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List of works by Itoshi Nikaido

An application of MeSH enrichment analysis in livestock

scientific article published on 02 June 2015

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

scientific article

Analysis of gene networks during adipogenesis and osteoblastgenesis focusing on the crosstalk and redundant pathways

scientific article published in December 2004

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

scientific article (publication date: 5 December 2002)

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

scientific article published on 01 February 2002

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

scientific article published on 20 January 2020

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

scientific article published on 06 April 2020

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

scientific article published on 11 February 2019

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

scientific article published on 9 February 2018

Comprehensive analysis of the mouse metabolome based on the transcriptome

scientific article published on June 2003

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

scientific article published on 10 October 2013

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

scientific article

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

scientific article published on 07 August 2020

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

scientific article

Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers

scientific article published on 01 June 2022

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

scientific article published on 18 January 2017

Functional annotation of a full-length mouse cDNA collection

scientific article (publication date: 8 February 2001)

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

scientific article published on 17 June 2020

Id4, a new candidate gene for senile osteoporosis, acts as a molecular switch promoting osteoblast differentiation

scientific journal article

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

scientific article

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

scientific article published on 23 February 2010

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

scientific article published on 01 August 2021

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

scientific article

Polysaccharide hydrolase of the hadal zone amphipods Hirondellea gigas

scientific article published on 06 April 2018

Quantitative expression profile of distinct functional regions in the adult mouse brain

scientific article

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

scientific article published on 9 March 2018

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

scientific article

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

scientific article published on 4 April 2017

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

scientific article published on 12 February 2018

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

scientific article published on 10 July 2021

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

scientific article published on 01 January 2019

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays

scientific article published on June 2003

Tracing the origin of hair follicle stem cells

Transcriptome tomography for brain analysis in the web-accessible anatomical space

scientific article

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