About me

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I have always been interested in science, especially biology, since I was little. This brought me to Osaka University, where I conducted research on transcription regulation during my undergraduate and master’s studies. I have since moved to the Okinawa Institute of Science and Technology in Okinawa, Japan, where I work on the transcriptional regulation of the scrambled genome of Oikopleura dioica.

My research combines genomics, single-cell transcriptomics, and epigenomics to understand how gene regulation contributes to the conservation of morphology despite extreme genome rearrangement. I am also trying to build a pangenome for O. dioica. I mostly use R, Python, bash, and Nextflow, with a focus on reproducibility, and I build tools for the lab and the wider community — including a genome browser for O. dioica at oikobrowser.jnicolaus.com (soon to be migrated to oikobrowser.com).

In my spare time, I take care of my carnivorous plants, 3D print, watch football, fish, and scuba dive.

Education

• Doctor of Philosophy Okinawa Institute of Science and Technology Graduate University · Okinawa, Japan · April 2022 – present
  • Unit: Genomics and Regulatory Systems Unit (PI: Nicholas Luscombe)
  • PhD project: gene regulation of the scrambled genome of Oikopleura dioica
  • Rotation: dental microwear analysis in the fish–tetrapod transition, Macroevolution Unit (PI: Lauren Sallan)
  • Rotation: metabolic gene duplication in Pomacentridae, Marine Eco-Evo-Devo Unit (PI: Vincent Laudet)
• Master of Science, Biological Sciences Graduate School of Science, Osaka University · Osaka, Japan · April 2020 – March 2022
  • Laboratory: Laboratory of Cell Systems (PI: Mariko Okada)
  • Project: NF-κB mediated transcriptional regulation in B cells — live fluorescence imaging and multi-omics analysis
  • Funding: Honjo International Scholarship Foundation Scholarship
• Bachelor of Science, Biological Sciences School of Science, Osaka University · Osaka, Japan · October 2016 – March 2020 (early graduation)
  • Major: Biological Sciences (G30 CBCMP programme)
  • Laboratory: Laboratory of Cell Systems (PI: Mariko Okada)
  • Project: NF-κB mediated transcriptional regulation in B cells — live fluorescence imaging and multi-omics analysis
  • Funding: Monbukagakusho (MEXT) Scholarship

Publications

Research articles

1. JN Wibisana*, RA Sallan*, T Ota, P Puchenkov, T Kubo, L Sallan* (2025). Modifiable clinical dental impression methods to obtain whole-mouth and detailed dental traits from vertebrates. Journal of Morphology.
2. G Sanchez-Serna, J Badia-Ramentol, P Bujosa, A Ferrandez-Roldan, NP Torres-Aguila, M Fabrega-Torrus, JN Wibisana*, MJ Mansfield, C Plessy, NM Luscombe, R Albalat, C Canestro (2025). Less, but More: New Insights From Appendicularians on Chordate Fgf Evolution and the Divergence of Tunicate Lifestyles. Molecular Biology and Evolution.
3. JN Wibisana, C Plessy*, N Diercxksens, J Miao, NM Luscombe (2025). The complete mitogenome of an unidentified Oikopleura species. F1000Research.
4. Y Harada, T Sasaki, JN Wibisana, M Okada, C Liu, H Ueno, PD Burrows, M Kubo* (2022). Type 2 helper T cells convert into Interleukin-13-expressing follicular helper T cells after antigen repriming. Translational and Regulatory Sciences.
5. JN Wibisana, T Inaba, H Shinohara, N Yumoto, T Hayashi, M Umeda, M Ebisawa, I Nikaido, Y Sako, M Okada* (2022). Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers. PLoS Genetics.
6. K Iida*, J Kondo, JN Wibisana, M Inoue, M Okada (2022). ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes. Bioinformatics.

Review articles

1. T Kon, K Kataoka, YJ Luo, JN Wibisana, K Toga, N Uno, Y Monden, M Hamada (2026). Transforming Life Science Through Chromosome-Level Genome Assemblies. Genes to Cells.
2. JN Wibisana, M Okada* (2022). Encoding and decoding NF-κB nuclear dynamics. Current Opinion in Cell Biology.
3. JN Wibisana, K Iida, M Okada (2021). Prediction of transcriptional regulation in immune cells through single-cell analysis. Journal of Clinical and Experimental Medicine (Igaku no Ayumi).

Book chapters

1. JN Wibisana, T Inaba, Y Sako, M Okada* (2023). Quantitative imaging analysis of NF-κB for mathematical modelling applications. Methods in Molecular Biology.

Conference presentations

International

• Gene regulation of the scrambled genome of Oikopleura dioica. CSHL Meeting: Mechanisms of Eukaryotic Transcription, Cold Spring Harbor, New York, USA, August 2025 (poster presentation).
• Gene regulation of the scrambled genome of Oikopleura dioica. EMBO Lecture Course: Evolutionary and Comparative Genomics, Nafplio, Greece, November 2024 (poster presentation).
• Epigenetic landscape of the cryptic tunicate Oikopleura dioica. EMBO Workshop: Animal Genomes, Sevilla, Spain, November 2021 (poster presentation).
• Imaging and single-cell sequencing analysis of super-enhancer activation mediated by NF-κB in B cells. Cell Symposia: Biological Assemblies — Phase Transitions and More, Online, November 2021 (poster presentation).
• NF-κB mediated transcriptional regulation in B cells. CSHL Meeting: Biology of Genomes, Online, May 2021 (poster presentation).
• NF-κB mediated transcriptional regulation in B cells. International Symposium on Structure and Folding of Disease Related Proteins, Seoul National University, South Korea, February 2020 (oral presentation).
• Multi-dimensional analysis of NF-κB nuclear dynamics. International Conference on Systems Biology, Okinawa Institute of Science and Technology, Japan, November 2019 (poster presentation).

Domestic

• Unraveling Genome Scrambling in a Miniature Chordate Genome Using Multiple Chromosome-level Assemblies. The 47th Annual Meeting of the Molecular Biology Society of Japan, Kanagawa, Japan, December 2025 (oral presentation).
• Enhancer-mediated transcriptional regulation in Oikopleura dioica. The 46th Annual Meeting of the Molecular Biology Society of Japan, Fukuoka, Japan, November 2024 (poster presentation).
• Enhancer-mediated transcriptional regulation in Oikopleura dioica. The 45th Annual Meeting of the Molecular Biology Society of Japan, Chiba, Japan, November 2022 (poster presentation).
• Imaging and single-cell sequencing analysis of super-enhancer activation mediated by NF-κB in B cells. The 19th IPR Retreat, Osaka University, Online, November 2021 (poster presentation).
• NF-κB mediated transcriptional regulation in B cells. The 58th Annual Meeting of the Biophysical Society of Japan, Online, September 2020 (poster presentation).
• Multi-dimensional analysis of NF-κB nuclear dynamics. The 18th IPR Retreat, Osaka University, Osaka, Japan, November 2019 (oral presentation).

Honors and awards

• Poster presentation award The 58th Annual Meeting of the Biophysical Society of Japan · Japan · September 2020
• Honjo International Scholarship Foundation Scholarship Japan · April 2020 – March 2022
• Bronze award BIOMOD 2018 Molecular Design Competition · USA · 2018
• Bronze award BIOMOD 2017 Molecular Design Competition · USA · 2017
• Monbukagakusho (MEXT) Scholarship Japan · September 2016 – March 2020

Research experience

• PhD student Genomics and Regulatory Systems Unit (PI: Nicholas Luscombe), Okinawa Institute of Science and Technology · Okinawa, Japan · March 2022 – present
  • Project: a genomic investigation of evolution and gene regulation in Oikopleura dioica
  • Analysis of genomic, transcriptomic and epigenomic data of O. dioica
  • Improved genome annotation of O. dioica
  • Developed a genome browser for O. dioica: oikobrowser.jnicolaus.com
  • Side project: O. dioica pangenomics
• PhD rotation student Macroevolution Unit (PI: Lauren Sallan), Okinawa Institute of Science and Technology · Okinawa, Japan · 2023
  • Project: dental microwear analysis in the fish–tetrapod transition
  • Established a fish facility for Polypterus
  • Performed dental molding of fossils and scanning using a confocal microscope
• PhD rotation student Marine Eco-Evo-Devo Unit (PI: Vincent Laudet), Okinawa Institute of Science and Technology · Okinawa, Japan · 2022
  • Project: metabolic gene duplication in clownfish
• Undergraduate and master's student Laboratory for Cell Systems (PI: Mariko Okada), Osaka University · Osaka, Japan · February 2019 – March 2022
  • Project: NF-κB mediated transcriptional regulation in B cells
  • Quantitative imaging analysis of NF-κB nuclear translocation using confocal microscopy and ImageJ
  • Single-cell RNA-seq and single-cell ATAC-seq analysis relating cis-regulatory elements to gene expression
  • In charge of training visiting researchers on RNA-seq analysis
• Research intern Laboratory of Cellular Life Science (PI: Naotada Ishihara), Osaka University · Osaka, Japan · September 2018 – February 2019
  • Project: quantification of mitochondrial morphology using ImageJ
  • Live imaging of mitochondria in cell culture
• Research assistant Laboratory of Science and Innovation for Pain, Osaka University · Osaka, Japan · April 2018 – February 2019
  • Mouse genotyping, RNA extraction, ELISA and MRI image analysis
• Associate project leader, Osaka University BIOMOD 2017–2018 Bio Medical Wet Robotics Laboratory (PI: Keisuke Morishima), Osaka University · Osaka, Japan · 2017 – 2018
  • DNA origami design, modelling and experiments
  • FRET observation using a confocal microscope for a live-cell tension sensor project
  • Team website and animation production
  • Bronze award in both BIOMOD 2017 and 2018
• Undergraduate researcher Department of Biotechnology, Pelita Harapan University · Tangerang, Indonesia · 2016
  • Antibiotic susceptibility evaluation of Bacillus amyloliquefaciens isolated from local pig gastrointestinal tract as a potential probiotic candidate

Teaching and training

• Mentor — Rotation student & Intern training Okinawa Institute of Science and Technology · Okinawa, Japan · 2022-2026
  • Trained 4 rotation students and a short internship student on genomics & transcriptomics analysis
• Mentor — RNA-seq analysis training for visiting researchers Laboratory for Cell Systems, Osaka University · Osaka, Japan · 2019 – 2022
• Coordinator — Bioinformatics training and website management Laboratory for Cell Systems, Osaka University · Osaka, Japan · 2019 – 2022

Workshops attended

• EMBO Practical Course: Single-cell omics — deeper to genomics Heidelberg, Germany · December 2022
• 第30回細胞生物学ワークショップ (The 30th Cell Biology Workshop) Hyogo, Japan · July 2020

Organizational experience

• Secretary General Indonesian Student Association in Japan (PPI Jepang) · 2020 – 2021
• Secretary General Indonesian Student Association in Japan (PPI Jepang) · 2019 – 2020
• President Indonesian Student Association in Osaka-Nara (PPI Osaka-Nara) · 2018 – 2019
  • In charge of ASSIGN, the annual symposium held by the Indonesian Student Association in Japan
• Head of academic division Indonesian Student Association in Osaka-Nara (PPI Osaka-Nara) · 2017 – 2018
  • Organized academic events such as group study sessions and career seminars