Studying Nature
Learning from Nature
Applying from Nature
Opening the Next

Sung-Joon Park
I'm a scientist in the Genome Informatics

About Me

About Me

生物学や医療・疾患関連研究において、膨大なデータの活用は非常に重要な課題です。特に、次世代シークエンシングなどの最先端実験技術によるゲノム・エピゲノム解析では、データサイエンスが欠かせません。また、ここから得られた知識を蓄積して共有することは、新しい価値の創造につながります。

 私は、データ駆動型情報科学で生命現象を研究し (Studying Nature)、その基本原理とメカニズムから学び (Learning from Nature)、それらを工学的に応用することで (Applying from Nature)、学術の発展と社会への貢献(Opening the Next)を目指しています。

Keywords: Omics, Bioinformatics, Computational Intelligence


  • 朴 聖俊(パク ソンジュン) (Sung-Joon Park), 博士（工学）
  • 東京大学医科学研究所 ヒトゲノム解析センター
    機能解析イン・シリコ分野

    〒108-8639
    東京都港区白金台4-6-1 総合研究棟8階
    Tel: 03-5449-5131
    Fax: 03-5449-5133
  •  sjpark AT ims.u-tokyo.ac.jp
My Resume

My Resume

学歴

博士（工学）

H13.4.1 - H17.3.26 (2001 - 2005)
東京工業大学大学院 総合理工学研究科 知能システム科学専攻
博士後期課程

修士（工学）

H10.4.1 - H12.3.26 (1998 - 2000)
東京工業大学大学院 総合理工学研究科 知能システム科学専攻
修士課程

学士（経営）

H6.4.1 - H10.3.22 (1994 - 1998)
専修大学 経営学部 情報管理学科（首席卒業, Valedictorian）

職歴・研究歴

准教授

R2.5.1 (2020 - ) - 現在
東京大学医科学研究所 ヒトゲノム解析センター
東京大学情報理工学系研究科 コンピュータ科学専攻
東京大学理学部 情報科学科 非常勤講師 (2021.9 - )

特任講師

H26.9.1 - R2.4.30 (2014 - 2020)
東京大学医科学研究所 ヒトゲノム解析センター

特任研究員

H22.4.1 - H26.8.30 (2010 - 2014)
東京大学医科学研究所 ヒトゲノム解析センター

特任助教

H19.4.1 - H22.3.30 (2007 - 2010)
京都大学大学院 情報学研究科 知能情報学専攻

学術研究員

H17.4.1 - H19.3.30 (2005 - 2007)
神戸大学 理学部 化学科

資格

システムアドミニストレータ (第 32703711 号)

第一種情報処理技術者 (第 12901663 号)

受賞

優秀口述講演者賞

Informatics In Biology, Medicine and Pharmacology 2023 (IIBMP 2023)

Informatics In Biology, Medicine and Pharmacology 2021 (IIBMP 2021)

The 19th International Conference on Bioinformatics (InCoB 2020)

Informatics In Biology, Medicine and Pharmacology 2020 (IIBMP 2020)

The 17th International Conference on Bioinformatics (InCoB 2018)

ベストポスター賞

The 28th International Conference on Genome Informatics (GIW/BIOINFO 2017)

The 18th HTLV and Related Viruses (HTLV 2017)

The 15th International Conference on Bioinformatics (InCoB 2016)

The 22nd International Conference on Genome Informatics (GIW 2011)

学術賞

川島記念学術賞, 専修大学, 1998

その他

奨学金

情報処理教育研修助成財団奨学金, 2002-2003
ロータリー米山記念奨学会, 1999
文部科学省外国人留学生学習奨励費, 1998, 2001
専修大学第二種奨学金, 1995-1997

所属学会

情報処理学会
人工知能学会
日本バイオインフォマティクス学会

学術活動など

  • Conference Committee
    International Conference on Biomedical and Bioinformatics Engineering (ICBBE) 2025, Program Chairs
    IEEE International Conference on AI x Medicine, Health, and Care (AIxMHC) 2025, Program Committee
    International Conference on Biomedical Engineering and Applications (ICBEA) 2023-2025, Program Committee
    International Conference on Computational Intelligence and Intelligent Systems (CIIS) 2024,2025, Program Committee
    IEEE International Conference on Bioinformatics and Bioengineering (BIBE) 2022, Program Committee
  • 国際協創海外拠点 UTokyo-KI LINK Lab 研究開発参加者 (2024.7-)
  • Accociate Editor, iScience (2025.7-)

    • Research Interest

    Research Interest

    Gene regulation, Chromatin structure, Diseases, Bioinformatics

    Data Analysis of Next-generation Sequencing

    We are analyzing high-throughput sequencing data from various cell types and tissues in which multimodal biological data are involved. The biological curiosities are broadly ranged such as embryo development, stem cell differentiation, and diseases.

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    Inferring Gene Regulation

    We are developing computational methods to infer mechanisms underlying gene regulation. Our approach includes probabilistic and heuristic methods for modeling promoter architectures, enhancer-promoter interactions, the correlation of chromosome 3D folding with transcriptome, etc.

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    AI in BI

    AI (Artificial Intelligence) techniques in BI (Bioinformatics) are greatly helping to model DNA language, regulatory codes, histone codes, and more. We are developing machine-learning-based tools embedding multimodal heterogeneous data into latent spaces and applying them to decipher biological cryptics.

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    Genome and Epigenome at Single Cell Level

    We are highlighting the computational methods to analyze transcriptomic and epigenetic characteristics of single-cell populations, which often give insights into intricate biological phenomena.

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    Online Resources

    By building up databases and web-based tools, we are providing windows to researchers that we open and share knowledge in public domains. In particular, we are expanding "OPEN" series (OpenTein, OpenLooper, OpenContami, etc), which promotes data-driven open-science.

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    Selected Publications

    Park SJ*, Nakai K. A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response. NAR Genom Bioinform. 2024 May 6;6(2):lqae050

    Ishii S, Kakizuka T, Park SJ, Tagawa A, Sanbo C, Tanabe H, Ohkawa Y, Nakanishi M, Nakai K, Miyanari Y. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nat Genet. 2024 Mar;56(3):473-482

    Hayashi R, Okubo T, Kudo Y, Ishikawa Y, Imaizumi T, Suzuki K, Shibata S, Katayama T, Park SJ, Young RD, Quantock AJ, Nishida K. Generation of 3D lacrimal gland organoids from human pluripotent stem cells. Nature. 2022 May;605(7908):126-131

    Park SJ, Onizuka S, Seki M, Suzuki Y, Iwata T, Nakai K. A systematic sequencing-based approach for microbial contaminant detection and functional inference. BMC Biol. 2019 Sep 13;17(1):72

    Sung-Joon Park. Genome-wide scanning of gene expression. in Encyclopedia of Bioinformatics and Computational Biology, Academic Press. 2019;3:452-462

    Park SJ, Shirahige K, Ohsugi M, Nakai K. DBTMEE: a database of transcriptome in mouse early embryos. Nucleic Acids Res. 2015 Jan;43(Database issue):D771-6

    Park SJ, Umemoto T, Saito-Adachi M, Shiratsuchi Y, Yamato M, Nakai K. Computational promoter modeling identifies the modes of transcriptional regulation in hematopoietic stem cells. PLoS One 2014 Apr 7;9(4):e93853

    Park SJ, Komata M, Inoue F, Yamada K, Nakai K, Ohsugi M, Shirahige K. Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. Genes Dev. 2013 Dec 15;27(24):2736-48

    DBTMEE

    DBTMEE

    Database of Transcriptome in Mouse Early Embryos

    More than 1.5x105 MII oocytes were sequenced to analyse the parental choreography during fertilization. DBTMEE is a database providing the gene expression profile established by this ultralarge-scale whole-transcriptome analysis.

    OpenTein

    OpenTein

    Open Teratoma Investigation

    Searchable, zoomable and annotatable web-based repository system that enables to archive and freely distribute high-resolution whole-slide images and relevant records for the stem cell-derived teratoma formation assay.

    OpenContami

    OpenContami

    Open Cell Microbial Contaminants by High-throughput Sequencing

    A web-based tool for profiling microbial contamination on NGS data and its database to help successful data analyses in biological and biomedical research.

    OpenLooper

    OpenLooper

    Open and Share Your Data. Loop with Your Co-workers

    A web-based platform to support opening and sharing high-throughput sequencing datasets, such as Hi-C, ChIP-seq, RNA-seq, and more.

    ChromOS

    ChromOS

    Data Portal of The Chromosome Orchestration System (OS)

    Providing online access to the data resources from Chromosome Orchestration System (OS), a research project supported by MEXT Japan.

    My Hobby

    My Hobby

    Playing Rock Guitar (Fender Stratocaster); Jimi Hendrix, Ritchie Blackmore, Yngwie Malmsteen

    › Always Remember Us This Way
    › Gurenge
    › Yuki 100%
    › Highway Star
    › Canon Rock
    › I'm alright
    › My grandfather's clock
    › Air on the G string


    Canon Rock

    Canon Rock

    Johann Pachelbel

    I'm Alright

    Neil Zaza

    My Grandfather's Clock

    (0:00 - 2:05)

    Highway Star

    Deep Purple

    勇気100%

    Ninja Boy Rantaro OP

    紅蓮華 (Gurenge)

    鬼滅の刃

    Always Remember Us This Way

    Lady GaGa

    Bookmark

    Bookmark

             
       

    Human Genome Center

    IMSUT

    The University of Tokyo

    Sung-Joon Park (Ph.D)
    Associate Professor
    Laboratory of Functional Analysis in silico
    Human Genome Center
    The Institute of Medical Science
    The University of Tokyo
    4-6-1 Shirokanedai Minato-ku Tokyo 108-8639, Japan
    +81-(0)3-5449-5131