Research Summary

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

• 1. *Matsuzawa R, Kawahara D, Kashima M, et al.
  "tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography."
  PLOS ONE 20(1), e0311296 (2025) doi: 10.1371/journal.pone.0311296
• 2. *Nakata S, Iwasaki K, Funato H, et al.
  "Neuronal subtype-specific transcriptomic changes in the cerebral neocortex associated with sleep pressure."
  Neuroscience Research 207, 13-25 (2024) doi: 10.1016/j.neures.2024.03.004
• 3. *Tahara S, Tsuchiya T, Matsumoto H, Ozaki H.
  "Transcription factor-binding k-mer analysis clarifies the cell type dependency of binding specificities and cis-regulatory SNPs in humans."
  BMC Genomics 24(1), 597 (2023) doi: 10.1186/s12864-023-09692-9
• 4. Arai Y, Takahashi K, Horinouchi T, et al.
  "SAGAS: Simulated annealing and greedy algorithm scheduler for laboratory automation."
  SLAS Technology 28(4), 264-277 (2023) doi: 10.1016/j.slast.2023.03.001
• 5. *Tsuchiya T, Hori H, Ozaki H.
  "CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells."
  Bioinformatics 38(21), 4868-4877 (2022) doi: 10.1093/bioinformatics/btac599
• 6. Itoh TD, Horinouchi T, Uchida H, et al.
  "Optimal Scheduling for Laboratory Automation of Life Science Experiments with Time Constraints."
  SLAS Technology 26(6), 650-659 (2021) doi: 10.1177/24726303211021790
• 7. *Minoshima F, Ozaki H, Odaka H, Tateno H.
  "Integrated analysis of glycan and RNA in single cells."
  iScience 24(8), 102882 (2021) doi: 10.1016/j.isci.2021.102882
• 8. 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(1), 177 (2020) doi: 10.1186/s12864-020-6542-z

Related Links

Lab Members

Contact Information