チームリーダー
二階堂 愛 Ph.D.

Lin CW, Septyaningtrias DE, Chao HW, et al.
A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model.
Molecular Psychiatry 27(8), 3343-3354 Mon Aug 01 00:00:00 JST 2022 doi: 10.1038/s41380-022-01566-y

Ochiai H, Hayashi T, Umeda M, et al.
Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.
Science Advances 6(25), eaaz6699 Tue Dec 01 00:00:00 JST 2020 doi: 10.1126/sciadv.aaz6699

Ozaki H, Hayashi T, Umeda M, Nikaido I.
Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets.
BMC Genomics 21, 177 Thu Oct 01 00:00:00 JST 2020 doi: 10.1186/s12864-020-6542-z

Tsuyuzaki K, Sato H, Sato K, Nikaido I.
Benchmarking principal component analysis for large-scale single-cell RNA-sequencing.
Genome Biology 21, 9 Tue Sep 01 00:00:00 JST 2020 doi: 10.1186/s13059-019-1900-3

Mereu E, Lafzi A, Moutinho C, et al.
Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.
Nature biotechnology 38(6), 747-755 Mon Jun 01 00:00:00 JST 2020 doi: 10.1038/s41587-020-0469-4

Sato K, Tsuyuzaki K, Shimizu K, Nikaido I.
CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing.
Genome Biology 20, 31 Sun Dec 01 00:00:00 JST 2019 doi: 10.1186/s13059-019-1639-x

Sasagawa Y, Danno H, Takada H et al.
Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.
Genome Biology 19, 29 Sat Dec 01 00:00:00 JST 2018 doi: 10.1186/s13059-018-1407-3

Hayashi T, Ozaki H, Sasagawa Y, et al.
Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.
Nature Communications 9, 619 Sat Dec 01 00:00:00 JST 2018 doi: 10.1038/s41467-018-02866-0

Matsumoto H, Kiryu H, Furusawa C, et al.
SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.
Bioinformatics 33(15), 2314-2321 Fri Dec 01 00:00:00 JST 2017 doi: 10.1093/bioinformatics/btx194

Tsuyuzaki K, Morota G, Ishii M, et al.
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis.
BMC Bioinformatics 16, 45 Tue Dec 01 00:00:00 JST 2015 doi: 10.1186/s12859-015-0453-z

Sasagawa Y, Nikaido I, Hayashi T, et al.
Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity.
Genome Biology 14, 3097 Sun Dec 01 00:00:00 JST 2013 doi: 10.1186/gb-2013-14-4-r31

Adachi K, Nikaido I, Ohta H, et al.
Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells.
Molecular Cell 52, 380-392 Fri Nov 01 00:00:00 JST 2013 doi: 10.1016/j.molcel.2013.09.002