Hideya Kawaji

Profile Information

Affiliation: Associate Center Director, Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science
: RIKEN Center for Integrative Medical Sciences, RIKEN

J-GLOBAL ID: 201901013468136481
researchmap Member ID: B000367691

Research Areas

Life sciences / Systems genomics /

Research History

Apr, 2023 - Present

RIKEN Center for Integrative Medical Sciences, RIKEN

Papers

165

An atlas of transcribed enhancers across helper T cell diversity for decoding human diseases.

Akiko Oguchi, Akari Suzuki, Shuichiro Komatsu, Hiroyuki Yoshitomi, Shruti Bhagat, Raku Son, Raoul Jean Pierre Bonnal, Shohei Kojima, Masaru Koido, Kazuhiro Takeuchi …

Science (New York, N.Y.), 385(6704) eadd8394, Jul 5, 2024
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Brian Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez …

Nature methods, 21(7) 1349-1363, Jul, 2024
Homologous recombination contributes to the repair of acetaldehyde-induced DNA damage.

Kosuke Yamazaki, Tomohiro Iguchi, Yutaka Kanoh, Kazuto Takayasu, Trinh Thi To Ngo, Ayaka Onuki, Hideya Kawaji, Shunji Oshima, Tomomasa Kanda, Hisao Masai …

Cell cycle (Georgetown, Tex.), 23(4) 369-384, Feb, 2024
Use of clinical variables for preoperative prediction of lymph node metastasis in endometrial cancer.

Yuta Ueno, Emiko Yoshida, Shuko Nojiri, Tomoyasu Kato, Takashi Ohtsu, Toshiyuki Takeshita, Shunji Suzuki, Hiroshi Yoshida, Ken Kato, Masayoshi Itoh …

Japanese journal of clinical oncology, 54(1) 38-46, Jan 7, 2024
ROR2 expression predicts human induced pluripotent stem cell differentiation into neural stem/progenitor cells and GABAergic neurons.

Takuya Kuroda, Satoshi Yasuda, Satoko Matsuyama, Takumi Miura, Rumi Sawada, Akifumi Matsuyama, Yumiko Yamamoto, Masaki Suimye Morioka, Hideya Kawaji, Takeya Kasukawa …

Scientific reports, 14(1) 690-690, Jan 6, 2024
mRNA-based generation of marmoset PGCLCs capable of differentiation into gonocyte-like cells.

Musashi Kubiura-Ichimaru, Christopher Penfold, Kazuaki Kojima, Constance Dollet, Haruka Yabukami, Katsunori Semi, Yasuhiro Takashima, Thorsten Boroviak, Hideya Kawaji, Knut Woltjen …

Stem cell reports, 18(10) 1987-2002, Oct 10, 2023
PLA2G2E-mediated lipid metabolism triggers brain-autonomous neural repair after ischemic stroke.

Akari Nakamura, Seiichiro Sakai, Yoshitaka Taketomi, Jun Tsuyama, Yoshimi Miki, Yuichiro Hara, Nobutaka Arai, Yuki Sugiura, Hideya Kawaji, Makoto Murakami …

Neuron, 111(19) 2995-3010, Oct 4, 2023
Single-Cell RNA-Seq Reveals LRRC75A-Expressing Cell Population Involved in VEGF Secretion of Multipotent Mesenchymal Stromal/Stem Cells Under Ischemia.

Takumi Miura, Tsukasa Kouno, Megumi Takano, Takuya Kuroda, Yumiko Yamamoto, Shinji Kusakawa, Masaki Suimye Morioka, Tohru Sugawara, Takamasa Hirai, Satoshi Yasuda …

Stem cells translational medicine, 12(6) 379-390, Jun 15, 2023
Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning.

Masaru Koido, Chung-Chau Hon, Satoshi Koyama, Hideya Kawaji, Yasuhiro Murakawa, Kazuyoshi Ishigaki, Kaoru Ito, Jun Sese, Nicholas F Parrish, Yoichiro Kamatani …

Nature biomedical engineering, 7(6) 830-844, Jun, 2023
Spatial transcriptome of developmental mouse brain reveals temporal dynamics of gene expressions and heterogeneity of the claustrum

Yuichiro Hara, Takuma Kumamoto, Naoko Yoshizawa-Sugata, Kumiko Hirai, Song Xianghe, Hideya Kawaji, Chiaki Ohtaka-Maruyama

Apr 13, 2023
CALML5 is a novel diagnostic marker for differentiating thymic squamous cell carcinoma from type B3 thymoma.

Koichiro Kanamori, Kentaro Suina, Takehito Shukuya, Fumiyuki Takahashi, Takuo Hayashi, Kieko Hara, Tsuyoshi Saito, Yoichiro Mitsuishi, Shoko Sonobe Shimamura, Wira Winardi …

Thoracic cancer, 14(12) 1089-1097, Apr, 2023
Urinary exosomal microRNAs as predictive biomarkers for persistent psychotic-like experiences.

Yasufumi Tomita, Kazuhiro Suzuki, Syudo Yamasaki, Kazuya Toriumi, Mitsuhiro Miyashita, Shuntaro Ando, Kaori Endo, Akane Yoshikawa, Koichi Tabata, Satoshi Usami …

Schizophrenia (Heidelberg, Germany), 9(1) 14-14, Mar 11, 2023
Application of spatial transcriptomics analysis using the Visium system for the mouse nasal cavity after intranasal vaccination.

Sakiko Toyama, Tomoko Honda, Sadahiro Iwabuchi, Shinichi Hashimoto, Kenzaburo Yamaji, Yuko Tokunaga, Yusuke Matsumoto, Hideya Kawaji, Takashi Miyazaki, Yoshiaki Kikkawa …

Frontiers in immunology, 14 1209945-1209945, 2023
Two ovarian candidate enhancers, identified by time series enhancer RNA analyses, harbor rare genetic variations identified in ovarian insufficiency.

Ryuichi Nakagawa, Kei Takasawa, Maki Gau, Atsumi Tsuji-Hosokawa, Hideya Kawaji, Yasuhiro Murakawa, Shuji Takada, Masashi Mikami, Satoshi Narumi, Maki Fukami …

Human molecular genetics, 31(13) 2223-2235, Jul 7, 2022
DUX4 is a multifunctional factor priming human embryonic genome activation.

Sanna Vuoristo, Shruti Bhagat, Christel Hydén-Granskog, Masahito Yoshihara, Lisa Gawriyski, Eeva-Mari Jouhilahti, Vipin Ranga, Mahlet Tamirat, Mikko Huhtala, Ida Kirjanov …

iScience, 25(4) 104137-104137, Apr 15, 2022
Exonic deletions in IMMP2L in schizophrenia with enhanced glycation stress subtype.

Akane Yoshikawa, Itaru Kushima, Mitsuhiro Miyashita, Kazuhiro Suzuki, Kyoka Iino, Kazuya Toriumi, Yasue Horiuchi, Hideya Kawaji, Norio Ozaki, Masanari Itokawa …

PloS one, 17(7) e0270506, 2022
Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset.

Vasanthan Jayakumar, Osamu Nishimura, Mitsutaka Kadota, Naoki Hirose, Hiromi Sano, Yasuhiro Murakawa, Yumiko Yamamoto, Masataka Nakaya, Tomoyuki Tsukiyama, Yasunari Seita …

Scientific data, 8(1) 159-159, Jun 28, 2021
Ex vivo conditioning of peripheral blood mononuclear cells of diabetic patients promotes vasculogenic wound healing.

Rica Tanaka, Rie Ito-Hirano, Satoshi Fujimura, Kayo Arita, Hiroko Hagiwara, Tomoya Mita, Masayoshi Itoh, Hideya Kawaji, Takasuke Ogawa, Hirotaka Watada …

Stem cells translational medicine, 10(6) 895-909, Jun, 2021
Dysregulation of post-transcriptional modification by copy number variable microRNAs in schizophrenia with enhanced glycation stress.

Akane Yoshikawa, Itaru Kushima, Mitsuhiro Miyashita, Kazuya Toriumi, Kazuhiro Suzuki, Yasue Horiuchi, Hideya Kawaji, Shunya Takizawa, Norio Ozaki, Masanari Itokawa …

Translational psychiatry, 11(1) 331-331, May 28, 2021
Cancer-associated fibroblast migration in non-small cell lung cancers is modulated by increased integrin α11 expression.

Moe Iwai, Miniwan Tulafu, Shinsaku Togo, Hideya Kawaji, Kotaro Kadoya, Yukiko Namba, Jin Jin, Junko Watanabe, Takahiro Okabe, Moulid Hidayat …

Molecular oncology, 15(5) 1507-1527, May, 2021

Misc.

INTRARED: a data platform for transcriptional regulation that integrates cis-regulatory elements, trans-factors, and epigenome information

粕川雄也, WALKER Scott, 長谷川哲, THALHATH Nishad, 信定知江, 沖真弥, 高田豊行, 桝屋啓志, 川路英哉

日本分子生物学会年会プログラム・要旨集(Web), 46th, 2023
尿中エキソソーム含有miRNAによる精神病様体験の持続の予測

富田康文, 鈴木一浩, 田畑光一, 川路英哉, 宮下光弘, 鳥海和也, 山崎修道, 安藤俊太郎, 笠井清登, 西田淳志 …

日本生化学会大会プログラム・講演要旨集, 95回 2P-315, Nov, 2022
糖化ストレスを伴う統合失調症におけるIMMP2L遺伝子欠失-臨床特徴と新規治療法開発の可能性

吉川茜, 久島周, 宮下光弘, 鈴木浩一, 鳥海和也, 堀内泰江, 川路英哉, 瀧澤俊也, 尾崎紀夫, 糸川昌成 …

精神神経学雑誌, (2021特別号) S573-S573, Sep, 2021
Predicting cell-type-specific non-coding RNA transcription from genome sequence

Masaru Koido, Chung-Chau Hon, Satoshi Koyama, Hideya Kawaji, Yasuhiro Murakawa, Kazuyoshi Ishigaki, Kaoru Ito, Jun Sese, Yoichiro Kamatani, Piero Carninci …

bioRxiv, Mar 30, 2020
遺伝子モデルと核酸医薬創薬に資するゲノム・RNAデータベース

78(2), Mar, 2020
非ヒト霊長類のトランスクリプトーム・アトラス

廣瀬直毅, 廣瀬直毅, 依馬正次, 佐々木えりか, GUSEV Oleg, GUSEV Oleg, 河合純, 村川泰裕, 村川泰裕, 川路英哉 …

日本分子生物学会年会プログラム・要旨集(Web), 43rd, 2020
腫瘍免疫と微小環境非小細胞肺癌における免疫関連分子の包括的遺伝子発現解析

高持一矢, 茂櫛薫, 林大久生, 川路英哉, 伊藤昌可, 林崎良英, 鈴木健司

肺癌, 59(6) 576-576, Nov, 2019
腫瘍免疫と微小環境非小細胞肺癌における免疫関連分子の包括的遺伝子発現解析

高持一矢, 茂櫛薫, 林大久生, 川路英哉, 伊藤昌可, 林崎良英, 鈴木健司

肺癌, 59(6) 576-576, Nov, 2019
心筋細胞に分化指向性を有するiPS細胞株を選択するためのバイオマーカーの探索

大橋文哉, 大橋文哉, 大橋文哉, 宮川繁, 安田智, 三浦巧, 黒田拓也, 伊藤昌可, 川路英哉, 伊東絵望子 …

日本再生医療学会総会(Web), 18th, 2019
核酸医薬創薬に資する霊長類オミックスデータベースの構築

廣瀬直毅, 村川泰裕, 川路英哉, 川路英哉, 川路英哉, 河合純

日本核酸医薬学会年会講演要旨集, 5th, 2019
非ヒト霊長類ゲノムの非コード領域の機能解析

廣瀬直毅, 依馬正次, 佐々木えりか, 河合純, 村川泰裕, 川路英哉, 川路英哉, 川路英哉

日本分子生物学会年会プログラム・要旨集(Web), 42nd, 2019
Hi-Cを用いたカニクイザルとマーモセットの染色体スケールゲノムスキャフォールディング

門田満隆, 西村理, JAYAKUMAR Vasanthan, 榊原康文, 井上貴史, 佐々木えりか, 依馬正次, 佐野浩美, 廣瀬直毅, 村川泰裕 …

日本分子生物学会年会プログラム・要旨集(Web), 42nd, 2019
【なぜ、いま核酸医薬なのか次なる創薬モダリティの本命】核酸医薬品開発とRNAデータベース

廣瀬直毅, 河合純, 川路英哉

実験医学, 37(1) 40-46, Jan, 2019 Invited
Primate DNA/RNA database; development and application for medicine

KAWAI Jun, NAKAYA Masataka, SASAKI Erika, INOUE Takashi, WATANABE Toshiaki, SAKAKIBARA Yasubumi, JAYAKUMAR Vasanthan, NAITO Yuki, MURAKAWA Yasuhiro, KAWAJI Hideya …

Annual Meeting of the Japanese Society of Toxicology, 46 S15-4, 2019
Databases for sequences and expression of non-coding RNAs

廣瀬直毅, 川路英哉

医学のあゆみ, 267(8) 603-608, Nov 24, 2018
肺腺癌における免疫関連分子の包括的遺伝子発現解析

高持一矢, 細谷理樹, 茂櫛薫, 林大久生, 川路英哉, 伊藤昌可, 林崎良英, 鈴木健司

肺癌, 58(6) 579-579, Oct, 2018
次世代ヒト科学を推進するゲノム基盤の構築

村川泰裕, 廣瀬直毅, 佐野浩美, 川路英哉, 川路英哉, 河合純

日本分子生物学会年会プログラム・要旨集(Web), 41st, 2018
非ヒト霊長類のトランスクリプトーム解析

廣瀬直毅, 佐野浩美, 八木研, 岡崎康司, 渡部聡朗, 井上貴史, 佐々木えりか, 中家雅隆, 築山智之, 清田弥寿成 …

日本分子生物学会年会プログラム・要旨集(Web), 41st, 2018
ヒトmRNA/pre-mRNA/lncRNA/pre-lncRNAデータベースの構築

廣瀬直毅, 内藤雄樹, 村川泰裕, 河合純, 川路英哉, 川路英哉

日本核酸医薬学会年会講演要旨集, 4th, 2018
心筋細胞への高い分化指向性を有するiPS細胞株のスクリーニング法の開発

大橋文哉, 大橋文哉, 大橋文哉, 宮川繁, 安田智, 三浦巧, 黒田拓也, 齋藤充弘, 八代健太, 増田茂夫 …

日本再生医療学会総会(Web), 17th, 2018

Books and Other Publications

RとBioconductorを用いたバイオインフォマティクス

Gentleman Robert, Carey Vincent J, Huber Wolfgang, Irizarry Rafael A, Dudoit Sandrine, 荒川和晴, 粕川雄也, 川路英哉, 河野信, 神田将和, 鈴木治夫, 田中伸也, 中尾光輝, 長嶋剛史, 二階堂愛, 宮本真理

丸善出版, 2012 (ISBN: 9784621062500)

Presentations

血管生検を用いた網羅的トランスクリプトーム解析による巨細胞性動脈炎の分子病態の解明

渡邊伸昌, 杉原誠人, 原雄一郎, 西藤泰昌, 鴻江真維, 川路英哉

第46回日本分子生物学会年会 2023年12月, Dec 7, 2023
Unraveling the genomic code in gene regulation

Hideya Kawaji

TMIMS International Symposium on Cells and Chromosomes, Oct 16, 2023
転写制御理解のためのゲノムワイドなシスエレメントデータベースfanta.bio

粕川雄也, SCOTT Walker, 長谷川哲, NISHAD Thalhath, 高田豊行, 桝屋啓志, 川路英哉

日本生化学会大会(Web), 2023
Genomics resource of non human primates: recent updates and future perspective

KAWAJI, Hideya

43th annual meeting of the molecular biology society of Japan,, Dec, 2020 Invited
Functional Annotation of Non-Coding Genomic Regions of Non-Human Primates

Hirose Naoki, Ema Masatsugu, Sasaki Erika, Gusev Oleg, Kawai Jun, Murakawa Yasuhiro, Hideya Kawaji

International Plant & Animal Genome XXVIII, 2020 Invited
Learn genomics from AI for interpreting GWAS findings, The 6th RIKEN-KI-SciLifeLab Symposium

Koido Masaru, Hon Chung Chau, Kawaji Hideya, Murakawa Yasuhiro, Kamatani Yoichiro, Carninci Piero, Terao Chikashi

Biomedical Data for Artificial Intelligence, 2019
Intratumoral heterogeneity of multiple myeloma revealed by single-cell RNA sequencing, EMBO Workshop

Hirabayashi Shigeki, Yamazaki Hiroyuki, Shirakawa Kotaro, Takaori-Kondo Akifumi, Kawaji Hideya, Murakawa Yasuhiro

Single cell biology, 2019
転写開始点リファレンスデータセットの構築

Abugessaisa Imad, Noguchi Shuhei, Hasegawa Akira, Kondo Atsushi, Kawaji Hideya, Carninci Piero, Kasukawa Takeya

第42会MBSJ, 2019
Chromosome-scale genome scaffolding of crab-eating macaque and common marmoset by Hi-C

Kadota Mitsutaka, Nishimura Osamu, Jayakumar Vasanthan, Sakakibara Yasubumi, Inoue Takashi, Sasaki Erika, Ema Masatsugu, Sano Hiromi, Hirose Naoki, Murakawa Yasuhiro, Hideya Kawaji, Kawai Jun, Kuraku Shigehiro

第42会MBSJ, 2019
Long-read sequencing and assembly of Common Marmoset and Crab-eating Macaque results in high-quality, chromosome-scale genome assemblies with over 100 fold improvements in contiguity

Jayakumar Vasanthan, Kadota Mitsutaka, Nishimura Osamu, Kuraku Shigehiro, Inoue Takashi, Sasaki Erika, Ema Masatsugu, Sano Hiromi, Hirose Naoki, Murakawa Yasuhiro, Hideya Kawaji, Kawai Jun, Sakakibara Yasubumi

第42会MBSJ, 2019
Development of a genome and RNA database of primates for nucleic acid-based drugs

Hirose Naoki, Murakawa Yasuhiro, Kawaji Hideya, Kawai Jun

第51回核酸医薬学会, 2019
Intratumoral heterogeneity of multiple myeloma revealed by single-cell RNA sequencing

Hirabayashi Shigeki, Yamazaki Hiroyuki, Shirakawa Kotaro, Takaori-Kondo Akifumi, Kawaji Hideya, Murakawa Yasuhiro

The 81st Annual Meeting of the Japanese Society of Hematology, 2019
"Transcribed cis-regulatory elements across primates

H. Kawaji, N. Hirose, M. Ema, E. Sasaki, J. Kawai

American Society of Human Genetics, 2019
Machine learning using nonlinear stacking method for predicting long non-coding RNA and enhancer transcription from genome sequence

Koido Masaru, Hon Chung Chau, Kawaji Hideya, Murakawa Yasuhiro, Kamatani Yoichiro, Carninci Piero, Terao Chikashi

American Society of Human Genetics, 2019
refTSS: a reference dataset of human and mouse transcription start sites

Abugessaisa Imad, Noguchi Shuhei, Hasegawa Akira, Kondo Atsushi, Kawaji Hideya, Carninci Piero, Kasukawa Takeya

Genome Informatics, 2019
Functional annotation of non-coding regions in the genome of non-human primates,

Hirose Naoki, Ema Masatsugu, Sasaki Erika, Kawai Jun, Murakawa Yasuhiro, Kawaji Hideya

The Non-Coding Genome, 2019
Functional annotation of non-coding genomic regions in non-human primates

Hirose Naoki, Ema Masatsugu, Sasaki Erika, Kawai Jun, Murakawa Yasuhiro, Kawaji Hideya

The 31st annual meeting on The Biology of Genomes, 2019
核酸医薬創薬に資する霊長類ゲノム・RNAデータベースの構築と活用

KAWAJI Hideya

第５回核酸医薬学会, 2019 Invited

Research Projects

Evaluating the role of cis-regulatory tandem DNA repeats in human disease and evolution

科学研究費助成事業, 基盤研究(B), 日本学術振興会, Apr, 2021 - Mar, 2024

ウォルツェンクヌート, 川路英哉, 依馬正次, 井上詞貴
Elucidation for genetic regulation of enhancer expression and interpretation of genetic architecture in autoimmune diseases

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (A), Japan Society for the Promotion of Science, Apr, 2020 - Mar, 2024
Reverse engineering of transcriptional regulatory regions through data modeling of transcription initiation activities

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2016 - Mar, 2021

KAWAJI Hideya
Development of a genomics data sharing platform in Asia

Grants-in-Aid for Scientific Research, Grant-in-Aid for Challenging Exploratory Research, Japan Society for the Promotion of Science, Apr, 2016 - Mar, 2018

Kawaji Hideya
Identification of biomarkers to diagnose lymph node metastasis based on gene expression patterns in primary lesion of endometrial carcinoma

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2015 - Mar, 2018

TERAO YASUHISA, ITO Masayoshi, KAWAJI Hideya, TAKEDA Satoru, HAYASHIZAKI Yoshihide
Research for blood RNA marker predicting prognosis of glaucoma focusing on the early and individualized medicine.

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2014 - Mar, 2017

Nakazawa Toru, ITO Masayoshi, KAWAJI Hideya
Comprehensive analysis of miRNA promoters

Grants-in-Aid for Scientific Research, Grant-in-Aid for Young Scientists (B), Japan Society for the Promotion of Science, 2010 - 2011

KAWAJI Hideya

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