About

Affiliation

• Education
  • Graduate School of Frontier Sciences, The University of Tokyo
    • JSPS Research Fellowship for Young Scientists 日本学術振興会特別研究員 DC1 (2021/04 -)
    • Doctoral course (2021/04 -)
    • Master of Science (2019/04 - 2021/03) Dean’s Award & Excellent Research Award
  • Department of Bioinformatics and Systems Biology, Faculty of Science, The University of Tokyo
    • Bachelor of Science (2015/04 - 2019/03)
• Research
  • Morishita Lab (bachelor/master/doctor) 2018/05 -
  • Iino Lab (part-time) 2017
  • Laboratory for Quantitative Biology, Kobayashi Lab (internship) 2015/10 - 2017/03
• Software Developer
  • Sony Computer Science Laboratories, Inc. Music Excellence Project (research assistant) 2020/10 -
  • Tier IV, Inc. (parttime engineer) 2019/05 - 2022/03
  • HAPT Lab, LLC (parttime) 2019/04 - 2020/03
  • OUXT Polaris (software developer) 2018/04 - 2019/03, Joined Maritime RobotX Challenge 2018 @ Honolulu
  • Beatrobo, Inc. (parttime) 2016/04 - 2019/04
  • Kph-Lab Kaijo High School Physics Club 2013/04 - 2016/03

Research Fields

• Accurate genome assembly of repetitive regions
• Genome Scaffolding with Hi-C

Papers

Peer-reviewed

• Ryo Nakabayashi, Shinichi Morishita, HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C, Bioinformatics, Volume 36, Issue 13, July 2020, Pages 3966–3974, https://doi.org/10.1093/bioinformatics/btaa288

Thesis for a degree

• Ryo Nakabayashi, A targeted haplotype-resolved assembly of the human killer cell immunoglobulin-like receptor region by chunking and clustering, 2021, master thesis
• Ryo Nakabayashi, A probabilistic model to determine contig orientation in chromosome-length scaffolds by Hi-C (日本語タイトル: Hi-C による染色体全長ゲノムアセンブリ内のコンティグの方向を推定する確率モデルの設計), 2019, bachelor thesis

Posters

• Ryo Nakabayashi, Shinichi Morishita, HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds by Hi-C, The Biology of Genomes, CSHL, Virtual Meeting, May 5-8, 2020
• Ryo Nakabayashi, Shinichi Morishita, HiC-Hiker: A probabilistic model to determine contig orientation in chromosome-length scaffolds by Hi-C, ASHG 2019 Annual Meeting, Houston, Oct 15-19, 2019
• Ryo Nakabayashi, Shinichi Morishita, A probabilistic model to determine contig orientation in chromosome-length scaffolds by Hi-C, 第13回国際ゲノム会議 AGW, Tokyo, June 25-27, 2019
• 中林 亮, 粘菌細胞集団の自己組織的回転運動の解析, 定量生物学の会 第八回年会, 2016

Teaching

• Teaching Assistant “Basic Laboratory Work in Information Science”(情報基礎実験) 2021/12

Talks

• 東京大学理学部 Open Campus 2022 Online 学生講演 “情報科学で読み解くゲノムの中身” YouTube

Programs

• UTokyo SFP09 (Summer Founders Program) 2020 アイデア共有のための誰でも使える3DCGアニメ作成ツール
• UTokyo Project Fund 2020

Musics

Button Accordion/Melodeon Player

• Fleadh Cheoil na hÉireann 2019 & Féile Tokyo 2019: Melodeon(Senior), Duets(Senior)
• Intercollegeate Celtic Festival (web)

Skills

• Languages: Python/C/C++(ROS)/Rust/GoLang/{Java,Type}Script/HTML/Bash

• Web
  • Frontend: HTML+CSS, TypeScript, frontend frameworks (vue.js, react), client side computing (WebGL, audio and video on browser), SPA
  • Backend: node.js, AWS/GCP/Lambda/EC2, docker/k8s
  • Scraping, Alexa Skills, Chrome extension, Tensorflow.js, Electron
• Mobile Apps
  • React Native
  • Android(Java), iOS(Swift)
• Analysis
  • data analysis / image processing with Python
  • Tensorflow, Keras, 3D segmentation
• Bioinformatics
  • Scaffolding with Hi-C
  • Assembly graph analysis
  • Image Segmentation
• Hardware/Robotics
  • Arduino/mbed, Rapid Prototyping
  • Robot software, ROS
  • Object Recognition
  • CI/CD
  • security, wireless networking
• 3DCG/CAD
  • blender
  • Autodesk Inventor, Fusion360, 3DS MAX
• Environment
  • vim
  • mac, ubuntu
• Personal Interest
  • Program Calculation, Haskell
  • Information Geometry
  • User Interface