Johannes Nicolaus Wibisana

A PhD student residing in Okinawa, Japan

About me

I have always been interested in science, especially biology since I was little. This brought me to Osaka University, where I was able to do research on transcription regulation for my undergraduate and master’s thesis. Currently, I have moved to Okinawa Institute of Science and Technology in Okinawa, Japan, currently working on the transcriptional regulation of the scrambled genome of O. dioica. In my spare time, I take care of my carnivorous plants, 3D print, watch football, fish and scuba dive.

I am currently using R and shell scripts for most of my work, and is learning nextflow during my PhD.

Education



  • Bachelor of Science, School of Science, Osaka University (October 2016-March 2020 early graduation)
    • Major: Biological Sciences (G30 CBCMP program)
    • Laboratory: Laboratory of Cell Systems (PI: Mariko Okada)
    • Project: NF-κB mediated transcriptional regulation in B cell
      • Live fluorescence imaging
      • Multi-omics analysis
    • Funding: Monbukagakusho (MEXT) Scholarship

Publications and conference presentations

  • Publications

    • JN Wibisana, R Sallan, T Kubo, L Sallan. Modification of clinical dental impression methods to obtain dental traits from living and whole non-mammalian vertebrates. BioRxiv, 2023. link
    • JN Wibisana, T Inaba, Y Sako, M Okada. Quantitative Imaging Analysis of NF-κB for Mathematical Modeling Applications. Methods in Molecular Biology: Computational Modeling of Signaling Networks, 2023. link
    • Y Harada, T Sasaki, JN Wibisana, […], M Kubo. Type 2 helper T cells convert into Interleukin-13-expressing follicular helper T cells after antigen repriming, 2023. link
    • K Iida, J Kondo, JN Wibisana, M Inoue, M Okada. ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes. Bioinformatics, 2022. link
    • JN Wibisana, M okada. Encoding and decoding NF-κB nuclear dynamics. Current Opinion in Cell Biology, 2022. link
    • JN Wibisana, Takehiko Inaba, Hisaaki Shinohara, […], M Okada. Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers. PLoS Genetics, 2022. link
    • JN Wibisana, K Iida, M Okada. 免疫系の 1 細胞解析による転写制御機構の予測. 医学のあゆみ, 2021. link

  • International conference

    *

    • 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, Nov 2021 (Poster presentation)
    • NF‑κB mediated transcriptional regulation in B cell, CSHL Biology of Genomes 2021, Online, May 2021. (Poster presentation)
    • NF-κB mediated transcriptional regulation in B cell, 2020 International Symposium on Structure and Folding of Disease Related Proteins, Seoul National University, Feb 2020. (Oral presentation)
    • Multi-dimensional analysis of NF-κB nuclear dynamics, International Conference on Systems Biology 2019, Okinawa Institute of Science and Technology, Nov 2019. (Poster presentation)

  • Domestic

    • Enhancer-mediated transcriptional regulation in \textit{Oikopleura dioica}, The 45th Annual Meeting of the Molecular Biology Society of Japan, Chiba, Japan, Nov 2022. (Poster presentation)
    • Imaging and single-cell sequencing analysis of super-enhancer activation mediated by NF-κB in B cells, 19th IPR retreat, Online, Nov 2021. (Poster presentation)
    • NF‑κB mediated transcriptional regulation in B cell, The 58th Annual Meeting of the Biophysical Society of Japan, Online, Sep 2020. (Poster presentation)
    • Multi-dimensional analysis of NF-κB nuclear dynamics, The 18th IPR Retreat, Osaka University, November 21-22, 2019. (Oral presentation) Feb 2020. (Oral presentation)

Honor and Awards

  • Honjo International Scholarship Foundation Scholarship. Apr 2020-Mar 2022
  • Poster presentation award. The 58th Annual meeting of the Biophysical Society of Japan. Sep 2020.
  • MEXT scholarship. Sep 2016-Mar 2020.

Research experience

  • Quantification of mitochondrial morphology (2018-2019)
    • Laboratory: Laboratory of Cellular Life Science, Osaka University (PI: Naotada ishihara)
    • Details:
      • Live imaging of mitochondria in cell culture
      • Quantification of mitochondrial morphology using ImageJ
  • Research assistant (2017-2018)
    • Laboratory: Laboratory of Science & Innovation for Pain, Osaka University (PI: Aya Nakae)
    • Details:
      • ELISA
      • Blood sample processing
      • Mouse genotyping
  • Research assistant (2017-2018)
    • Laboratory: Bio Medical Wet Robotics Laboratory, Osaka University (PI: Morishima Keisuke)
    • Project: Tension sensor using live cells
    • Details:
      • FRET observation using confocal microscope
      • Mammalian cell culture
      • PCR validation
  • BIOMOD 2018
    • Laboratory: Bio Medical Wet Robotics Laboratory, Osaka University (PI: Morishima Keisuke)
    • Details:
      • DNA origami design
      • Website making
    • Award: Bronze award
  • BIOMOD 2017
    • Laboratory: Bio Medical Wet Robotics Laboratory, Osaka University (PI: Morishima Keisuke)
    • Details:
      • DNA origami design
      • Website making
      • Animation
    • Award: Bronze award
  • Antibiotic susceptibility evaluation of Bacillus amyloliquefaciens isolated from local pig gastrointestinal tract as potentially probiotic candidate
    • Laboratory: Department of Biotechnology, Pelita Harapan University
    • Details:
      • Bacterial cell culture
      • Antibiotic susceptibility testing

Organizational experience

  • Secretary General - Indonesian Student Association in Japan (2020-2021)

  • Secretary General - Indonesian Student Association in Japan (2019-2020)

  • President - Indonesian Student Association in 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 (2017-2018)
    • In charge of organizing academic events such as group study and career seminars