I. Nikaido

发表

Comprehensive analysis of the mouse metabolome based on the transcriptome.

Y. Hayashizaki, H. Bono, Y. Okazaki, 2003, Genome research.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

E. Birney, E. Lander, C. Bult, 2002, Nature.

Functional annotation of a full-length mouse cDNA collection

C. Bult, S. Batalov, Y. Matsuo, 2001, Nature.

Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

H. Kimura, Zhe Liu, I. Nikaido, 2019, bioRxiv.

Benchmarking principal component analysis for large-scale single-cell RNA-sequencing

Hiroyuki Sato, I. Nikaido, K. Tsuyuzaki, 2020, Genome Biology.

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing

I. Nikaido, K. Shimizu, K. Tsuyuzaki, 2019, Genome Biology.

Erratum to: Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

H. Ueda, Kenichiro D. Uno, I. Nikaido, 2017, Genome Biology.

An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data

H. Okano, I. Nikaido, Tetsutaro Hayashi, 2019, NAR genomics and bioinformatics.

A NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data

H. Okano, I. Nikaido, Tetsutaro Hayashi, 2019, bioRxiv.

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays.

Y. Hayashizaki, H. Bono, Y. Okazaki, 2003, Genome research.

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

I. Nikaido, Tetsutaro Hayashi, Mana Umeda, 2018, Nature Communications.

An efficient gene regulatory network inference algorithm for early Drosophila melanogaster embryogenesis

H. Kiryu, I. Nikaido, Hirotaka Matsumoto, 2017, bioRxiv.

Integration of exogenous DNA into mouse embryonic stem cell chromosomes shows preference into genes and frequent modification at junctions

Y. Okazaki, F. Ohbayashi, Keiichiro Suzuki, 2010, Chromosome Research.

Single Molecule and Single Cell Sequencing

Yutaka Suzuki, I. Nikaido, Tetsutaro Hayashi, 2019, Advances in Experimental Medicine and Biology.

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

I. Nikaido, A. Kurisaki, Tetsutaro Hayashi, 2017, bioRxiv.

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

I. Nikaido, Tetsutaro Hayashi, Mana Umeda, 2020, BMC Genomics.

The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression.

Yutaka Suzuki, T. Kasukawa, N. Yumoto, 2020, Cell reports.

Best practices for reporting throughput in biomedical research

K. Goda, R. Damoiseaux, D. Di Carlo, 2022, Nature Methods.

Polysaccharide hydrolase of the hadal zone amphipods Hirondellea gigas

H. Watanabe, I. Nikaido, Tetsutaro Hayashi, 2018, Bioscience, biotechnology, and biochemistry.

An application of MeSH enrichment analysis in livestock

F. Peñagaricano, G. Morota, J. Petersen, 2015, Animal genetics.

A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model

K. Honda, T. McHugh, I. Nikaido, 2022, Molecular Psychiatry.

RIKEN cDNA Microarrays Systematic Expression Profiling of the Mouse Transcriptome Using Material Supplemental

Y. Hayashizaki, Y. Okazaki, D. Hume, 2017 .

Tracing the origin of hair follicle stem cells

T. Abe, H. Kiyonari, T. Shibata, 2021, Nature.

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

Oliver Stegle, Christian Conrad, Aviv Regev, 2019, bioRxiv.

Local states of chromatin compaction at transcription start sites control transcription levels

S. Ishihara, I. Nikaido, Mana Umeda, 2021, Nucleic acids research.

The local state of chromatin compaction at transcription start sites controls transcription levels

S. Ishihara, I. Nikaido, Mana Umeda, 2019, bioRxiv.

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing

Kentaro Shimizu, Koki Tsuyuzaki, Itoshi Nikaido, 2018, Genome Biology.

Benchmarking principal component analysis for large-scale single-cell RNA-sequencing

Hiroyuki Sato, Koki Tsuyuzaki, Itoshi Nikaido, 2019, Genome Biology.

Identification of novel PPARgamma target genes by integrated analysis of ChIP-on-chip and microarray expression data during adipocyte differentiation.

H. Bono, Y. Okazaki, C. Schönbach, 2008, Biochemical and biophysical research communications.

Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors

H. Okano, J. Kohyama, I. Nikaido, 2018, Genes & development.

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Hideo Matsuda, John Quackenbush, Yoshihide Hayashizaki, 2003, Genome research.

Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray.

Jun Kawai, Yoshihide Hayashizaki, Tomohiro Kono, 2002, Biochemical and biophysical research communications.

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

I. Nikaido, Tetsutaro Hayashi, Mana Umeda, 2018, Nature Communications.

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation

Hisanori Kiryu, Itoshi Nikaido, Minoru S. H. Ko, 2016, bioRxiv.

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

H. Ueda, Kenichiro D. Uno, I. Nikaido, 2013, Genome Biology.

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

Oliver Stegle, Christian Conrad, Aviv Regev, 2020, Nature Biotechnology.

Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling.

Yoshihide Hayashizaki, Tomohiro Kono, Hidemasa Bono, 2003, Genome research.

READ: Practical Analysis System of Mouse Transcriptome with the FANTOM Database

Yoshihide Hayashizaki, Hidemasa Bono, Itoshi Nikaido, 2001 .

Biological Systems as Heterogeneous Information Networks: A Mini-review and Perspectives pdf

Koki Tsuyuzaki, Itoshi Nikaido, I. Nikaido, 2017, ArXiv.

Erratum to: Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

H. Ueda, Kenichiro D. Uno, I. Nikaido, 2017, Genome Biology.

Quartz-Seq : a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity

H. Ueda, Kenichiro D. Uno, I. Nikaido, 2012 .

Uncovering hypergraphs of cell-cell interaction from single cell RNA-sequencing data

Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido, 2019, bioRxiv.

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads

I. Nikaido, A. Kurisaki, Tetsutaro Hayashi, 2017, bioRxiv.

Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids

Jennifer A. Erwin, Y. Goda, I. Nikaido, 2020, Molecular Psychiatry.

Quantitative Expression Profile of Distinct Functional Regions in the Adult Mouse Brain

Takeya Kasukawa, Itoshi Nikaido, Hiroki R. Ueda, 2011, PloS one.

Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra syndrome

S. Itohara, I. Nikaido, Y. Shinkai, 2021, iScience.

Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells

H. Kimura, I. Nikaido, Y. Ohkawa, 2020, Science Advances.

Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells.

H. Ueda, I. Nikaido, H. Niwa, 2013, Molecular cell.

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis

Satoru Miyazaki, Takeru Nakazato, Koki Tsuyuzaki, 2015, BMC Bioinformatics.

Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

N. Yumoto, Y. Sako, I. Nikaido, 2022, PLoS genetics.

Imaging and single cell sequencing analyses of super-enhancer activation mediated by NF-κB in B cells

N. Yumoto, Y. Sako, I. Nikaido, 2021, bioRxiv.

Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis.

Y. Nakamura, S. Tabata, I. Nikaido, 2000, DNA research : an international journal for rapid publication of reports on genes and genomes.

Sctensor detects many-to-many cell–cell interactions from single cell RNA-sequencing data

I. Nikaido, K. Tsuyuzaki, Manabu Ishii, 2022, bioRxiv.

Primed to naïve-like conversion of the common marmoset embryonic stem cells.

H. Okano, Mari Nakamura, E. Sasaki, 2020, Stem cells and development.

Cell type‐specific transcriptome analysis unveils secreted signaling molecule genes expressed in apical epithelial cap during appendage regeneration

I. Nikaido, Tetsutaro Hayashi, M. Yoshimura, 2019, Development, growth & differentiation.

Comprehensive Quantification of Gene Expression Fluctuation by Single-cell RNA-seq

I. Nikaido, 2016 .

EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes

Yoshihide Hayashizaki, Itoshi Nikaido, Yasushi Okazaki, 2004, Nucleic Acids Res..

Strategies for Converting RNA to Amplifiable cDNA for Single-Cell RNA Sequencing Methods.

I. Nikaido, Tetsutaro Hayashi, Y. Sasagawa, 2019, Advances in experimental medicine and biology.

Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space

Gang Song, Hideo Yokota, Ryutaro Himeno, 2012, PloS one.

A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model

K. Honda, T. McHugh, I. Nikaido, 2022, Molecular Psychiatry.

Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of thalamus

Yasuyuki Shima, Henrik Skibbe, I. Nikaido, 2022, bioRxiv.

Single‐oocyte transcriptome analysis reveals aging‐associated effects influenced by life stage and calorie restriction

T. Kitajima, I. Nikaido, H. Hamada, 2021, Aging cell.

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets

Haruka Ozaki, Tetsutaro Hayashi, Mana Umeda, 2019, BMC Genomics.

A centrifugation-based method for high-throughput biomaterial separation using magnetic microbeads

I. Nikaido, Tetsutaro Hayashi, Yuki Gotoh, 2023, bioRxiv.

Id4, a New Candidate Gene for Senile Osteoporosis, Acts as a Molecular Switch Promoting Osteoblast Differentiation

S. Wakana, H. Bono, Y. Okazaki, 2010, PLoS genetics.

An automated system for high-throughput single cell-based breeding

Ikuo Fujii, Akihiko Kondo, Itoshi Nikaido, 2013, Scientific Reports.

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity

Kenichiro D. Uno, I. Nikaido, Tetsutaro Hayashi, 2013, Genome Biology.

Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System

C. Bult, D. Hill, John Quackenbush, 2003 .

I. Nikaido, Y. Sasagawa, Takamasa Suzuki, 2023, Science advances.

WormTensor: a clustering method for time-series whole-brain activity data from C. elegans

Y. Iino, T. Ishihara, Hirofumi Sato, 2023, BMC Bioinformatics.

Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

I. Nikaido, A. Kurisaki, Tetsutaro Hayashi, 2023, Nature communications.

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing

I. Nikaido, K. Shimizu, Kenta Sato, 2018, Genome Biology.