Gina M. Oba

github.com/G708 ORCID Email: gina-oba {at} iqb.u-tokyo.ac.jp

Current position

Project Researcher

Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo.

Education

PhD in Science | Department of Computational Biology and Medical Sciences, Graduate School Of Frontier Sciences , The University of Tokyo - Apr. 2020 - June 2024

MA in Life Science | Department of Biological Sciences, Graduate School of Humanities and Sciences, Ochanomizu University - Apr 2018 - Mar 2020

B.S. in Biology | Department of Biology, Faculty of Science, Ochanomizu University - Apr 2014 - Mar 2018

Publication

Hattori, N., Takamatsu, H., Iida, N., Asano, N., Yamashita, S., Oba, G. M., Kimura, K., Yoshida, A., Kobayashi, E., Nakayama, R., Matsumoto, M., Nakamura, M., Kawai, A. & Ushijima, T. Epigenetic disruption of adipogenic gene enhancers in dedifferentiated liposarcomas and its therapeutic value. Front. Oncol. 15, 1419877 (2025)
Oba, G. M. & Nakato, R. A beginner’s guide to ChIP-seq analysis. The Biochemist 47, 21–26 (2025)
Oba, G. M. & Nakato, R. Clover: An unbiased method for prioritizing differentially expressed genes using a data-driven approach. Genes to Cells 29, 456–470 (2024)
Nakato, R., Sakata, T., Wang, J., Nagai, L. A. E., Nagaoka, Y., Oba, G. M., Bando, M. & Shirahige, K. Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors. Nat Commun 14, 5647 (2023)
Sato, A., Oba, G. M., Aubert-Kato, N., Yura, K. & Bishop, J. Co-expression network analysis of environmental canalization in the ascidian ciona. BMC Ecology and Evolution 22, 53 (2022)

Tool

Clover
Prioritize differentially expressed genes by rarity. https://github.com/G708/Clover
Clover-dash
Interactive dashboard implementation of Clover. https://github.com/G708/clover-dash

Presentation

  • Oba, G. M., Nakato, R. “Integrative gene clustering analysis of coessentiality and expression data using graph Neural Network” JST-EMBO meeting Feb 2025 | Talk & Poster

  • Oba, G. M., Nakato, R. “Differences in Gene Regulatory Insights Based on Network References” APBJC2024 Oct 2024 | Poster

  • Oba, G. M., Nakato, R. “Gene features validation to enhance the interpretation of differentially expressed gene (DEG)” MBSJ2023 Dec 2023 | Poster

  • Oba, G. M., Nakato, R. “Clover: An unbiased method for prioritizing differentially expressed genes using a data-driven approach” IIBMP2023 Sep 2023 | Talk

  • Oba, G. M., Nakato, R. “Clover: Prioritization score to find surprising gene from differentially expressed genes list” OKO Intrenational Symposium 2023 Aug 2023 | Poster

  • Oba, G. M., Sato, A. “Gene Identification of Developmental Buffering in Hybrids of Ciona robusta and Ciona intestinalis” the 71th meeting of the Zoological Society of Japan (ZSJ) Kanto Branch May 2019 | Poster | Poster presentation Prize

Skills

  • Python
  • R
  • HTML, CSS
  • Git
  • Docker/Singularity
  • Linux
  • Japanease
  • English

Science Communication & Science Education

  • Volunteer Museum staff | Exedra, Chiba, Japan - Since Aug 2023
  • Research coach for Junior high school, high school students | Marine challenge program 2023 - Apr 2023 - Mar 2024
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