Quantifying the recovery process of skeletal muscle on hematoxylin and eosin stained images via learning from label proportion

Yu Yamaoka, Weng Ian Chan, Shigeto Seno, Kanako Iwamori, So-ichiro Fukada, Hideo Matsuda

Scientific Reports　Vol. 14　No. 1　2024/11/07　Research paper (scientific journal)

網羅的生体情報の統合解析の課題 全血球トランスクリプトームと血漿プロテオームの関連性の評価

松本 寿健, 蛯原 健, 伊藤 弘, 瀬尾 茂人, 奥崎 大介, 織田 順

日本救急医学会雑誌　Vol. 35　No. 11　p. 877-877　2024/11

HER2陽性乳癌における高いHER2腫瘍内不均一性は不良予後の予測因子である

多根井 智紀, 瀬尾 茂人, 草田 義昭, 波多野 高明, 北原 友梨, 阿部 かおり, 増永 奈苗, 三嶋 千恵子, 塚部 昌美, 吉波 哲大, 三宅 智博, 下田 雅史, 松田 秀雄, 島津 研三

日本癌治療学会学術集会抄録集　Vol. 62回　p. O72-1　2024/10

A single fast Hebbian-like process enabling one-shot class addition in deep neural networks without backbone modification

Kazufumi Hosoda, Keigo Nishida, Shigeto Seno, Tomohiro Mashita, Hideki Kashioka, Izumi Ohzawa

Frontiers in Neuroscience　Vol. 18　2024/06/12　Research paper (scientific journal)

Periportal macrophages protect against commensal-driven liver inflammation

Yu Miyamoto, Junichi Kikuta, Takahiro Matsui, Tetsuo Hasegawa, Kentaro Fujii, Daisuke Okuzaki, Yu-chen Liu, Takuya Yoshioka, Shigeto Seno, Daisuke Motooka, Yutaka Uchida, Erika Yamashita, Shogo Kobayashi, Hidetoshi Eguchi, Eiichi Morii, Karl Tryggvason, Takashi Shichita, Hisako Kayama, Koji Atarashi, Jun Kunisawa, Kenya Honda, Kiyoshi Takeda, Masaru Ishii

Nature　2024/04/24　Research paper (scientific journal)

Regulation of muscle hypertrophy through granulin: Relayed communication among mesenchymal progenitors, macrophages, and satellite cells

Lidan Zhang, Hayato Saito, Tatsuyoshi Higashimoto, Takayuki Kaji, Ayasa Nakamura, Kanako Iwamori, Ryoko Nagano, Daisuke Motooka, Daisuke Okuzaki, Akiyoshi Uezumi, Shigeto Seno, So ichiro Fukada

Cell Reports　Vol. 43　No. 4　2024/04/23　Research paper (scientific journal)

Plasma Proteomics Profile-Based Comparison of Torso Versus Brain Injury: A Prospective Cohort Study.

Jotaro Tachino, Yuki Togami, Hisatake Matsumoto, Tsunehiro Matsubara, Shigeto Seno, Hiroshi Ogura, Jun Oda

The journal of trauma and acute care surgery　2024/04/10　Research paper (scientific journal)

Association between tranexamic acid administration and mortality based on the trauma phenotype: a retrospective analysis of a nationwide trauma registry in Japan.

Jotaro Tachino, Shigeto Seno, Hisatake Matsumoto, Tetsuhisa Kitamura, Atsushi Hirayama, Shunichiro Nakao, Yusuke Katayama, Hiroshi Ogura, Jun Oda

Critical care (London, England)　Vol. 28　No. 1　p. 89-89　2024/03/19　Research paper (scientific journal)

High HER2 Intratumoral Heterogeneity Is a Predictive Factor for Poor Prognosis in Early-Stage and Locally Advanced HER2-Positive Breast Cancer

Tomonori Tanei, Shigeto Seno, Yoshiaki Sota, Takaaki Hatano, Yuri Kitahara, Kaori Abe, nanae masunaga, Masami Tsukabe, Tetsuhiro Yoshinami, Tomohiro Miyake, Masafumi Shimoda, Hideo Matsuda, Kenzo Shimazu

Cancers　2024/03　Research paper (scientific journal)

A Novel Approach to Detection Algorithms for Artifacts in Clinical Endoscopy

Seiryo Watanabe, Hironori Shigeta, Shigeto Seno, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 17　p. 18-26　2024　Research paper (scientific journal)

血漿プロテオミクスプロファイルによる体幹部外傷と外傷性脳損傷の比較 前向きコホート研究

舘野 丈太郎, 松本 寿健, 戸上 由貴, 松原 庸博, 瀬尾 茂人, 小倉 裕司, 織田 順

日本救急医学会雑誌　Vol. 34　No. 12　p. 641-641　2023/12

Biodiversity and Constrained Information Dynamics in Ecosystems: A Framework for Living Systems

Kazufumi Hosoda, Shigeto Seno, Rikuto Kamiura, Naomi Murakami, Michio Kondoh

Entropy　2023/12　Research paper (scientific journal)

Synthetic model ecosystem of 12 cryopreservable microbial species allowing for a noninvasive approach.

Kazufumi Hosoda, Shigeto Seno, Naomi Murakami, Hideo Matsuda, Yutaka Osada, Rikuto Kamiura, Michio Kondoh

Bio Systems　Vol. 235　p. 105087-105087　2023/11/19　Research paper (scientific journal)

Cell Tracking via Reinforcement Learning with Microscopic Image Simulator

Toru Nagamura, Shigeto Seno, Hironori Shigeta, Tomohiro Mashita, Hideo Matsuda

Proceedings of the 2023 13th International Conference on Biomedical Engineering and Technology　2023/06/15　Research paper (international conference proceedings)

Pseudotime-based Deep Learning of Gene Regulatory Relationships from Single-Cell Expression Data

Koki Nishi, Junko Yoshida, Shigeto Seno, Kyoji Horie, Hideo Matsuda

Proceedings of the 2023 13th International Conference on Biomedical Engineering and Technology　2023/06/15　Research paper (international conference proceedings)

A Cell Tracking Method for Dynamic Analysis of Immune Cells Based on Deep Learning

Aya Watanabe, Kenji Fujimoto, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Masaru Ishii, Hideo Matsuda

International Journal of Machine Learning　Vol. 13　No. 2　p. 64-69　2023/04　Research paper (scientific journal)

UCP1レポーター脂肪細胞株を用いたβ-アドレナリンシグナル調節遺伝子の探索

川原崎 聡子, 瀬尾 茂人, 岡松 優子, 高橋 春弥, 野村 亘, 神戸 大朋, 木村 和弘, 斉藤 昌之, 松田 秀雄, 井上 和生, 後藤 剛

日本栄養・食糧学会大会講演要旨集　Vol. 77回　p. 267-267　2023/03

Identification of a unique subset of tissue-resident memory CD4+ T cells in Crohn's disease.

Takehito Yokoi, Mari Murakami, Takako Kihara, Shigeto Seno, Mitsuru Arase, James Badger Wing, Jonas Nørskov Søndergaard, Ryuichi Kuwahara, Tomohiro Minagawa, Eri Oguro-Igashira, Daisuke Motooka, Daisuke Okuzaki, Ryota Mori, Atsuyo Ikeda, Yuki Sekido, Takahiro Amano, Hideki Iijima, Keiichi Ozono, Tsunekazu Mizushima, Seiichi Hirota, Hiroki Ikeuchi, Kiyoshi Takeda

Proceedings of the National Academy of Sciences of the United States of America　Vol. 120　No. 1　2023/01/03　Research paper (scientific journal)

Combination of WFDC2, CHI3L1, and KRT19 in Plasma Defines a Clinically Useful Molecular Phenotype Associated with Prognosis in Critically Ill COVID-19 Patients.

Takeshi Ebihara, Tsunehiro Matsubara, Yuki Togami, Hisatake Matsumoto, Jotaro Tachino, Hiroshi Matsuura, Takashi Kojima, Fuminori Sugihara, Shigeto Seno, Daisuke Okuzaki, Haruhiko Hirata, Hiroshi Ogura

Journal of clinical immunology　Vol. 43　No. 2　p. 1-13　2022/11/04　Research paper (scientific journal)

レポーター脂肪細胞株を用いたβ-アドレナリン刺激応答性UCP1発現誘導調節遺伝子の探索

川原崎 聡子, 瀬尾 茂人, 岡松 優子, 高橋 春弥, 野村 亘, 神戸 大朋, 木村 和弘, 斉藤 昌之, 松田 秀雄, 井上 和生, 後藤 剛

肥満研究　Vol. 28　No. Suppl.　p. 318-318　2022/11

Myeloid cell-specific ablation of Runx2 gene exacerbates post-infarct cardiac remodeling.

Masashi Tomimatsu, Kotaro Matsumoto, Moe Ashizuka, Shohei Kumagai, Shota Tanaka, Takafumi Nakae, Kosei Yokota, Shunsuke Kominami, Ryota Kajiura, Daisuke Okuzaki, Daisuke Motooka, Aki Shiraishi, Takaya Abe, Hideo Matsuda, Yoshiaki Okada, Makiko Maeda, Shigeto Seno, Masanori Obana, Yasushi Fujio

Scientific reports　Vol. 12　No. 1　p. 16656-16656　2022/10/05　Research paper (scientific journal)

Development of clinical phenotypes and biological profiles via proteomic analysis of trauma patients

Jotaro Tachino, Hisatake Matsumoto, Fuminori Sugihara, Shigeto Seno, Daisuke Okuzaki, Tetsuhisa Kitamura, Sho Komukai, Yoshiyuki Kido, Takashi Kojima, Yuki Togami, Yusuke Katayama, Yuko Nakagawa, Hiroshi Ogura

Critical Care　Vol. 26　No. 1　2022/08/06　Research paper (scientific journal)

MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus.

Naoko Fujiwara, Maki Shigemoto, Mizuki Hirayama, Ken-Ichi Fujita, Shigeto Seno, Hideo Matsuda, Masami Nagahama, Seiji Masuda

Nucleic acids research　Vol. 50　No. 15　p. 8779-8806　2022/07/29　Research paper (scientific journal)

A Novel Method for Gene Regulatory Network Inference with Pseudotime Data Using Information Criterion

Shuhei Yao, Kaito Uemura, Shigeto Seno, Hideo Matsuda

International Jounral of Bioscience, Biochemistry and Bioinformatics　Vol. 12　No. 3　p. 43-52　2022/07　Research paper (scientific journal)

Relayed signaling between mesenchymal progenitors and muscle stem cells ensures adaptive stem cell response to increased mechanical load

Akihiro Kaneshige, Takayuki Kaji, Lidan Zhang, Hayato Saito, Ayasa Nakamura, Tamaki Kurosawa, Madoka Ikemoto-Uezumi, Kazutake Tsujikawa, Shigeto Seno, Masatoshi Hori, Yasuyuki Saito, Takashi Matozaki, Kazumitsu Maehara, Yasuyuki Ohkawa, Michael Potente, Shuichi Watanabe, Thomas Braun, Akiyoshi Uezumi, So-ichiro Fukada

Cell Stem Cell　Vol. 29　No. 2　p. 265-280　2021/12/02　Research paper (scientific journal)

Osteoclasts adapt to physioxia perturbation through DNA demethylation

Keizo Nishikawa, Shigeto Seno, Toshitada Yoshihara, Ayako Narazaki, Yuki Sugiura, Reito Shimizu, Junichi Kikuta, Reiko Sakaguchi, Norio Suzuki, Norihiko Takeda, Hiroaki Semba, Masamichi Yamamoto, Daisuke Okuzaki, Daisuke Motooka, Yasuhiro Kobayashi, Makoto Suematsu, Haruhiko Koseki, Hideo Matsuda, Masayuki Yamamoto, Seiji Tobita, Yasuo Mori, Masaru Ishii

EMBO reports　Vol. 22　No. 12　2021/10/18　Research paper (scientific journal)

SC-JNMF: Single-cell clustering integrating multiple quantification methods based on joint non-negative matrix factorization

Mikio Shiga, Shigeto Seno, Makoto Onizuka, Hideo Matsuda

PeerJ　Vol. 9　2021/08/27　Research paper (scientific journal)

A CNN-based cell tracking method for multi-slice intravital imaging data.

Kenji Fujimoto, Tsubasa Mizugaki, Utkrisht Rajkumar, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Masaru Ishii, Vineet Bafna, Hideo Matsuda

Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics 2021　p. 35-7　2021/08　Research paper (international conference proceedings)

SLPI is a critical mediator that controls PTH-induced bone formation.

Akito Morimoto, Junichi Kikuta, Keizo Nishikawa, Takao Sudo, Maki Uenaka, Masayuki Furuya, Tetsuo Hasegawa, Kunihiko Hashimoto, Hiroyuki Tsukazaki, Shigeto Seno, Akira Nakamura, Daisuke Okuzaki, Fuminori Sugihara, Akinori Ninomiya, Takeshi Yoshimura, Ryoko Takao-Kawabata, Hideo Matsuda, Masaru Ishii

Nature communications　Vol. 12　No. 1　p. 2136-2136　2021/04/09　Research paper (scientific journal)

Determining homologous recombination deficiency scores with whole exome sequencing and their association with responses to neoadjuvant chemotherapy in breast cancer.

Seung Jin Kim, Yoshiaki Sota, Yasuto Naoi, Keiichiro Honma, Naofumi Kagara, Tomohiro Miyake, Masafumi Shimoda, Tomonori Tanei, Shigeto Seno, Hideo Matsuda, Shinzaburo Noguchi, Kenzo Shimazu

Translational oncology　Vol. 14　No. 2　p. 100986-100986　2021/02　Research paper (scientific journal)

Dlk1 regulates quiescence in calcitonin receptor-mutant muscle stem cells.

Lidan Zhang, Manami Kubota, Ayasa Nakamura, Takayuki Kaji, Shigeto Seno, Akiyoshi Uezumi, Ditte Caroline Andersen, Charlotte Harken Jensen, So-Ichiro Fukada

Stem cells (Dayton, Ohio)　Vol. 39　No. 3　p. 306-317　2020/12/08　Research paper (scientific journal)

Correlated chromosomal periodicities according to the growth rate and gene expression

Liu Liu, Masaomi Kurokawa, Motoki Nagai, Shigeto Seno, Bei-Wen Ying

Scientific Reports　Vol. 10　No. 1　2020/12　Research paper (scientific journal)

Development of an intravital imaging system for the synovial tissue reveals the dynamics of CTLA-4 Ig in vivo

Tetsuo Hasegawa, Junichi Kikuta, Takao Sudo, Erika Yamashita, Shigeto Seno, Tsutomu Takeuchi, Masaru Ishii

Scientific Reports　Vol. 10　No. 1　p. 13480-13480　2020/12　Research paper (scientific journal)

A model ecosystem of twelve cryopreservable microbial species allowing for a non-invasive approach

Kazufumi Hosoda, Shigeto Seno, Naomi Murakami, Hideo Matsuda, Yutaka Osada, Michio Kondoh

2020/10/23　Research paper (other academic)

Glycerol kinase stimulates uncoupling protein 1 expression by regulating fatty acid metabolism in beige adipocytes.

Mari Iwase, Soshi Tokiwa, Shigeto Seno, Takako Mukai, Yu-Sheng Yeh, Haruya Takahashi, Wataru Nomura, Huei-Fen Jheng, Sigenobu Matsumura, Tatsuya Kusudo, Naoki Osato, Hideo Matsuda, Kazuo Inoue, Teruo Kawada, Tsuyoshi Goto

The Journal of biological chemistry　Vol. 295　No. 20　p. 7033-7045　2020/05/15　Research paper (scientific journal)

Anti-Inflammatory and Antioxidative Properties of Isoflavones Provide Renal Protective Effects Distinct from Those of Dietary Soy Proteins against Diabetic Nephropathy.

Huei-Fen Jheng, Kanako Hayashi, Yasuki Matsumura, Teruo Kawada, Shigeto Seno, Hideo Matsuda, Kazuo Inoue, Wataru Nomura, Haruya Takahashi, Tsuyoshi Goto

Molecular nutrition & food research　Vol. 64　No. 10　2020/05　Research paper (scientific journal)

In vivo dynamic analysis of BMP-2-induced ectopic bone formation

Kunihiko Hashimoto, Takashi Kaito, Masayuki Furuya, Shigeto Seno, Daisuke Okuzaki, Junichi Kikuta, Hiroyuki Tsukazaki, Hideo Matsuda, Hideki Yoshikawa, Masaru Ishii

SCIENTIFIC REPORTS　Vol. 10　No. 1　2020/03　Research paper (scientific journal)

Long non-coding RNA 2310069B03Rik functions as a suppressor of Ucp1 expression under prolonged cold exposure in murine beige adipocytes.

Mari Iwase, Shoko Sakai, Shigeto Seno, Yu-Sheng Yeh, Tony Kuo, Haruya Takahashi, Wataru Nomura, Huei-Fen Jheng, Paul Horton, Naoki Osato, Hideo Matsuda, Kazuo Inoue, Teruo Kawada, Tsuyoshi Goto

Bioscience, biotechnology, and biochemistry　Vol. 84　No. 2　p. 305-313　2020/02　Research paper (scientific journal)

URH49 exports mRNA by remodeling complex formation and mediating the NXF1-dependent pathway.

Ken-Ichi Fujita, Tomohiro Yamazaki, Kotaro Harada, Shigeto Seno, Hideo Matsuda, Seiji Masuda

Biochimica et biophysica acta. Gene regulatory mechanisms　Vol. 1863　No. 2　p. 194480-194480　2020/01/07　Research paper (scientific journal)

Migration arrest of chemoresistant leukemia cells mediated by MRTF-SRF pathway.

Maho Morimatsu, Erika Yamashita, Shigeto Seno, Takao Sudo, Junichi Kikuta, Hiroki Mizuno, Daisuke Okuzaki, Daisuke Motooka, Masaru Ishii

Inflammation and regeneration　Vol. 40　p. 15-15　2020　Research paper (scientific journal)

Tracking and Analysis of FUCCI-Labeled Cells Based on Particle Filters and Time-to-Event Analysis

Kenji Fujimoto, Shigeto Seno, Hironori Shigeta, Tomohiro Mashita, Masaru Ishii, Hideo Matsuda

International Journal of Bioscience, Biochemistry and Bioinformatics　Vol. 10　No. 2　p. 94-109　2020　Research paper (scientific journal)

Thrombomodulin induces anti-inflammatory effects by inhibiting the rolling adhesion of leukocytes in vivo

Shino Nishizawa, Junichi Kikuta, Shigeto Seno, Masahiro Kajiki, Ryuichi Tsujita, Hiroki Mizuno, Takao Sudo, Tomoka Ao, Hideo Matsuda, Masaru Ishii

Journal of Pharmacological Sciences　2020/01

Food-Derived Compounds Apigenin and Luteolin Modulate mRNA Splicing of Introns with Weak Splice Sites.

Masashi Kurata, Naoko Fujiwara, Ken-Ichi Fujita, Yasutaka Yamanaka, Shigeto Seno, Hisato Kobayashi, Yusaku Miyamae, Nobuyuki Takahashi, Yasuyuki Shibuya, Seiji Masuda

iScience　Vol. 22　p. 336-352　2019/12/20　Research paper (scientific journal)

Single-cell transcriptome analysis of mouse leukocytes in inflammatory stimulation

Naoki Osato, Hironori Shigeta, Shigeto Seno, Yutaka Uchida, Junichi Kikuta, Masaru Ishii, Hideo Matsuda

2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)　p. 1229-1231　2019/11　Research paper (international conference proceedings)

Analyzing Leukocyte Migration Trajectories by Deformable Image Matching

Hironori Shigeta, Shigeto Seno, Shino Nishizawa, Yutaka Uchida, Junichi Kikuta, Masaru Ishii, Hideo Matsuda

IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)　p. 94-98　2019/10　Research paper (international conference proceedings)

Cell Tracking based on Deep Learning with Depth Information for Intravital Fluorescence Imaging Data

Ayato Shimada, Shigeto Seno, Hironori Shigeta, Tomohiro Mashita, Yutaka Uchida, Masaru Ishii, Hideo Matsuda

IPSJ, Transactions on Mathematical Modeling and its Applications　Vol. 12　No. 2　p. 82-91　2019/07　Research paper (scientific journal)

Improvement of detection performance of fusion genes from RNA-seq data by clustering short reads”

Yoshiaki Sota, Shigeto Seno, Hironori Shigeta, Naoki Osato, Masafumi Shimoda, Shinzabro Noguchi, Hideo Matsuda

Journal of Bioinformatics and Computational Biology　Vol. 17　No. 3　p. 1940008-1940008　2019/07　Research paper (scientific journal)

In vivo Multicolor Imaging with Fluorescent Probes Revealed the Dynamics and Function of Osteoclast Proton Pumps

Masafumi Minoshima, Junichi Kikuta, Yuta Omori, Shigeto Seno, Riko Suehara, Hiroki Maeda, Hideo Matsuda, Masaru Ishii, Kazuya Kikuchi

ACS Central Science　Vol. 5　No. 6　p. 1059-1066　2019/05　Research paper (scientific journal)

Asymmetric Integration of Single-Cell Transcriptomic Data using Latent Dirichlet Allocation and Procrustes Analysis

Mitsuhiro Eto, Wataru Hirota, Shigeto Seno, Hideo Matsuda

2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)　p. 2129-2135　2018/12　Research paper (international conference proceedings)

Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR

Yukako Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii

Scientific Reports　Vol. 8　No. 1　2018/12/01　Research paper (scientific journal)

細胞画像のセグメンテーション精度向上のための画像類推を用いた学習データ拡張

赤沢 秀樹, 渡邊 誓旅, 繁田 浩功, 間下 以大, 瀬尾 茂人, 松田 秀雄

2018/08　Research paper (other academic)

Rising Stars in Skeletal Biology 二光子励起生体イメージングを用いた骨芽細胞・破骨細胞コミュニケーションの解明

古家 雅之, 菊田 順一, 瀬尾 茂人, 前田 拓樹, 吉川 秀樹, 石井 優

日本骨代謝学会学術集会プログラム抄録集　Vol. 36回　p. 117-117　2018/07

The dipeptidyl peptidase‐4 (DPP‐4) inhibitor teneligliptin enhances brown adipose tissue function, thereby preventing obesity in mice

Kenichiro Takeda, Honami Sawazaki, Haruya Takahashi, YuSheng Yeh, HueiFen Jheng, Wataru Nomura, Takeshi Ara, Nobuyuki Takahashi, Shigeto Seno, Naoki Osato, Hideo Matsuda, Teruo Kawada, Tsuyoshi Goto

FEBS openbio　Vol. 8　No. 11　2018/07　Research paper (scientific journal)

Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells

Yoichi Takenaka, Kazuma Mikami, Shigeto Seno, Hideo Matsuda

BMC Bioinformatics　Vol. 19　No. 89　p. 49-59　2018/05/08　Research paper (scientific journal)

生体骨イメージング技術と計測解析の最前線 生体骨イメージングで見る破骨細胞・骨芽細胞間の4D相互作用

古家 雅之, 菊田 順一, 瀬尾 茂人, 前田 拓樹, 吉川 秀樹, 石井 優

日本骨形態計測学会雑誌　Vol. 28　No. 2　p. S57-S57　2018/05

Chromatin 3D reconstruction from chromosomal contacts using a genetic algorithm

Kapilevich, V., Seno, S., Matsuda, H., Takenaka, Y.

IEEE/ACM Transactions on Computational Biology and Bioinformatics　Vol. 16　No. 5　2018/03　Research paper (scientific journal)

A Phytol-Enriched Diet Activates PPAR-α in the Liver and Brown Adipose Tissue to Ameliorate Obesity-Induced Metabolic Abnormalities

Ji-Yeong An, Huei-Fen Jheng, Hiroyuki Nagai, Kohei Sanada, Haruya Takahashi, Mari Iwase, Natsumi Watanabe, Young-Il Kim, Aki Teraminami, Nobuyuki Takahashi, Rieko Nakata, Hiroyasu Inoue, Shigeto Seno, Hideo Mastuda, Teruo Kawada, Tsuyoshi Goto

Molecular Nutrition and Food Research　Vol. 62　No. 6　2018/03/01　Research paper (scientific journal)

Direct cell-cell contact between mature osteoblasts and osteoclasts dynamically controls their functions in vivo.

Masayuki Furuya, Junichi Kikuta, Sayumi Fujimori, Shigeto Seno, Hiroki Maeda, Mai Shirazaki, Maki Uenaka, Hiroki Mizuno, Yoriko Iwamoto, Akito Morimoto, Kunihiko Hashimoto, Takeshi Ito, Yukihiro Isogai, Masafumi Kashii, Takashi Kaito, Shinsuke Ohba, Ung-Il Chung, Alexander C Lichtler, Kazuya Kikuchi, Hideo Matsuda, Hideki Yoshikawa, Masaru Ishii

Nature communications　Vol. 9　No. 1　p. 300-300　2018/01/19　Research paper (scientific journal)

Detection of Fusion Genes from Human Breast Cancer Cell-line RNA-Seq Data Using Shifted Short Read Clustering

Yoshiaki Sota, Shigeto Seno, Hironori Shigeta, Naoki Osato, Masafumi Shimoda, Shinzaburo Noguchi, Hideo Matsuda

PROCEEDINGS 2018 IEEE 18TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE)　p. 159-162　2018　Research paper (international conference proceedings)

Diagnostic Assessment of Deep Learning Algorithms for Detection of Lymph Node Metastases in Women With Breast Cancer

Babak Ehteshami Bejnordi, Mitko Veta, Paul Johannes van Diest, Bram van Ginneken, Nico Karssemeijer, Geert Litjens, Jeroen A. W. M. van der Laak

JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION　Vol. 318　No. 22　p. 2199-2210　2017/12　Research paper (scientific journal)

Bone marrow cavity segmentation using graph-cuts with wavelet-based texture feature

Hironori Shigeta, Tomohiro Mashita, Junichi Kikuta, Shigeto Seno, Haruo Takemura, Masaru Ishii, Hideo Matsuda

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY　Vol. 15　No. 5　2017/10　Research paper (scientific journal)

Over-expression of PPARα in obese mice adipose tissue improves insulin sensitivity

Haruya Takahashi, Kohei Sanada, Hiroyuki Nagai, Yongjia Li, Yumeko Aoki, Takeshi Ara, Shigeto Seno, Hideo Matsuda, Rina Yu, Teruo Kawada, Tsuyoshi Goto

Biochemical and Biophysical Research Communications　Vol. 493　No. 1　p. 108-114　2017/09　Research paper (scientific journal)

The hepatokine FGF21 is crucial for peroxisome proliferator-activated receptor-alpha agonist-induced amelioration of metabolic disorders in obese mice

Tsuyoshi Goto, Mariko Hirata, Yumeko Aoki, Mari Iwase, Haruya Takahashi, Minji Kim, Yongjia Li, Huei-Fen Jheng, Wataru Nomura, Nobuyuki Takahashi, Chu-Sook Kim, Rina Yu, Shigeto Seno, Hideo Matsuda, Megumi Aizawa-Abe, Ken Ebihara, Nobuyuki Itoh, Teruo Kawada

JOURNAL OF BIOLOGICAL CHEMISTRY　Vol. 292　No. 22　p. 9175-9190　2017/06　Research paper (scientific journal)

A simple comparison of the extrinsic noise in gene expression between native and foreign regulations in Escherichia coli

Bei-Wen Ying, Shigeto Seno, Hideo Matsuda, Tetsuya Yomo

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS　Vol. 486　No. 3　p. 852-857　2017/05　Research paper (scientific journal)

Correlation between genome reduction and bacterial growth

Masaomi Kurokawa, Shigeto Seno, Hideo Matsuda, Bei-Wen Ying

DNA RESEARCH　Vol. 23　No. 6　p. 517-525　2016/12　Research paper (scientific journal)

模様特徴量とグラフカットを利用した生体骨組織の骨髄腔の領域分割

繁田 浩功, 間下 以大, 菊田 順一, 瀬尾 茂人, 石井 優, 松田 秀雄

2016/09　Research paper (other academic)

ウェーブレット特徴量を用いた生体骨組織の骨髄腔の領域分割手法

繁田浩功, 間下以大, 菊田順一, 瀬尾茂人, 竹村治雄, 松田秀雄, 石井優

2016/06　Research paper (other academic)

Comparative Analysis of Transformation Methods for Gene Expression Profiles in Breast Cancer Datasets

Yoshiaki Sota, Shigeto Seno, Yoichi Takenaka, Shinzaburo Noguchi, Hideo Matsuda

2016 IEEE 16TH INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOENGINEERING (BIBE)　p. 328-333　2016　Research paper (international conference proceedings)

Proinflammatory cytokine interleukin-1 beta suppresses cold-induced thermogenesis in adipocytes

Tsuyoshi Goto, Supaporn Naknukool, Rieko Yoshitake, Yuki Hanafusa, Soshi Tokiwa, Yongjia Li, Tomoya Sakamoto, Takahiro Nitta, Minji Kim, Nobuyuki Takahashi, Rina Yu, Hiromi Daiyasu, Shigeto Seno, Hideo Matsuda, Teruo Kawada

CYTOKINE　Vol. 77　p. 107-114　2016/01　Research paper (scientific journal)

A Bone Marrow Cavity Segmentation Method using Wavelet-based Texture Feature

Hironori Shigeta, Tomohiro Mashita, Junichi Kikutat, Shigeto Seno, Haruo Takemura, Hideo Matsuda, Masaru Ishii

2016 23RD INTERNATIONAL CONFERENCE ON PATTERN RECOGNITION (ICPR)　Vol. 15　No. 5　p. 2133-2138　2016　Research paper (international conference proceedings)

生体イメージング技術を駆使したトロンボモジュリンの新たな作用機序解明

西澤 志乃, 菊田 順一, 瀬尾 茂人, 松田 秀雄, 石井 優

日本生化学会大会・日本分子生物学会年会合同大会講演要旨集　Vol. 88回・38回　p. [3T23p-05(3P0080)]　2015/12

Functional specialization in regulation and quality control in thermal adaptive evolution

Kazuma Yama, Yuki Matsumoto, Yoshie Murakami, Shigeto Seno, Hideo Matsuda, Kazuyoshi Gotoh, Daisuke Motooka, Shota Nakamura, Bei-Wen Ying, Tetsuya Yomo

GENES TO CELLS　Vol. 20　No. 11　p. 943-955　2015/11　Research paper (scientific journal)

Detecting shifts in gene regulatory networks during time-course experiments at single-time-point temporal resolution

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY　Vol. 13　No. 5　2015/10　Research paper (scientific journal)

Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages

Bei-Wen Ying, Tomoya Honda, Saburo Tsuru, Shigeto Seno, Hideo Matsuda, Yasuaki Kazuta, Tetsuya Yomo

PLOS ONE　Vol. 10　No. 8　2015/08　Research paper (scientific journal)

コンポーネントツリーを用いたグローバルデータアソシエーションによる細胞追跡手法

Kohei Kurashige, Shigeto Seno, Tomohiro Mashita, Junichi Kikuta, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda

2015/06　Research paper (other academic)

A Bone-marrow Space Segmentation Method Using Graph-cuts

Vol. 8　No. 3　p. 18-27　2015/03　Research paper (scientific journal)

生体骨組織における骨髄腔画像のウェーブレット変換を用いた骨髄腔領域の認識手法

繁田 浩功, 間下 以大, 金子 雄, 菊田 順一, 瀬尾 茂人, 竹村 治雄, 松田 秀雄, 石井 優

2015/01　Research paper (other academic)

Directed evolution of cell size in Escherichia coli

Mari Yoshida, Saburo Tsuru, Naoko Hirata, Shigeto Seno, Hideo Matsuda, Bei-Wen Ying, Tetsuya Yomo

BMC EVOLUTIONARY BIOLOGY　Vol. 14　No. 1　2014/12　Research paper (scientific journal)

Improvement approach of cell tracking accuracy by using inter-frame information

Kohei Kurashige, Shigeto Seno, Tomohiro Mashita, Junichi Kikuta, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda

2014/10

An automatic event detection method using semi-supervised learning for time-lapse imaging data

Kojiro Fukuda, Shigeto Seno, Tomohiro Mashita, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda

2014/10

大域データ対応付けの反復実行による細胞追跡精度の改善手法

藏重 昂平, 福田浩二郎, 瀬尾茂人, 間下以大, 竹中要一, 松田秀雄

情報処理学会研究報告　2014/09　Research paper (other academic)

Metagenome fragment classification based onmultiple motif-occurrence profiles

Naoki Matsushita, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

PEERJ　Vol. 2　2014/09　Research paper (scientific journal)

A Segmentation Method for Bone Marrow Cavity Imaging Using Graph Cuts

Tomohiro Mashita, Jun Usam, Hironori Shigeta, Yoshihiro Kuroda, Junichi Kikuta, Shigeto Senoo, Masaru Ishi, Hideo Matsuda, Haruo Takemura

2014 1st Workshop on Pattern Recognition Techniques for Indirect Immunofluorescence Images　2014/08　Research paper (international conference proceedings)

タイムラプスイメージングによる細胞周期観測画像の時空間解析

福田浩二郎, 瀬尾茂人, 間下以大, 竹中要一, 松田秀雄

2014/06　Research paper (other academic)

マルチチャンネル蛍光顕微鏡動画のためのパーティクルフィルタを用いた細胞追跡手法

小森康祐, 瀬尾茂人, 間下以大, 竹中要一, 松田秀雄

第76回全国大会講演論文集　Vol. 2014　No. 1　p. 291-292　2014/03　Research paper (other academic)

Gene expression scaled by distance to the genome replication site

Bei-Wen Ying, Saburo Tsuru, Shigeto Seno, Hideo Matsuda, Tetsuya Yomo

MOLECULAR BIOSYSTEMS　Vol. 10　No. 3　p. 375-379　2014　Research paper (scientific journal)

A Robust Method for Estimating Gene Regulatory Networks Using Multiple Time Series Gene Expression Profiles

Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

情報処理学会論文誌. 数理モデル化と応用　Vol. 6　No. 3　p. 151-162　2013/12/27

Segmentation and Tracking Method of Cell Nuclei for Time-lapse Fluorescent Microscopy Images Based on Gaussian Mixture Model

Shigeto Seno, Tomohiro Mashita, Sakae Maeda, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda

情報処理学会論文誌. 数理モデル化と応用　Vol. 6　No. 3　p. 140-150　2013/12/27

Integrative prediction of miRNA-mRNA interactions from high-throughput sequencing data

Tomoshige Ohno, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges 2013　2013/11

経時観測蛍光画像からのモーションヒストリーイメージを用いた細胞分裂の検出方法

福田浩二郎, 瀬尾茂人, 間下以大, 前田栄, 竹中要一, 石井優, 松田秀雄

2013/08　Research paper (other academic)

Global Data Associationによる経時観察画像における破骨前駆細胞の自動追跡手法

尾野貴広, 瀬尾茂人, 間下以大, 竹中要一, 石井優, 松田秀雄

2013/07　Research paper (other academic)

An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles

Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

Gene　Vol. 518　No. 1　p. 17-25　2013/04/10　Research paper (scientific journal)

Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome

Bei-Wen Ying, Shigeto Seno, Fuyuro Kaneko, Hideo Matsuda, Tetsuya Yomo

BMC GENOMICS　Vol. 14　2013/01　Research paper (scientific journal)

多色蛍光イメージングによる経時観測データのための細胞追跡手法

瀬尾茂人, 間下以大, 前田栄, 竹中要一, 石井優, 松田秀雄

2012/12　Research paper (other academic)

Estimate Dynamic Gene Regulatory Networks in Adipocyte Differentiation for Detecting Changes of Gene Regulations by Splitting Time Course Data

Tomoyoshi Nakayama, Yoshiyuki Kido, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

2012/12

多色蛍光タイムラプスイメージングによる細胞周期観測データのための細胞自動追跡手法

瀬尾茂人, 間下以大, 前田栄, 竹中要一, 石井優, 松田秀雄

2012/11　Research paper (other academic)

Automatic cell tracking for time-lapse fluorescent images of cell cycle

Shigeto Seno, Sakae Maeda, Tomohiro Mashita, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda

2012/10　Research paper (international conference proceedings)

Estimation of Dynamic Gene Regulatory Networks for Cell Differentiation by Splitting Time Course Data

Tomoyoshi Nakayama, Yoshiyuki Kido, Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

2012/10

A cell-tracking method for time-lapse multicolor fluorescent images

Shigeto Seno, Tomohiro Mashita, Yoichi Takenaka, Masaru Ishii, Hideo Matsuda

2012/09　Research paper (international conference proceedings)

A Method for Isoform Prediction from RNA-Seq Data by Iterative Mapping

Ohno Tomoshige, Seno Shigeto, Takenaka Yoichi, Matsuda Hideo

IMT　Vol. 7　No. 2　p. 921-927　2012

An estimation method for inference of gene regulatory net-work using Bayesian network with uniting of partial problems

Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

Series on Advances in Bioinformatics and Computational Biology　Vol. 13　2012　Research paper (international conference proceedings)

A method for isoform prediction from RNA-seq data by iterative mapping

Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 5　p. 27-33　2012　Research paper (scientific journal)

An estimation method for inference of gene regulatory net-work using Bayesian network with uniting of partial problems

Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

BMC GENOMICS　Vol. 13　2012/01　Research paper (scientific journal)

INFERENCE OF S-SYSTEM MODELS OF GENE REGULATORY NETWORKS USING IMMUNE ALGORITHM

Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY　Vol. 9　p. 75-86　2011/12　Research paper (scientific journal)

Reduction in genome size decreased fluctuation in gene expression.

Bei-Wen Ying, Shigeto Seno, Tetsuya Yomo

2011/12　Research paper (other academic)

細胞分化クロストークのモデル化と細胞分化クロストーク遺伝子の推定手法

吉澤陽志, 瀬尾茂人, 竹中要一, 松田秀雄

情報処理学会論文誌 数理モデル化と応用　Vol. 4　No. 4　p. 59-68　2011/11　Research paper (scientific journal)

Perfect Hamming code with a hash table for faster genome mapping

Yoichi Takenaka, Shigeto Seno, Hideo Matsuda

BMC GENOMICS　Vol. 12　2011/11　Research paper (scientific journal)

Size evolution with a laboratory Escherichia coli strain.

Mari Yoshida, Nao Hiramoto, Shigeto Seno, Saburo Tsuru, Bei-Wen Ying, Tetsuya Yomo

2011/10　Research paper (international conference proceedings)

A method for using REST service in bioinformatics workflow by converting to SOAP service

Seigo Ikeda, Yoshiyuki kido, Shigeto Senoo, Yoichi Takenaka, Hideo Matsuda

IPSJ SIG Technical Reports (2011-BIO-25)　Vol. 2011　No. 9　p. 1-7　2011/06　Research paper (other academic)

Exploration of Potential Genomic Portraits Associated with Intrahepatic Recurrence in Human Hepatocellular Carcinoma

Nobuyoshi Kittaka, Ichiro Takemasa, Shigeto Seno, Yutaka Takeda, Shogo Kobayashi, Shigeru Marubashi, Keizo Dono, Koji Umeshita, Hiroaki Nagano, Hideo Matsuda, Morito Monden, Masaki Mori, Yuichiro Doki

ANNALS OF SURGICAL ONCOLOGY　Vol. 17　No. 12　p. 3145-3154　2010/12　Research paper (scientific journal)

A Proposal for a Method to Support Bioinformatics Workflow Composition using Metadata

Takanori Fukumoto, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

Proceedings of Kansai Branch Annual Meeting, Information Processing Society of Japan, Kansai Branch　Vol. 2010　2010/09　Research paper (other academic)

A Metadata Management System for Composing Bioinformatics Workflows

Takuya Ishibashi, Yoshiyuki Kido, Takanori Fukumoto, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

9th International Conference on Bioinformatics (InCoB2010)　2010/09　Research paper (international conference proceedings)

Gene Expression Profile Prospectively Predicts Peritoneal Relapse After Curative Surgery of Gastric Cancer

Atsushi Takeno, Ichiro Takemasa, Shigeto Seno, Makoto Yamasaki, Masaaki Motoori, Hiroshi Miyata, Kiyokazu Nakajima, Shuji Takiguchi, Yoshiyuki Fujiwara, Toshiro Nishida, Toshitsugu Okayama, Kenichi Matsubara, Yoichi Takenaka, Hideo Matsuda, Morito Monden, Masaki Mori, Yuichiro Doki

ANNALS OF SURGICAL ONCOLOGY　Vol. 17　No. 4　p. 1033-1042　2010/04　Research paper (scientific journal)

立体構造情報と機能情報によるタンパク質間相互作用予測法の改良

吉川達也, 瀬尾茂人, 竹中要一, 松田秀雄

情報処理学会研究報告　Vol. 2010　No. 1　p. 1-8　2010/03

Improved Prediction Method for Protein Interactions Using Both Structural and Functional Characteristics of Proteins

Yoshikawa Tatsuya, Seno Shigeto, Takenaka Yoichi, Matsuda Hideo

Information and Media Technologies　Vol. 5　No. 2　p. 489-502　2010

Improved prediction method for protein interactions using both structural and functional characteristics of proteins

Tatsuya Yoshikawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 3　No. 2　p. 10-23　2010　Research paper (scientific journal)

A METHOD FOR EFFICIENT EXECUTION OF BIOINFORMATICS WORKFLOWS

JUNYA SEO, YOSHIYUKI KIDO, SHIGETO SENO, YOICHI TAKENAKA, HIDEO MATSUDA

Genome Informatics 2009　Vol. 23　p. 139-148　2009/10　Research paper (international conference proceedings)

A proposal of repository federation method for integration of Web service information

Takefumi Nonaka, Junya Seo, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ SIG Technical Reports (2009-BIO-16-1)　Vol. 2009　No. 25　p. 1-4　2009/03　Research paper (other academic)

Architecture of an Efficient Data Transfer System and Manager for Genome-wide Analysis Workflows

Junya Seo, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

The 3rd MEI International Symposium 2008　2008/12　Research paper (other academic)

A Method for Reducing Bounds of Compound Search by Dividing Structure Key

Takashi Shimizu, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

The Proceedings of the 2008 Annual Conference of the Japanese Society for Bioinformatics　2008/12　Research paper (international conference proceedings)

A Method for Making a New Reference Set of PDB Entries for Retrieving Protein 3D Structures with Structural Annotations

Masahiko Hamada, Yoshiyuki Kido, Shigeto Seno, Hiromi Daiyasu, Yoichi Takenaka, Hideo Matsuda

The Proceedings of the 2008 Annual Conference of the Japanese Society for Bioinformatics　2008/12　Research paper (international conference proceedings)

Inference of gene regulatory network for adipocyte/osteoblast differentiation

Hideo Matsuda, Yoichi Takenaka, Yosuke Mizuno, Shigeto Seno, Yoshimi Tokuzawa, Yutaka Nakachi, Hidemasa Bono, Yasushi Okazaki

2008/12

A method for refinement of the calculation range by divided structure key of the compound search using Tanimoto coefficient

Takashi Shimizu, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ SIG Technical Reports (2008-BIO-14)　Vol. 2008　No. 86　p. 5-8　2008/09　Research paper (other academic)

A Distributed-Processing System for Accelerating Biological Research using Data-Staging

Yoshiyuki Kido, Shigeto Seno, Susumu Date, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 49　No. 5　p. 58-64　2008/03　Research paper (scientific journal)

A Combination Method of the Tanimoto Coefficient and Proximity Measure of Random Forest for Compound Activity Prediction

Gen Kawamura, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 49　No. 5　p. 46-57　2008/03　Research paper (scientific journal)

A Distributed-Processing System for Accelerating Biological Research Using Data-Staging

Kido Yoshiyuki, Seno Shigeto, Date Susumu, Takenaka Yoichi, Matsuda Hideo

ipsjdc　Vol. 4　p. 250-256　2008

A Combination Method of the Tanimoto Coefficient and Proximity Measure of Random Forest for Compound Activity Prediction

Kawamura Gen, Seno Shigeto, Takenaka Yoichi, Matsuda Hideo

ipsjdc　Vol. 4　p. 238-249　2008

A Method for Retrieving Functionally Similar Bioinformatics Workflows

Junya Seo, Shigeto Seno, Yoichi Takenaka

Proceedings of 2007 Annual Conference of Japanese Society for Bioinformatics　2007/12

A Method for the Efficient Data Transmission in Bioinformatics Workflows

Junya Seo, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

2007/09

Retrieving Functionally Similar Bioinformatics Workflows using TF-IDF Filtering.

Junya Seo, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

IPSJ Transactions on Bioinformatics　Vol. 2007　No. 128　p. 259-266　2007/03　Research paper (scientific journal)

Retrieving Functionally Similar Bioinformatics Workflows Using TF-IDF Filtering

Seo Junya, Seno Shigeto, Takenaka Yoichi, Matsuda Hideo

ipsjdc　Vol. 3　p. 164-173　2007

A method for similarity search of genomic positional expression using CAGE

Shigeto Seno, Yoichi Takenaka, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Hideo Matsuda

PLOS GENETICS　Vol. 2　No. 4　p. 578-586　2006/04　Research paper (scientific journal)

The transcriptional landscape of the mammalian genome

P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, R Oyama, T Ravasi, B Lenhard, C Wells, R Kodzius, K Shimokawa, VB Bajic, SE Brenner, S Batalov, ARR Forrest, M Zavolan, MJ Davis, LG Wilming, Aidinis, V, JE Allen, Ambesi-Impiombato, X, R Apweiler, RN Aturaliya, TL Bailey, M Bansal, L Baxter, KW Beisel, T Bersano, H Bono, AM Chalk, KP Chiu, Choudhary, V, A Christoffels, DR Clutterbuck, ML Crowe, E Dalla, BP Dalrymple, B de Bono, G Della Gatta, D di Bernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, CF Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, TR Gingeras, T Gojobori, RE Green, S Gustincich, M Harbers, Y Hayashi, TK Hensch, N Hirokawa, D Hill, L Huminiecki, M Iacono, K Ikeo, A Iwama, T Ishikawa, M Jakt, A Kanapin, M Katoh, Y Kawasawa, J Kelso, H Kitamura, H Kitano, G Kollias, SPT Krishnan, A Kruger, SK Kummerfeld, Kurochkin, IV, LF Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, MM Babu, M Madera, L Marchionni, H Matsuda, S Matsuzawa, H Miki, F Mignone, S Miyake, K Morris, S Mottagui-Tabar, N Mulder, N Nakano, H Nakauchi, P Ng, R Nilsson, S Nishiguchi, S Nishikawa, F Nori, O Ohara, Y Okazaki, Orlando, V, KC Pang, WJ Pavan, G Pavesi, G Pesole, N Petrovsky, S Piazza, J Reed, JF Reid, BZ Ring, M Ringwald, B Rost, Y Ruan, SL Salzberg, A Sandelin, C Schneider, C Schonbach, K Sekiguchi, CAM Semple, S Seno, L Sessa, Y Sheng, Y Shibata, H Shimada, K Shimada, D Silva, B Sinclair, S Sperling, E Stupka, K Sugiura, R Sultana, Y Takenaka, K Taki, K Tammoja, SL Tan, S Tang, MS Taylor, J Tegner, SA Teichmann, HR Ueda, E van Nimwegen, R Verardo, CL Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, A Zimmer, W Hide, C Bult, SM Grimmond, RD Teasdale, ET Liu, Brusic, V, J Quackenbush, C Wahlestedt, JS Mattick, DA Hume, C Kai, D Sasaki, Y Tomaru, S Fukuda, M Kanamori-Katayama, M Suzuki, J Aoki, T Arakawa, J Iida, K Imamura, M Itoh, T Kato, H Kawaji, N Kawagashira, T Kawashima, M Kojima, S Kondo, H Konno, K Nakano, N Ninomiya, T Nishio, M Okada, C Plessy, K Shibata, T Shiraki, S Suzuki, M Tagami, K Waki, A Watahiki, Y Okamura-Oho, H Suzuki, J Kawai, Y Hayashizaki

SCIENCE　Vol. 309　No. 5740　p. 1559-1563　2005/09　Research paper (scientific journal)

A method for clustering gene expression data based on graph structure.

Seno S, Teramoto R, Takenaka Y, Matsuda H

Genome informatics. International Conference on Genome Informatics　Vol. 15　No. 2　p. 151-160　2004　Research paper (scientific journal)

P-quasi complete linkage analysis for gene-expression data

S. Seno, R. Teramoto, H. Matsuda

Proceedings - IEEE Computer Society Bioinformatics Conference, CSB 2002　2002　Research paper (international conference proceedings)