Itoshi Nikaido

Tokyo Medical and Dental University — Japan

Biochemistry, Genetics and Molecular Biology · Life Sciences

30h-index6.4kcitations118works1.12yr avg
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Research Topics

Single-cell and spatial transcriptomics(52), RNA Research and Splicing(16), Cancer-related molecular mechanisms research(12), Genomics and Chromatin Dynamics(9), Pluripotent Stem Cells Research(9)

Publications118 total

scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase
Nature Communications·2025Open Access
MitoDelta: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data
BMC Genomics·2025Open Access
Elucidation of the mechanism of byproduct DNA synthesis in whole-transcript amplification by poly-A tagging and development of its specific suppression
2025Open Access
Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells that drive retinal layer structure
2025
MitoDelta: identifying mitochondrial DNA deletions at cell-type resolution from single-cell RNA sequencing data
2025Open Access
Transfer learning using generative pretrained genomic DNA models for predicting perturbation-induced changes in gene expression
2025Open Access
The Effect of Multi-Task Learning on the Prediction of Neoantigen–MHC Class II Binding
IEEE Transactions on Computational Biology and Bioinformatics·2025· 1 cited
Transcriptomic signatures of WNT-driven pathways and granulosa cell-oocyte interactions during primordial follicle activation
PLoS ONE·2024· 7 citedOpen Access
Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interactions during Primordial Follicle Activation
2024· 2 citedOpen Access
Sctensor detects many-to-many cell–cell interactions from single cell RNA-sequencing data
BMC Bioinformatics·2023· 30 citedOpen Access
Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis
Nature Communications·2023Open Access
Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of the thalamus
Cell Reports·2023· 30 citedOpen Access
WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus
Science Advances·2023· 63 citedOpen Access
Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis
Nature Communications·2023· 28 citedOpen Access
WormTensor: a clustering method for time-series whole-brain activity data from C. elegans
BMC Bioinformatics·2023· 3 citedOpen Access
A centrifugation-based method for high-throughput biomaterial separation using magnetic microbeads
2023Open Access
nnTensor: An R package for non-negative matrix/tensordecomposition
The Journal of Open Source Software·2023· 2 citedOpen Access
Maternal epigenetic factors in embryonic and postnatal development
Genes to Cells·2023· 7 citedOpen Access
WormTensor: a clustering method for time-series whole-brain activity data from C. elegans
Research Square (Research Square)·2022· 1 citedOpen Access
scTensor detects many-to-many cell–cell interactions from single cell RNA-sequencing data
2022· 1 citedOpen Access
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Frequent Co-authors

Tetsutaro Hayashi(20), Yohei Sasagawa(18), Mana Umeda(10), Yasushi Okazaki(9), Mika Yoshimura(9), Takeya Kasukawa(8), Hidemasa Bono(8), Kaori Tanaka(7), Koki Tsuyuzaki(7), Yoshihide Hayashizaki(6), Hiroki R. Ueda(6), Hiroki Danno(5), Masashi Ebisawa(5), Ken Yagi(4), Christian Schönbach(4), David Hume(4), Marta Gut(4), Masaaki Furuno(3), Hidenori Kiyosawa(3), Richard M. Baldarelli(3)