):3635-3637. doi: 10.1093/bioinformatics/btx445. Bioinformatics. 2017. PMID: 29036533 Free PMC article.

7

Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters.

Nabeshima R, Nishimura O, Maeda T, Shimizu N, Ide T, Yashiro K, Sakai Y, Meno C, Kadota M, Shiratori H, Kuraku S, Hamada H. Nabeshima R, et al. Among authors: nishimura o. Elife. 2018 Aug 2;7:e36435. doi: 10.7554/eLife.36435. Elife. 2018. PMID: 30070635 Free PMC article.

8

Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei.

Tanegashima C, Nishimura O, Motone F, Tatsumi K, Kadota M, Kuraku S. Tanegashima C, et al. Among authors: nishimura o. Sci Data. 2018 Oct 8;5:180200. doi: 10.1038/sdata.2018.200. Sci Data. 2018. PMID: 30295675 Free PMC article.

9

Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates.

Hara Y, Yamaguchi K, Onimaru K, Kadota M, Koyanagi M, Keeley SD, Tatsumi K, Tanaka K, Motone F, Kageyama Y, Nozu R, Adachi N, Nishimura O, Nakagawa R, Tanegashima C, Kiyatake I, Matsumoto R, Murakumo K, Nishida K, Terakita A, Kuratani S, Sato K, Hyodo S, Kuraku S. Hara Y, et al. Among authors: nishimura o. Nat Ecol Evol. 2018 Nov;2(11):1761-1771. doi: 10.1038/s41559-018-0673-5. Epub 2018 Oct 8. Nat Ecol Evol. 2018. PMID: 30297745

10

Evaluating Genome Assemblies and Gene Models Using gVolante.

Nishimura O, Hara Y, Kuraku S. Nishimura O, et al. Methods Mol Biol. 2019;1962:247-256. doi: 10.1007/978-1-4939-9173-0_15. Methods Mol Biol. 2019. PMID: 31020565

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