Nakai K - Search Results

1

Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina.

Zeng X, Gyoja F, Cui Y, Loza M, Kusakabe TG, Nakai K. Zeng X, et al. Among authors: nakai k. NAR Genom Bioinform. 2024 Nov 12;6(4):lqae149. doi: 10.1093/nargab/lqae149. eCollection 2024 Sep. NAR Genom Bioinform. 2024. PMID: 39534499 Free PMC article.

2

Profiling ascidian promoters as the primordial type of vertebrate promoter.

Okamura K, Yamashita R, Takimoto N, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K. Okamura K, et al. Among authors: nakai k. BMC Genomics. 2011 Nov 30;12 Suppl 3(Suppl 3):S7. doi: 10.1186/1471-2164-12-S3-S7. Epub 2011 Nov 30. BMC Genomics. 2011. PMID: 22369359 Free PMC article.

3

HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.

Zhang W, Cui Y, Liu B, Loza M, Park SJ, Nakai K. Zhang W, et al. Among authors: nakai k. Brief Bioinform. 2024 Mar 27;25(3):bbae152. doi: 10.1093/bib/bbae152. Brief Bioinform. 2024. PMID: 38581422 Free PMC article.

4

Characterization of trans-spliced chimeric RNAs: insights into the mechanism of trans-splicing.

Yokomori R, Kusakabe TG, Nakai K. Yokomori R, et al. Among authors: nakai k. NAR Genom Bioinform. 2024 Jun 6;6(2):lqae067. doi: 10.1093/nargab/lqae067. eCollection 2024 Jun. NAR Genom Bioinform. 2024. PMID: 38846348 Free PMC article.

5

TF-EPI: an interpretable enhancer-promoter interaction detection method based on Transformer.

Liu B, Zhang W, Zeng X, Loza M, Park SJ, Nakai K. Liu B, et al. Among authors: nakai k. Front Genet. 2024 Aug 9;15:1444459. doi: 10.3389/fgene.2024.1444459. eCollection 2024. Front Genet. 2024. PMID: 39184348 Free PMC article.

6

Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.

Yokomori R, Shimai K, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K. Yokomori R, et al. Among authors: nakai k. Genome Res. 2016 Jan;26(1):140-50. doi: 10.1101/gr.184648.114. Epub 2015 Dec 14. Genome Res. 2016. PMID: 26668163 Free PMC article.

7

Characterizing Promoter and Enhancer Sequences by a Deep Learning Method.

Zeng X, Park SJ, Nakai K. Zeng X, et al. Among authors: nakai k. Front Genet. 2021 Jun 15;12:681259. doi: 10.3389/fgene.2021.681259. eCollection 2021. Front Genet. 2021. PMID: 34211503 Free PMC article.

8

Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression.

Loza M, Vandenbon A, Nakai K. Loza M, et al. Among authors: nakai k. Nucleic Acids Res. 2024 Feb 9;52(3):1107-1119. doi: 10.1093/nar/gkad1164. Nucleic Acids Res. 2024. PMID: 38084904 Free PMC article.

9

Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization.

Zhang Y, Yang W, Kumagai Y, Loza M, Zhang W, Park SJ, Nakai K. Zhang Y, et al. Among authors: nakai k. Front Immunol. 2023 Dec 20;14:1304778. doi: 10.3389/fimmu.2023.1304778. eCollection 2023. Front Immunol. 2023. PMID: 38173717 Free PMC article.

10

DBTGR: a database of tunicate promoters and their regulatory elements.

Sierro N, Kusakabe T, Park KJ, Yamashita R, Kinoshita K, Nakai K. Sierro N, et al. Among authors: nakai k. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D552-5. doi: 10.1093/nar/gkj064. Nucleic Acids Res. 2006. PMID: 16381930 Free PMC article.

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