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Research

>Genome Informatics
>Structural Bioinformatics

[Publications]
""
"Genome-wide scanning of gene expression",
   Sung-Joon Park,
  Encyclopedia of Bioinformatics and Computational Biology, Academic Press, 2019, Pages 452-462, 2018,
  [ScienceDirect]
"Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s",
   Jong-Hun Lee, Sung-Joon Park, Kenta Nakai,
  Scientific Reports (2017), 7(1):11295,   [SREP]   [PUBMED]
"Multidisciplinary insight into clonal expansion of HTLV-1-infected cells in adult T-cell leukemia via modeling by deterministic finite automata coupled with high-throughput sequencing",
  Amir Farmanbar, Sanaz Firouzi, Sung-Joon Park, Kenta Nakai, Kaoru Uchimaru and Toshiki Watanabe,
  BMC Med Genomics (2017), 10(1):4,   [BMC]   [PUBMED]
"Transcriptional regulation of a horizontally transferred gene from bacterium to chordate",
  Yasunori Sasakura, Yosuke Ogura, Nicholas Treen, Rui Yokomori, Sung-Joon Park, Kenta Nakai, Hidetoshi Saiga, Tetsushi Sakuma, Takashi Yamamoto, Shigeki Fujiwara, and Keita Yoshida,
  Proc. R. Soc. B (2016), 283:20161712,  [RSPB]   [PUBMED]
"ZBTB16 as a Downstream Target Gene of Osterix Regulates Osteoblastogenesis of Human Multipotent Mesenchymal Stromal Cells",
  Satoru Onizuka, Takanori Iwata, Sung-Joon Park, Kenta Nakai, Masayuki Yamato, Teruo Okano and Yuichi Izumi,
  J. Cell. Biochem. (2016), 117:2423-2434,   [JCB]   [PUBMED]
"Advances, Practice, and Clinical Perspectives in High-throughput Sequencing",
  Sung-Joon Park, Mihoko Saito-Adachi, Yusuke Komiyama and Kenta Nakai,
  Oral Diseases (2016), 22:353-364,   [ODI]   [PUBMED]
"PAX6 isoforms, along with reprogramming factors, differentially regulate the induction of cornea-specific genes",
  Yuzuru Sasamoto, Ryuhei Hayashi, Sung-Joon Park, Mihoko Saito-Adachi, Yutaka Suzuki, Satoshi Kawasaki, Andrew Quantock, Kenta Nakai, Motokazu Tsujikawa and Kohji Nishida,
  Scientific Reports (2016), 6:20807,   [SREP]   [PUBMED]
"OpenTein: a database of digital whole-slide images of stem cell-derived teratomas",
  Sung-Joon Park, Yusuke Komiyama, Hirofumi Suemori, Akihiro Umezawa and Kenta Nakai,
  Nucl. Acids Res. (2016), 44(D1):D1000-D1004,   [NAR]   [PUBMED]   [OpenTein]
"An integrative approach for efficient analysis of whole genome bisulfite sequencing data",
  Jong-Hun Lee, Sung-Joon Park and Kenta Nakai,
  BMC Genomics (2015), 16(Suppl 12):S14,   [BMC]   [PUBMED]
"DBTMEE: a database of transcriptome in mouse early embryos",
  Sung-Joon Park, Katsuhiko Shirahige, Miho Ohsugi and Kenta Nakai,
  Nucl. Acids Res. (2015), 43(D1):D771-D776,   [NAR]   [PUBMED]   [DBTMEE]
"Computational promoter modeling identifies the modes of transcriptional regulation in hematopoietic stem cells",
  Sung-Joon Park, Terumasa Umemoto, Mihoko Saito-Adachi, Yoshiko Shiratsuchi, Masayuki Yamato and Kenta Nakai,
  PLoS One (2014), 9(4):e93853, [PUBMED]
"Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis",
  Sung-Joon Park, Makiko Komata, Fukashi Inoue, Kaori Yamada, Kenta Nakai, Miho Ohsugi and Katsuhiko Shirahige,
  Genes Dev (2013), 27:2736-2748, [PUBMED]   [Press Release]   [BRIC]   [RESEARCH HIGHLIGHTS] Nature Genetics
"Predicting promoter activities of primary human DNA sequences",
  Takuma Irie, Sung-Joon Park, Riu Yamashita, Masahide Seki, Tetsushi Yada, Sumio Sugano, Kenta Nakai and Yutaka Suzuki,
  Nucl. Acids Res. (2011), 39(11):e75, [PUBMED]
"A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns",
  Sung-Joon Park and Kenta Nakai,
  BMC Bioinformatics (2011), 12 (Suppl 1):S50, [BMC]   [PUBMED]   [Suppl.]
"Probabilistic Graphical Modeling for Large-scale Combinatorial Regulation of Transcription Factors",
  Sung-Joon Park, Natsuhiro Ichinose and Tetsushi Yada,
  Proc. the workshop on Knowledge, Language, and Learning in Bioinformatics (KLLBI), 72-86, 2008, [WEB]
"Applying a Grid Technology to Protein Structure Predictor ROKKY",
  Kazutoshi Fujikawa, Wenzhen Jin, Sung-Joon Park, Tadaomi Furuta, Shoji Takada, Hiroshi Arikawa, Susumu Date and Shinji Shimojo,
  Stud Health Technol Inform. (Proc. HealthGrid 2005), 112:27-36, 2005, [PUBMED]
"A Study of Fragment-Based Protein Structure Prediction: Biased Fragment Replacement for Searching Low-energy Conformation",
  Sung-Joon Park, Genome Informatics, 16(2):104-113, 2005, [PUBMED]
"A Computing System for Protein Structure Prediction with Trial-and-error Process",
  Hiroshi Arikawa,Shingo Masuda, Tadaomi Furuta,Wenzhen Jin, Sung-Joon Park, Shoji Takada, Kazutoshi Fujikawa and Hideki Sunahara,
  ACS Transaction, IPSJ, 46(11):407-419, 2005, [CiNii]
"Two-layered Comparison of Protein Structures by Real-coded GA",
  Sung-Joon Park, Shoji Takada and Masayuki Yamamura,
  IPSJ Journal, 46(3):898-910, 2005, [CiNii]
"GA-based Generic Method for Protein Structure Comparison",
  Sung-Joon Park and Masayuki Yamamura,
  Proc. The 2003 IEEE Congress on Evolutionary Computation (CEC 2003), 1528-1535, 2003, [IEEE Xplore]
"Two-layer Protein Structure Comparison",
  Sung-Joon Park and Masayuki Yamamura,
  Proc. The 15th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2003), 435-440, 2003, [IEEE Xplore]
"Asynchronous Real-coded Genetic Algorithm for Simultaneous Protein Structure-based Alignment",
  Sung-Joon Park and Masayuki Yamamura,
  Proc. Genetic and Evolutionary Computation Conference (GECCO-2003) Graduate Student Workshop, 276-279, 2003
"Real-coded Genetic Algorithm to Reveal Biological Significant Sites of Remotely Homologous Proteins",
  Sung-Joon Park and Masayuki Yamamura,
  Genetic and Evolutionary Computation Conference (GECCO-2003), 1602-1603, 2003, [Springer]

[Writings]

"Chapter 7: Computational Inference of Gene Regulation from Whole-Transcriptome Analysis of Early Embryos",
Sung-Joon Park and Kenta Nakai,
 in (I. Ivanov, X. Qian and R. Pal ed.) Emerging Research in the Analysis and Modeling of Gene Regulatory Networks,
 pp. 241-279, IGI Global, 2016  DOI: 10.4018/978-1-5225-0353-8.ch007,  [Sample PDF]

"バイオインフォマティクス(第9章 プロテオミクス)", Andrzej Polanski and Marek Kimmel(原著)、
  朴 聖俊(和訳), Springer-Verlag, 2010

"Template-free Prediction by Fragment Assembly with SimFold Energy Function at CASP7",
  S.J. Park, N. Hori, K. Okazaki and S. Takada,
  CASP7 Abstracts, 110-112, 2006, [PDF]   [WEB]

"De novo Structure Prediction Server by Fragment Assembly with SimFold Energy Function",
  W. Jin, S.J. Park and S. Takada, CASP7 Abstracts, 112-113, 2006, [PDF]

"タンパク質立体構造予測の現状と未来",
  朴 聖俊,千見寺 浄慈,広川 貴次,富井 健太郎,高田 彰二, 人工知能学会誌, 20(4):479-485, 2005, [CiNii]

"タンパク質立体構造の2層比較",
  朴 聖俊,山村 雅幸, 第48回 数理モデル化と問題解決(MPS)研究会, 2004, [CiNii]


[Talks]

"Applying Joint Non-Negative Matrix Factorization to Functional Analysis of Microbial Infection",
Sung-Joon Park and Kenta Nakai,
The 17th International Conference On BioInformatics (InCOB-2018), Sep. 26-28, New Delhi, India

"Analyzing the 3D Chromatin Organization Coordinating with Gene Expression Regulation in B-cell Lymphoma",
 Luis A.E. Nagai, Sung-Joon Park and Kenta Nakai,
The 17th International Conference On BioInformatics (InCOB-2018), Sep. 26-28, New Delhi, India

"Three-Dimensional Chromatin Structures Coordinate with Gene Expression Levels and Reveals Inter-chromosomal Interactions in B-Cell Lymphoma",
 Luis A.E. Nagai, Sung-Joon Park and Kenta Nakai,
生命医薬情報学連合大会 (IIBMP2018), P-31 (oral presentation), 2018年9月19日~21日, 鶴岡、日本

"OpenLooper: A web-based platform for managing multi-layered NGS data"
Sung-Joon Park and Kenta Nakai,
生命医薬情報学連合大会 (IIBMP2018), P-32, 2018年9月19日~21日, 鶴岡、日本

"脂肪由来幹細胞(Adipose-derived stem cell)の分化に関与するエピジェネティック因子の探索",
 山谷恭代, 朴聖俊, 中井謙太,
生命医薬情報学連合大会 (IIBMP2018), P-37 (oral presentation), 2018年9月19日~21日, 鶴岡、日本

"DNAヒドロキシメチル化とヒストンH4K8アセチル化によるヒト多能性幹細胞遺伝子発現変動",
 石川靖久, 朴聖俊, 中井謙太,
生命医薬情報学連合大会 (IIBMP2018), P-73, 2018年9月19日~21日, 鶴岡、日本

"The establishment of safety and efficacy evaluation for allogeneic periodontal ligament derived multipotent mesenchymal stromal cell sheet with next-generation sequencer",
 Takanori Iwata, Satoru Onizuka, Sung-Joon Park, Yuka Tsumanuma, Kenta Nakai, Yuichi Izumi, Tomohiro Ando,
5th TERMIS World Congress, 36-SY-2, Sep. 4-7, 2018, Kyoto, Japan

"Detecting Microbial Contamination from NGS Data and Analyzing Its Functional Impact",
Sung-Joon Park and Kenta Naka
BIO UT, P70, June 9, 2018, Tokyo, Japan

"Profiling of Cell Microbial Contamination by NGS data",
Sung-Joon Park,
配列解析シンポジウム (36 years since the Smith-Waterman-Gotoh algorithm),
 2018年3月28日,産業技術総合研究所 臨海副都心センター別館

"同種歯根膜細胞シートの安全性・有効性評価指標の確立と歯周組織の再建",
 岩田 隆紀, 鬼塚 理, 朴 聖俊, 妻沼 有香, 和泉 雄一, 中井 謙太, 安藤 智博,
 第17回 日本再生医療学会総会, 2018年3月21-23日, 横浜, 日本



"Non-CpGメチル化パターンによる脳の老化関連遺伝子の分類",
 李 鍾勳, 朴 聖俊, 中井 謙太,
 2017年度生命科学系学会合同年次大会, 1P-0670, 2017年12月6日, 神戸, 日本

"生殖細胞においてトランスポゾンに富んだ染色体領域が一過的に緩む",
 山中 総一郎, Sung-Joon Park, 渋谷 あおい, Piero Carninci, 中井 謙太, 塩見 春彦,
 2017年度生命科学系学会合同年次大会, 3P-0559 (3PT18-13), 2017年12月8日, 神戸, 日本

"Development of a Pipeline for Contamination Profiling of Cells with Next Generation Sequencing Data",
  Sung-Joon Park, Satoru Onizuka, Takanori Iwata, Kenta Nakai,
  The 28th International Conference on Genome Informatics Workshop (GIW)/BIOINFO 2017, P35, Oct.31-Nov.3, 2017, Seoul, Korea
  BEST POSTER AWARD

"Whole transcriptome analysis of MSCs derived from different types of tissue reveals unique profiles",
  Satoru Onizuka, Yasuharu Yamazaki, Takayuki Sugimoto, Yumiko Sone, Akira Takeda, Sung-Joon Park, Kenta Nakai, Takanori Iwata, Masayuki Yamato, Teruo Okano,
  The American Society for Bone and Mineral Research (ASBMR) 2017 Annual Meeting, Sep.8-11, 2017, Denver, Colorado, USA

"腸骨・顎骨組織由来間葉系幹細胞に対する網羅的遺伝子発現解析による検討",
  鬼塚 理, 山崎安晴, 杉本孝之, 曽根由美子, 武田 啓, 朴 聖俊, 中井謙太, 岩田隆紀, 大和雅之, 岡野光夫,
  第16回日本再生医療学会総会, 2017年3月7日, 仙台, 日本

"歯根膜細胞シートを用いた歯周組織の再生と展望",
  岩田隆紀, 鬼塚 理, 伊豆原 るな, 鷲尾 薫, 妻沼有香, Park Sung-Joon, 中井謙太, 和泉雄一, 安藤智博,
  第16回日本再生医療学会総会, 2017年3月8日, 仙台, 日本

"An Empirical Model for Visualizing Clonal Expansion of HTLV-1-Infected Cells in Adult T-Cell Leukemia Derived from High-Throughput Sequencing",
  Amir Farmanbar, Sanaz Firouzi, Sung-Joon Park, Kaoru Uchimaru, Toshiki Watanabe, Kenta Nakai,
  18th International Conference on Human Retrovirology HTLV and Related Viruses, March 7-10 2017, Tokyo, Japan
  BEST POSTER AWARD

"Comprehensive Clonality Analysis of HTLV-1 Infected Cells Integrating Cell Surface Markers of ATL Progression, Genome Wide Profiling of Provirus Integration Sites and Mutation Patterns",
  Sanaz Firouzi, Amir Farmanbar, Sereewattanawoot Sarun (Ball), Seiichiro Kobayashi,Kazumi Nakano, Sung-Joon Park, Kenta Nakai, Toshiki Watanabe, Yutaka Suzuki, Kaoru Uchimaru,
  18th International Conference on Human Retrovirology HTLV and Related Viruses, March 7-10 2017, Tokyo, Japan



"Assessing the Impact of Contamination on RNA-seq Transcriptome Profiles",
  Sung-Joon Park, Josep Basha Gutierrez, Myungjin Moon, Kenta Nakai,
  The 15th International Conference On BioInformatics (InCOB 2016), Sep.21-23, Biopolis, Singapore
  BEST POSTER AWARD (GOLD) [photo]

"多施設培養幹細胞のトランスクリプトーム比較解析",
  朴 聖俊, 中井 謙太
  BMB2015 (第38回日本分子生物学会年会、第88回日本生化学会大会 合同大会), 2W12-p-4, Dec.1-4, 2015, Kobe, Japan

"次世代シークエンサーによる再生医療のためのヒト間葉系幹細胞の品質管理",
  岩田 隆紀, 朴 聖俊, 各務 秀明, 中井 謙太, 大和 雅之
  BMB2015 (第38回日本分子生物学会年会、第88回日本生化学会大会 合同大会), 2W12-p-2, Dec.1-4, 2015, Kobe, Japan

"ゲノム編集した患者由来疾患iPS細胞の全ゲノム解析によって明らかになったこと",
  曽根 岳史, 朴 聖俊, 田中 泰圭, 太田 悦朗, 日暮 憲道, 中井 謙太, 廣瀬 伸一, 岡野 栄之
  BMB2015 (第38回日本分子生物学会年会、第88回日本生化学会大会 合同大会), 2W12-p-3, Dec.1-4, 2015, Kobe, Japan

"Integrin αvβ3 による双方向的な造血幹細胞活性の制御",
  梅本 晃正, 松崎 優, 大和 雅之, 古澤 純一, 善本 隆之, 朴 聖俊, 中井 謙太, 須田 年生
  BMB2015 (第38回日本分子生物学会年会、第88回日本生化学会大会 合同大会), 2W12-p-5, Dec.1-4, 2015, Kobe, Japan

"OpenTein: a database of whole-slide digital images of stem cell teratomas",
  Sung-Joon Park, Yusuke Komiyama, Hirofumi Suemori, Akihiro Umezawa, Kenta Nakai,
  GIW/InCoB 2015, P166, Sept.9-11, 2015, Odaiba, Tokyo

"マウス初期胚を用いた大規模トランスクリプトーム解析",
   井上 玄志, 朴 聖俊, 古俣 麻希子, 山田 かおり, 岸本 健雄, 中井 謙太, 白髭 克彦, 大杉 美穂
  Journal of Mammalian Ova Research 31(2): 5111-5111 2014, [PDF]

"Analysis of differential regulatory network dynamics in hematopoietic stem and progenitor cells",
  Sung-Joon Park, Terumasa Umemoto, Mihoko Saito-Adachi, Masayuki Yamato, Kenta Nakai,
  Annual Conference of Japanese Society for Bioinformatics, P48, 2013

"Inferring gene regulatory network from RNA-seq data of mouse hematopoietic stem and progenitor cells",
  Sung-Joon Park, Terumasa Umemoto, Masayuki Yamato, Kenta Nakai,
  The 8th International Symposium of the Institute Network, P1, 2013

"タウリンによるTXNIP発現制御に関する研究",
   権藤 祐輔, 薩 秀夫, 朴 聖俊, 若林 俊一, 中井 謙太, 清水 誠
   日本農芸化学会2013年度大会, 3月24-28日, 仙台, 2013

"Massive-scale RNA-Seq analysis of mouse early embryo development",
  Sung-Joon Park, Makiko Komata, Fukashi Inoue, Kaori Yamada, Kenta Nakai, Miho Ohsugi, Katsuhiko Shirahige,
  The 22nd International Conference on Genomic Informatics (GIW 2011), Posters and Software Demonstrations, P-017, 2011,
  OUTSTANDING POSTER AWARD [photo]

"Transcriptome analysis of mouse early embryo development by RNA sequencing",
  Sung-Joon Park, Makiko Komata, Fukashi Inoue, Kaori Yamada, Kenta Nakai, Miho Ohsugi, Katsuhiko Shirahige,
  Annual Conference of Japanese Society for Bioinformatics, Selected oral presentation (JSBi-46), 2011

"Predicting Promoter Activities of Primary Human DNA Sequences",
  Takuma Irie, Sung-Joon Park, Riu Yamashita, Masahide Seki, Tetsushi Yada, Sumio Sugano, Yutaka Suzuki,
  The 34th Annual Meeting of the Molecular Biology Society of Japan, 3P-0196, 2011

"Predicting Promoter Activities of Primary Human DNA Sequences",
  Takuma Irie, Sung-Joon Park, Riu Yamashita, Masahide Seki, Tetsushi Yada, Sumio Sugano, Kenta Nakai, Yutaka Suzuki,
  Biochemistry and Molecular Biology (BMB2010), 3P-0694, 2010

"真核生物の遺伝子転写制御機構のモデル化と解析", 朴 聖俊, 九州工業大学情報工学部生命情報工学科講演会 (Jan.28), 2010

"大規模遺伝子プロモータ活性におけるシス制御因子の重要度推定", 朴 聖俊, 第41回 人工知能学会 分子生物情報研究会, 2009

"Comprehensive Modeling for the Combinatorial Regulation of Transcription Factors",
  Sung-Joon Park, Natsuhiro Ichinose and Tetsushi Yada,
  Annual Conference of Japanese Society for Bioinformatics, Selected oral presentation (P006/T08), 2008

"Template-free Predictionの現状と今後", 朴 聖俊, 第7回GSICシンポジウム(34回分子生物情報研究会), 2006

"粗視化モデルによるタンパク質の局所構造変化とトポロジー形成との相関解析", 朴 聖俊, 第16回 生命情報科学特別講義(CBRC), 2005.9.26

"アミノ酸配列情報からの蛋白質立体構造予測へ向けて:配列プロファイル比較に基づく部分立体構造ライブラリの構築", 朴 聖俊, 高田 彰二, 第32回知能システムシンポジウム, 289-294, 2005

"タンパク質立体構造予測技術の現状と未来:Rokko, Rokky 神戸大学理学部チーム", 高田 章二,朴 聖俊, IPAB公開セミナー, 2005

"フラグメントアセンブリ法によるタンパク質立体構造予測のための戦略的フラグメント探索", 朴 聖俊, 千見寺 浄慈, 藤墳 佳見, 高田 彰二, 日本生物物理学会第42回年会, 2P042, 2004

"タンパク質立体構造予測サーバーROKKYの開発", 朴 聖俊, 金 文珍,古田 忠臣, 高田 彰二, バイオグリッド研究会, 2004

"非同期並列GAによるタンパク質の立体構造アラインメント", 朴 聖俊,山村 雅幸, 分子プログラミング夏季セミナー, 2003

"ローカルとグローバル立体構造比較から眺めるタンパク質進化", 朴 聖俊,山村 雅幸, 第24回 SIG-MBI研究会, 2003

"Protein Structure-based Alignment - Optimized Meaningful Fragment Posture by Real-coded Genetic Algorithm -",
   Sung-Joon Park and Masayuki Yamamura, SICE Sympossium on Systems and Information 2002, 269-272, 2002

"Comparative Sensitivity of Protein Structure-based Alignment Algorithms: An Essential Approach to Identifying Positional Conservation",
   Sung-Joon Park and Masayuki Yamamura, SICE The 29th Intelligent System Symposium, 65-68, 2002

"二つのタンパク質における構造的類似度を発見するための遺伝的アルゴリズムの適用", 朴 聖俊,山村 雅幸, 第10回 SIG-MBI研究会, 2000

"遺伝的立体構造アラインメント:マルチプル立体構造アラインメントへ向けて", 朴 聖俊,山村 雅幸, SICE第27回知能システムシンポジウム, 123-126, 2000

"GAによる立体構造アラインメント", 朴 聖俊,山村 雅幸, SICE第12回自律分散システム, 323-328, 2000



Human Genome Center The University of Tokyo