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	A computational approach for deciphering the interactions between proximal and distal gene regulators in GC B-cell response Sung-Joon Park* and Kenta Nakai NAR Genomics and Bioinformatics in press (2024)
	HyGAnno: Hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data Weihang Zhang, Yang Cui, Bowen Liu, Martin Loza, Sung-Joon Park, and Kenta Nakai Briefings in Bioinformatics 25:bbae152 (2024)  [BIB]  [PUBMED]
	Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility Satoko Ishii, Taishi Kakizuka, Sung-Joon Park, Ayako Tagawa, Chiaki Sanbo, Hideyuki Tanabe, Yasuyuki Ohkawa, Mahito Nakanishi, Kenta Nakai, Yusuke Miyanari Nature Genetics 56:473-482 (2024)  [Nat Genet]  [PUBMED]  [Press Release]
	Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization Yubo Zhang, Wenbo Yang, Yutaro Kumagai, Martin Loza, Weihang Zhang, Sung-Joon Park and Kenta Nakai Frontiers in Immunology 14:1304778 (2023)  [Front. Immunol]  [PUBMED]
	Signaling Pathway of Taurine-Induced Upregulation of TXNIP Hideo Satsu, Yusuke Gondo, Hana Shimanaka, Masato Imae, Shigeru Murakami, Kenji Watari, Shunichi Wakabayashi, Sung-Joon Park, Kenta Nakai & Makoto Shimizu Metabolites 12:636 (2022)  [MDPI]  [PUBMED]
	Generation of 3D lacrimal gland organoids from human pluripotent stem cells Ryuhei Hayashi, Toru Okubo, Yuji Kudo, Yuki Ishikawa, Tsutomu Imaizumi, Kenji Suzuki, Shun Shibata, Tomohiko Katayama, Sung-Joon Park, Robert D. Young, Andrew J. Quantock & Kohji Nishida Nature 605:126-131 (2022)  [Nature]  [PUBMED]  [Press Release]
	Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A. Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Shohei Noma, Shuhei Noguchi, Takeya Kasukawa, Akira Hasegawa, Harukazu Suzuki, Hiromi Nishiyori-Sueki, Martin C. Frith, FANTOM consortium (incl. Sung-Joon Park, Kenta Nakai), Clément Chatelain, Piero Carninci, Michiel J. L. de Hoon, Wyeth W. Wasserman, Laurent Bréhélin & Charles-Henri Lecellier Nature Communications 12:3297 (2021)  [Nat Commun.]  [PUBMED]
	Characterizing promoter and enhancer sequences by a deep learning method Xin Zeng, Sung-Joon Park and Kenta Nakai Frontiers in Genetics 12:681259 (2021)  [Front. Genet.]  [PUBMED]
	OpenContami: A web-based application for detecting microbial contaminants in next-generation sequencing data Sung-Joon Park* and Kenta Nakai Bioinformatics 37(18):3021-3022 (2021)  [Bioinformatics]  [PUBMED]
	A semi-supervised deep learning approach for predicting the functional effects of genomic non-coding variations Hao Jia, Sung-Joon Park and Kenta Nakai BMC Bioinformatics 22(Suppl 6):128 (2021)  [BMC]  [PUBMED]
	Existence and possible roles of independent non-CpG methylation in the mammalian brain Jong-Hun Lee, Yutaka Saito, Sung-Joon Park, Kenta Nakai DNA Research 27:dsaa020 (2020)  [DNA Res]  [PUBMED]
	RNA-sequencing reveals positional memory of multipotent mesenchymal stromal cells from oral and maxillofacial tissue transcriptomes Satoru Onizuka, Yasuharu Yamazaki, Sung-Joon Park, Takayuki Sugimoto, Yumiko Sone, Sebastian Sjöqvist, Michihiko Usui, Akira Takeda, Kenta Nakai, Keisuke Nakashima, Takanori Iwata BMC Genomics 21, 417 (2020)  [BMC]  [PUBMED]
	HHEX promotes myeloid transformation in cooperation with mutant ASXL1 Reina Takeda, Shuhei Asada, Sung-Joon Park, Akihiko Yokoyama, Hans Becker, Akinori Kanai, Valeria Visconte, Courtney Hershberger, Yasutaka Hayashi, Taishi Yonezawa, Moe Tamura, Tsuyoshi Fukushima, Yosuke Tanaka, Tomofusa Fukuyama, Akiko Matsumoto, Satoshi Yamasaki, Kenta Nakai, Satoshi Yamazaki, Toshiya Inaba, Tatsuhiro Shibata, Daichi Inoue, Hiroaki Honda, Susumu Goyama, Jaroslaw Maciejewski, and Toshio Kitamura Blood, blood.2019004613 (2020)  [Blood]  [PUBMED]
	A systematic sequencing-based approach for microbial contaminant detection and functional inference Sung-Joon Park, Satoru Onizuka, Masahide Seki, Yutaka Suzuki, Takanori Iwata, and Kenta Nakai BMC Biology (2019), 17(1):72  [BMC]  [PUBMED]
	Broad heterochromatic domains open in gonocyte development prior to de novo DNA methylation Soichiro Yamanaka, Hidenori Nishihara, Hidehiro Toh, Luis Augusto Eijy Nagai, Kosuke Hashimoto, Sung-Joon Park, Aoi Shibuya, Ana Maria Suzuki, Yujiro Tanaka, Kenta Nakai, Piero Carninci, Hiroyuki Sasaki, and Haruhiko Siomi Dev. Cell (2019), S1534-5807(19)30629-X  [Dev.Cell]  [PUBMED]
	Analyzing the 3D chromatin organization coordinating with gene expression regulation in B-cell lymphoma Luis A.E. Nagai, Sung-Joon Park and Kenta Nakai BMC Med Genomics (2019), 11 (Suppl 7):127  [BMC]  [PUBMED]
	Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s Jong-Hun Lee, Sung-Joon Park and 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]
	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]
	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
	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]

	NGSによる細胞製品の有効性及び安全性の評価 朴 聖俊 特集:歯根膜由来細胞シートによる歯周組織再生治療, Precision Medicine (北隆館), 7(1):20-23, 2024
	タウリンによるTXNIP転写活性亢進機構の解析 薩 秀夫, 権藤 祐輔, 嶋中 花, 井前 正人, 村上 茂, 和多利 研二, 若林 俊一, 朴 聖俊, 中井 謙太, 清水 誠 タウリンリサーチ, 8:11-13, 2022
	スパイクイン，NGS定量標準化の「量叉」 朴 聖俊 実験医学別冊 「クロマチン解析実践プロトコール」（羊土社）, 編集：大川恭行, 宮成悠介, pp 22-24, 2020
	Homeobox Transcription Factor Hhex Promotes Myeloid Leukemia in Cooperation with Mutant ASXL1 Reina Takeda, Shuhei Asada, Sung-Joon Park, Akihiko Yokoyama, Akinori Kanai, Valeria Visconte, Courtney Hershberger, Yasutaka Hayashi, Taishi Yonezawa, Moe Tamura, Tomofusa Fukuyama, Akiko Matsumoto, Satoshi Yamasaki, Kenta Nakai, Toshiya Inaba, Tatsuhiro Shibata, Daichi Inoue, Hiroaki Honda, Susumu Goyama, Jaroslaw P. Maciejewski, Toshio Kitamura Blood (2019), 134(Supplement_1): 2525  doi.org/10.1182/blood-2019-126663
	Genome-wide scanning of gene expression Sung-Joon Park* in Encyclopedia of Bioinformatics and Computational Biology, Academic Press, Vol.3, Pages 452-462, 2019  [ScienceDirect]
	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]
	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 Investigative Ophthalmology & Visual Science (2016), 57(12):4906, ARVO Annual Meeting Abstract  [IOVS]
	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]

STAIG: Spatial Transcriptomics Analysis via Image-Aided Graph Contrastive Learning for Domain Exploration and Alignment-Free Integration

Yitao Yang, Yang Cui, Sung-Joon Park, Xin Zeng, Yubo Zhang, Martin Loza Lopez, Kenta Nakai
2023,   bioRxiv 2023.12.18.572279, doi: https://doi.org/10.1101/2023.12.18.572279

HyGAnno: Hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data

Weihang Zhang, Yang Cui, Bowen Liu, Martin Loza Lopez, Sung-Joon Park, Kenta Nakai
2023,   bioRxiv 2023.11.29.569114, doi: https://doi.org/10.1101/2023.11.29.569114

A computational approach for deciphering the interactions between proximal and distal regulators in B cell differentiation

Sung-Joon Park and Kenta Nakai
2023,   bioRxiv 2023.11.02.565268, doi: https://doi.org/10.1101/2023.11.02.565268

Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization

Yubo Zhang, Wenbo Yang, Yutaro Kumagai, Martin Loza, Sung-Joon Park, Kenta Nakai
2023,  bioRxiv 2023.09.27.559849, doi: https://doi.org/10.1101/2023.09.27.559849

RNA-sequencing reveals positional memory of multipotent mesenchymal stromal cells from oral and maxillofacial tissue transcriptomes

Satoru Onizuka, Yasuharu Yamazaki, Sung-Joon Park, Takayuki Sugimoto, Yumiko Sone, Sebastian Sjöqvist, Michihiko Usui, Akira Takeda, Kenta Nakai, Keisuke Nakashima, Takanori Iwata
2020,  [Research Square]

Existence and possible roles of independent non-CpG methylation in mammalian brain

Jong-Hun Lee, Yutaka Saito, Sung-Joon Park, Kenta Nakai
2020,  [Research Square]

A systematic NGS-based approach for contaminant detection and functional inference

Sung-Joon Park, Satoru Onizuka, Masahide Seki, Yutaka Suzuki, Takanori Iwata, Kenta Nakai
2019,  bioRxiv 741934, doi: https://doi.org/10.1101/741934

RNA-Sequencing Reveals Unique Features of Multipotent Mesenchymal Stromal Cells from Oral and Maxillofacial Tissue Transcriptomes

Satoru Onizuka, Yasuharu Yamazaki, Sung-Joon Park, Takayuki Sugimoto, Yumiko Sone, Sebastian Sjöqvist, Michihiko Usui, Akira Takeda, Kenta Nakai, Keisuke Nakashima, Takanori Iwata
2019,  [SSRN]

機械学習法によるびまん性B細胞リンパ腫の新規バイオマーカーCOPS5の同定

戴 彧童, 朴 聖俊, 李 婧美, ⼭本 圭太, 合⼭ 進, 中井 謙太
第46回日本分子生物学会年会, 1P-819, Dec. 6-8, 2023, 神戸

Exploring the role of hysteresis in macrophage lipid metabolism and repolarization memory

Yubo Zhang, Yutaro Kumagai, Sung-Joon Park and Kenta Nakai
The 22nd International Conference on Bioinformatics (InCoB 2023), Nov. 12-15, 2023, Brisbane, Australia

Identification of COPS5 as a novel biomarker of diffuse large B cell lymphoma by a machine-learning algorithm

Yutong Dai, Sung-Joon Park, Jingmei Li, Keita Yamamoto, Susumu Goyama and Kenta Nakai
The 22nd International Conference on Bioinformatics (InCoB 2023), Nov. 12-15, 2023, Brisbane, Australia

A graph-embedding approach dissecting enhancer-cofactor-promoter interactions

Sung-Joon Park and Kenta Nakai
The 22nd International Conference on Bioinformatics (InCoB 2023), Nov. 12-15, 2023, Brisbane, Australia

Computational modeling of the interactions between proximal and distal transcriptional regulators

Sung-Joon Park and Kenta Nakai
The 4th GENOME MODALITY Annual meeting, Sep. 21-23, 2023, Karolinska Institute, Sweden

A BERT-based prediction model of human protein sub-cellular localization

Wanzhe Xu, Sung-Joon Park, and Kenta Nakai
The 4th GENOME MODALITY Annual meeting, Sep. 21-23, 2023, Karolinska Institute, Sweden

Prediction of global splice-site selection considering long-range effects using Transformer

Yuna Miyachi, Sung-Joon Park, and Kenta Nakai
The 4th GENOME MODALITY Annual meeting, Sep. 21-23, 2023, Karolinska Institute, Sweden

長距離および短距離転写制御因子間相互作用の計算モデリング手法の開発

朴 聖俊, 中井 謙太
第12回生命医薬情報学連合大会 (IIBMP 2023), OS-3/P-46, Sep. 7-9, 2023, Kashiwa, Japan
 BEST ORAL PRESENTATION AWARD

Meta co-expression analysis of genetic heterogeneity in GBM using single-cell RNA-seq data

Taisuke Hori, Sung-Joon Park and Kenta Nakai
生命医薬情報学連合大会 (IIBMP 2021), Sep. 27-29, 2021, Japan
 BEST ORAL PRESENTATION AWARD

A Semi-supervised Deep Learning Approach for Predicting the Functional Effects of Genomic Non-coding Variations

Hao Jia, Sung-Joon Park and Kenta Nakai
The 19th International Conference on Bioinformatics (InCoB 2020), Oral, Nov. 25-29, 2020, VIRTUALLY
 BEST PAPER PRESENTATION AWARD

Characterizing Promoter and Enhancer Sequences by a Deep Learning Method

Xin Zeng, Sung-Joon Park and Kenta Nakai
The 19th International Conference on Bioinformatics (InCoB 2020), Oral, Nov. 25-29, 2020, VIRTUALLY

Analyzing the impact of inter-chromosomal interactions on B cell development by linear regression modeling

Sung-Joon Park
生命医薬情報学連合大会 (IIBMP 2020), Oral O-6, Sep. 1-3, 2020, Japan
 EXCELLENT ORAL PRESENTATION AWARD

Co-expression network analysis of E3 ligase genes in embryonic stem cells and cell fate specification

Darina Obukhova, Sung-Joon Park and Kenta Nakai
生命医薬情報学連合大会 (IIBMP 2020), Poster P-40, Sep. 1-3, 2020, Japan

歯根膜組織由来間葉系幹細胞シートによる歯周組織再生

鬼塚 理, 朴 聖俊, 貝淵 信之, 妻沼 有香, 安藤 智博, 中井 謙太, 岩田 隆紀
第19回日本再生医療学会総会, Mar. 12-14, 2020, PACIFICO Yokohama, Japan

Regression-based promoter modeling with local 3D chromatin structure

Sung-Joon Park
CHROMOSOME DYNAMICS (An international symposium on chromatin and chromosome stability), Dec. 8-10, 2019, Basel, Switzerland

脂肪由来幹細胞の運命決定と分化制御に関する時空間特異的ヒストン修飾のin-silico特定

山谷 恭代, 朴 聖俊, 中井 謙太
第42回 日本分子生物学会年会, 2P-0091, Dec. 3-6, 2019, 福岡, 日本

Genome-wide chromatin structural analysis reveals inter-chromosomal translocations in B-cell lymphoma

Luis A.E. Nagai, Sung-Joon Park, Kenta Nakai
The 42nd Annual Meeting of the Molecular Biology Society of Japan, 1P-0002, Dec. 3-6, 2019, Fukuoka, Japan

脂肪由来幹細胞の分化制御に働くエピジェネティック因子のin-silico同定

山谷 恭代, 朴 聖俊, 中井 謙太
IIBMP2019, O-1 (oral), Sep.9-11, 2019, Tokyo, Japan

Analyzing the 3D Chromatin Organization Coordinating with Gene Expression Regulation in B-cell Lymphoma

Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai
IIBMP2019, O-3 (oral), Sep.9-11, 2019, Tokyo, Japan

OpenContami: A Web-based Application for Detecting Microbial Contaminants in Next-generation Sequencing

Sung-Joon Park, Satoru Onizuka, Masahide Seki, Yutaka Suzuki, Takanori Iwata and Kenta Nakai
IIBMP2019, O-10 (oral), Sep.9-11, 2019, Tokyo, Japan

Analyzing the 3D Chromatin Organization Coordinating with Gene Expression Regulation in B-cell Lymphoma

Luis Augusto Eijy Nagai, Sung-Joon Park and Kenta Nakai
IIBMP2019, P-1 (poster), Sep.9-11, 2019, Tokyo, Japan

脂肪由来幹細胞の分化制御における時期特異的ヒストン修飾のin-silico検出

山谷 恭代, 朴 聖俊, 中井 謙太
IIBMP2019, P-56 (poster), Sep.9-11, 2019, Tokyo, Japan

マウス胎仔期生殖細胞におけるクロマチンリプログラミング

山中 総一郎, 西原 秀典, 藤 英博, Luis Augusto Eijy Nagai, 橋本 浩介, 朴 聖俊, 渋谷 あおい, Ana Maria Suzuki, 田中 悠二郎, 中井 謙太, Piero Carninci, 佐々木 裕之, 塩見 春彦
第21回日本RNA学会年会, P-45, Jul.17-19, 2019, Tokyo, Japan

Host-unmapped NGS reads shape the prevalence of microbial contamination

Sung-Joon Park and Kenta Nakai
The Biology of Genomes, P188, May 7-11, 2019, Cold Spring Harbor Laboratory, NY, USA

Genome-wide chromatin structural analysis reveals inter-chromosomal translocations in B-cell lymphoma cell line

Luis AE Nagai, Sung-Joon Park and Kenta Nakai
The Biology of Genomes, P177, May 7-11, 2019, Cold Spring Harbor Laboratory, NY, USA

Profiling microbial contamination by exploiting host-unmapped NGS reads

Sung-Joon Park and Kenta Nakai
Revolutionizing Next-Generation Sequencing 2019 (RNGS19), P36, Mar. 25-26, 2019, Antwerp, Belgium

同種歯根膜由来間葉系幹細胞シートによる歯周組織の再建

岩田 隆紀, 鬼塚 理, 妻沼 有香, 朴 聖俊, 中井 謙太, 安藤 智博
第18回日本再生医療学会総会, SY-45-3, Mar. 21-23, 2019, Kobe, Japan

ゴノサイトでの新規DNAメチル化に付随して起こる多段階のクロマチンの緩み

山中 総一郎, 西原 秀典, 藤 英博, 永井 映司, 橋本 浩介, 朴 聖俊, 渋谷 あおい, Ana Maria Suzuki, 田中 悠二郎, 中井 謙太, Piero Carninci, 佐々木 裕之, 塩見 春彦
第41回日本分子生物学会年会, 3AW-09-1 (2P-0007), Nov. 28-30, 2018, Yokohama, Japan

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), P-55, Sep. 26-28, 2018, 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, 2018, New Delhi, India
  BEST ORAL PRESENTATION AWARD

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

精子エピジェネティックマップ：その本質とリプログラミング様式の解明に向けて

岡田 由紀, 山口 幸佑, 牧野 吉倫, 朴 聖俊, 加藤 由起, 中井 謙太, 白髭 克彦
第44回日本毒性学会学術年会, 2017年7月10日-12日, S6-3, 横浜, 日本

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)

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

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