Johannes Nicolaus Wibisana

Johannes Nicolaus Wibisana

A computational biologist

About me

Download my CV Google Scholar

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
  • Master of Science, Biological Sciences Graduate School of Science, Osaka University · Osaka, Japan · April 2020 – March 2022
  • 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

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

Peer review

  • Nature Communications Reviewer · 2025
  • Trends in Genetics Reviewer · 2025

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

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