Identification of the differences in molecular networks between idiopathic pulmonary fibrosis and lung squamous cell carcinoma using machine learning

Yosui Nojima, Kenji Mizuguchi

Computational Biology and Chemistry　2025/06　Research paper (scientific journal)

A Novel Method for Endometrial Cancer Patient Stratification Considering ARID1A Protein Expression and Activity with Effective Use of Multi-omics Data

Junsoo Song, Ayako Ui, Kenji Mizuguchi, Reiko Watanabe

Computational and Structural Biotechnology Journal　2025/06　Research paper (scientific journal)

Dual antioxidant and cytotoxic activities of novel 1,2,3-triazole-decorated unsymmetrical monocarbonyl curcumin analogs

Bayu Ardiansah, Ahmad Farhan, Novita Sari Nurhasanah, Mochammad Arfin Fardiansyah Nasution, Noordini M. Salleh, Kenji Mizuguchi, Antonius Herry Cahyana, Lina Mardiana

Case Studies in Chemical and Environmental Engineering　Vol. 11　p. 101031-101031　2025/06　Research paper (scientific journal)

Improving the accuracy of prediction models for small datasets of Cytochrome P450 inhibition with deep learning

Elpri Eka Permadi, Reiko Watanabe, Kenji Mizuguchi

Journal of Cheminformatics　Vol. 17　No. 1　2025/04/30　Research paper (scientific journal)

Biological age prediction using a DNN model based on pathways of steroidogenesis

Qiuyi Wang, Zi Wang, Kenji Mizuguchi, Toshifumi Takao

Science Advances　Vol. 11　No. 11　2025/03/14　Research paper (scientific journal)

Effects of Malted Rice Amazake Consumption on Nutritional Status and Gut Microbiome in Older Patients and Residents of an Integrated Facility for Medical and Long-Term Care

Miki Doi, Rikako Inoue, Koji Hosomi, Jonguk Park, Hitomi Yumioka, A. Yasmin Syauki, Suzumi Kageyama, Haruka Sakaue, Kozo Tanabe, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie

Journal of Nutrition in Gerontology and Geriatrics　p. 1-23　2025/01/16　Research paper (scientific journal)

Clinical Phenotypes Associated with the Gut Microbiome in Older Japanese People with Care Needs in a Nursing Home

Rikako Inoue, Koji Hosomi, Jonguk Park, Haruka Sakaue, Hitomi Yumioka, Hiroko Kamitani, Yoshiharu Kinugasa, Kaori Harano, A. Yasmin Syauki, Miki Doi, Suzumi Kageyama, Kazuhiro Yamamoto, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie

Nutrients　Vol. 16　No. 22　p. 3839-3839　2024/11/08　Research paper (scientific journal)

High barley intake in non-obese individuals is associated with high natto consumption and abundance of butyrate-producing bacteria in the gut: a cross-sectional study

Satoko Maruyama, Tsubasa Matsuoka, Koji Hosomi, Jonguk Park, Haruka Murakami, Motohiko Miyachi, Hitoshi Kawashima, Kenji Mizuguchi, Toshiki Kobayashi, Tadao Ooka, Zentaro Yamagata, Jun Kunisawa

Frontiers in Nutrition　Vol. 11　2024/10/31　Research paper (scientific journal)

Association Between Gut Microbiome Composition and Physical Characteristics in Patients with Severe Motor and Intellectual Disabilities: Perspectives from Microbial Diversity

Suzumi Kageyama, Rikako Inoue, Koji Hosomi, Jonguk Park, Hitomi Yumioka, Miki Doi, Miyuu Miyake, Yuka Nagashio, Yoshiko Shibuya, Nobue Oka, Hirofumi Akazawa, Susumu Kanzaki, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie

Nutrients　Vol. 16　No. 20　p. 3546-3546　2024/10/19　Research paper (scientific journal)

A modern multi-omics data exploration experience with Panomicon

Rodolfo S Allendes Osorio, Yuji Kosugi, Johan T Nyström-Persson, Kenji Mizuguchi, Yayoi Natsume-Kitatani

Bioinformatics Advances　2024/10/03　Research paper (scientific journal)

Phosphoproteomic subtyping of gastric cancer reveals dynamic transformation with chemotherapy and guides targeted cancer treatment

Hirokazu Shoji, Hidekazu Hirano, Yosui Nojima, Daigo Gunji, Akina Shinkura, Satoshi Muraoka, Yuichi Abe, Ryohei Narumi, Chioko Nagao, Masahiko Aoki, Kazutaka Obama, Kazufumi Honda, Kenji Mizuguchi, Takeshi Tomonaga, Yutaka Saito, Takaki Yoshikawa, Ken Kato, Narikazu Boku, Jun Adachi

Cell Reports　p. 114774-114774　2024/10　Research paper (scientific journal)

Group X phospholipase A2 links colonic lipid homeostasis to systemic metabolism via host-microbiota interaction

Hiroyasu Sato, Yoshitaka Taketomi, Remi Murase, Jonguk Park, Koji Hosomi, Takayuki Jujo Sanada, Kenji Mizuguchi, Makoto Arita, Jun Kunisawa, Makoto Murakami

Cell Reports　Vol. 43　No. 10　p. 114752-114752　2024/10　Research paper (scientific journal)

Construction of a Tm-Value Prediction Model and Molecular Dynamics Study of AmNA-Containing Gapmer Antisense Oligonucleotide

Masataka Kuroda, Yuuya Kasahara, Masako Hirose, Harumi Yamaguma, Masayuki Oda, Chioko Nagao, Kenji Mizuguchi

Molecular Therapy - Nucleic Acids　p. 102272-102272　2024/07/16　Research paper (scientific journal)

Effect of resistance training and chicken meat on muscle strength and mass and the gut microbiome of older women: A randomized controlled trial

Masataka Uchida, Jonguk Park, Shumpei Fujie, Koji Hosomi, Naoki Horii, Kohei Watanabe, Kiyoshi Sanada, Yasushi Shinohara, Kenji Mizuguchi, Jun Kunisawa, Motoyuki Iemitsu, Motohiko Miyachi

Physiological Reports　Vol. 12　No. 12　2024/06/18　Research paper (scientific journal)

SFTPB in serum extracellular vesicles as a biomarker of progressive pulmonary fibrosis

Takatoshi Enomoto, Yuya Shirai, Yoshito Takeda, Ryuya Edahiro, Shigeyuki Shichino, Mana Nakayama, Miho Takahashi-Itoh, Yoshimi Noda, Yuichi Adachi, Takahiro Kawasaki, Taro Koba, Yu Futami, Moto Yaga, Yuki Hosono, Hanako Yoshimura, Saori Amiya, Reina Hara, Makoto Yamamoto, Daisuke Nakatsubo, Yasuhiko Suga, Maiko Naito, Kentaro Masuhiro, Haruhiko Hirata, Kota Iwahori, Izumi Nagatomo, Kotaro Miyake, Shohei Koyama, Kiyoharu Fukushima, Takayuki Shiroyama, Yujiro Naito, Shinji Futami, Yayoi Natsume-Kitatani, Satoshi Nojima, Masahiro Yanagawa, Yasushi Shintani, Mari Nogami-Itoh, Kenji Mizuguchi, Jun Adachi, Takeshi Tomonaga, Yoshikazu Inoue, Atsushi Kumanogoh

JCI Insight　Vol. 9　No. 11　2024/06/10　Research paper (scientific journal)

Galectin-10 in serum extracellular vesicles reflects asthma pathophysiology

Hanako Yoshimura, Yoshito Takeda, Yuya Shirai, Makoto Yamamoto, Daisuke Nakatsubo, Saori Amiya, Takatoshi Enomoto, Reina Hara, Yuichi Adachi, Ryuya Edahiro, Moto Yaga, Kentaro Masuhiro, Taro Koba, Miho Itoh-Takahashi, Mana Nakayama, So Takata, Yuki Hosono, Sho Obata, Masayuki Nishide, Akinori Hata, Masahiro Yanagawa, Satoko Namba, Michio Iwata, Momoko Hamano, Haruhiko Hirata, Shohei Koyama, Kota Iwahori, Izumi Nagatomo, Yasuhiko Suga, Kotaro Miyake, Takayuki Shiroyama, Kiyoharu Fukushima, Shinji Futami, Yujiro Naito, Takahiro Kawasaki, Kenji Mizuguchi, Yusuke Kawashima, Yoshihiro Yamanishi, Jun Adachi, Mari Nogami-Itoh, Shigeharu Ueki, Atsushi Kumanogoh

Journal of Allergy and Clinical Immunology　2024/03　Research paper (scientific journal)

Structural and accessibility studies highlight the differential binding of clemizole to TRPC5 and TRPC6

Uzma Saqib, Isaac S. Demaree, Alexander G. Obukhov, Mirza S. Baig, Mohd Shahnawaz Khan, Nojood Altwaijry, Mochammad Arfin Fardiansyah Nasution, Kenji Mizuguchi, Krishnan Hajela

Journal of Biomolecular Structure and Dynamics　2024/01/27　Research paper (scientific journal)

Idiopathic pulmonary fibrosis-specific Bayesian network integrating extracellular vesicle proteome and clinical information

Mei Tomoto, Yohei Mineharu, Noriaki Sato, Yoshinori Tamada, Mari Nogami-Itoh, Masataka Kuroda, Jun Adachi, Yoshito Takeda, Kenji Mizuguchi, Atsushi Kumanogoh, Yayoi Natsume-Kitatani, Yasushi Okuno

Scientific Reports　Vol. 14　No. 1　2024/01/15　Research paper (scientific journal)

Impact of Hydrogen Bonding on P-Glycoprotein Efflux Transport as Revealed by Evaluation of a De Novo Prediction Model

Yulong Gou, Suyong Re, Kenji Mizuguchi, Chioko Nagao

ACS Medicinal Chemistry Letters　2023/12/21　Research paper (scientific journal)

Attention network for predicting T-cell receptor–peptide binding can associate attention with interpretable protein structural properties

Kyohei Koyama, Kosuke Hashimoto, Chioko Nagao, Kenji Mizuguchi

Frontiers in Bioinformatics　Vol. 3　2023/12/18　Research paper (scientific journal)

Association of skeletal muscle function, quantity, and quality with gut microbiota in Japanese adults: A cross-sectional study.

Chiharu Iwasaka, Hinako Nanri, Takashi Nakagata, Harumi Ohno, Kumpei Tanisawa, Kana Konishi, Haruka Murakami, Koji Hosomi, Jonguk Park, Yosuke Yamada, Rei Ono, Kenji Mizuguchi, Jun Kunisawa, Motohiko Miyachi

Geriatrics & gerontology international　2023/12/14　Research paper (scientific journal)

Effects of energy loads on energy and nutrient absorption rates and gut microbiome in humans: A randomized crossover trial

Eiichi Yoshimura, Yuka Hamada, Yoichi Hatamoto, Takashi Nakagata, Hinako Nanri, Yui Nakayama, Takanori Hayashi, Ippei Suzuki, Takafumi Ando, Kazuko Ishikawa‐Takata, Shigeho Tanaka, Rei Ono, Jonguk Park, Koji Hosomi, Kenji Mizuguchi, Jun Kunisawa, Motohiko Miyachi

Obesity　2023/11/05　Research paper (scientific journal)

Changes in Fecal Gut Microbiome of Home Healthcare Patients with Disabilities through Consumption of Malted Rice Amazake

Suzumi Kageyama, Rikako Inoue, Jonguk Park, Koji Hosomi, Hitomi Yumioka, Tomo Suka, Kazuaki Teramoto, A. Yasmin Syauki, Miki Doi, Haruka Sakaue, Miyuu Miyake, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie

Physiological Genomics　2023/09/11　Research paper (scientific journal)

Ramen Consumption and Gut Microbiota Diversity in Japanese Women: Cross-Sectional Data from the NEXIS Cohort Study

Jonguk Park, Hiroto Bushita, Ayatake Nakano, Ai Hara, Hiroshi M. Ueno, Naoki Ozato, Koji Hosomi, Hitoshi Kawashima, Yi-An Chen, Attayeb Mohsen, Harumi Ohno, Kana Konishi, Kumpei Tanisawa, Hinako Nanri, Haruka Murakami, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi, Michihiro Araki

Microorganisms　Vol. 11　No. 8　p. 1892-1892　2023/07/26　Research paper (scientific journal)

Gut microbiota alternation with training periodization and physical fitness in Japanese elite athletes

Nobuhiko Akazawa, Mariko Nakamura, Nobuhiko Eda, Haruka Murakami, Takashi Nakagata, Hinako Nanri, Jonguk Park, Koji Hosomi, Kenji Mizuguchi, Jun Kunisawa, Motohiko Miyachi, Masako Hoshikawa

Frontiers in Sports and Active Living　Vol. 5　2023/07/14　Research paper (scientific journal)

DruMAP: A Novel Drug Metabolism and Pharmacokinetics Analysis Platform

Hitoshi Kawashima, Reiko Watanabe, Tsuyoshi Esaki, Masataka Kuroda, Chioko Nagao, Yayoi Natsume-Kitatani, Rikiya Ohashi, Hiroshi Komura, Kenji Mizuguchi

Journal of Medicinal Chemistry　2023/07/14　Research paper (scientific journal)

Predicting thrombotic cardiovascular outcomes induced by waterpipe-associated chemicals using comparative toxicogenomic database: Genes, phenotypes, and pathways

Ahmed B. Alarabi, Attayab Mohsen, Ziyad Ben Taleb, Kenji Mizuguchi, Fatima Z. Alshbool, Fadi T. Khasawneh

Life Sciences　Vol. 323　p. 121694-121694　2023/06　Research paper (scientific journal)

Evidence-Based Prediction of Cellular Toxicity for Amorphous Silica Nanoparticles

Martin, Reiko Watanabe, Kosuke Hashimoto, Kazuma Higashisaka, Yuya Haga, Yasuo Tsutsumi, Kenji Mizuguchi

ACS Nano　2023/05/30　Research paper (scientific journal)

Characteristic Gut Bacteria in High Barley Consuming Japanese Individuals without Hypertension

Satoko Maruyama, Tsubasa Matsuoka, Koji Hosomi, Jonguk Park, Mao Nishimura, Haruka Murakami, Kana Konishi, Motohiko Miyachi, Hitoshi Kawashima, Kenji Mizuguchi, Toshiki Kobayashi, Tadao Ooka, Zentaro Yamagata, Jun Kunisawa

Microorganisms　Vol. 11　No. 5　2023/05/09　Research paper (scientific journal)

Integration of pharmacoproteomic and computational approaches reveals the cellular signal transduction pathways affected by apatinib in gastric cancer cell lines

Yosui Nojima, Masahiko Aoki, Suyong Re, Hidekazu Hirano, Yuichi Abe, Ryohei Narumi, Satoshi Muraoka, Hirokazu Shoji, Kazufumi Honda, Takeshi Tomonaga, Kenji Mizuguchi, Narikazu Boku, Jun Adachi

Computational and Structural Biotechnology Journal　2023/03　Research paper (scientific journal)

RDFization of Interview Forms for Effective Use of Pharmaceutical Documents

Nagao Chioko, Kamada Mayumi, Nakatsui Masahiko, Fukagawa Akiko, Katayama Toshiaki, Kawashima Shuichi, Mizuguchi Kenji, Abe Rika

Japanese Journal of Drug Informatics　Vol. 24　No. 4　p. 187-195　2023/02/28　Research paper (scientific journal)

DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein–protein interactions

Kazuyoshi Ikeda, Yuta Maezawa, Tomoki Yonezawa, Yugo Shimizu, Toshiyuki Tashiro, Satoru Kanai, Nobuyoshi Sugaya, Yoshiaki Masuda, Naoko Inoue, Tatsuya Niimi, Keiichi Masuya, Kenji Mizuguchi, Toshio Furuya, Masanori Osawa

Frontiers in Chemistry　Vol. 10　2023/01/09　Research paper (scientific journal)

Prediction of the Contribution Ratio of a Target Metabolic Enzyme to Clearance from Chemical Structure Information

Reiko Watanabe, Toshio Kawata, Shinya Ueda, Takumi Shinbo, Mitsuo Higashimori, Yayoi Natsume-Kitatani, Kenji Mizuguchi

Molecular Pharmaceutics　2022/12/20　Research paper (scientific journal)

Identification of Human Gut Microbiome Associated with Enterolignan Production

Kento Sawane, Koji Hosomi, Jonguk Park, Kouta Ookoshi, Hinako Nanri, Takashi Nakagata, Yi-An Chen, Attayeb Mohsen, Hitoshi Kawashima, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa

Microorganisms　Vol. 10　No. 11　p. 2169-2169　2022/10/31　Research paper (scientific journal)

Structural dynamics of the N‐terminal SH2 domain of PI3K in its free and CD28‐bound states

Yuhi Hosoe, Yohei Miyanoiri, Suyong Re, Saki Ochi, Yuya Asahina, Toru Kawakami, Masataka Kuroda, Kenji Mizuguchi, Masayuki Oda

The FEBS Journal　Vol. 290　No. 9　p. 2366-2378　2022/10/25　Research paper (scientific journal)

Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota

Koji Hosomi, Mayu Saito, Jonguk Park, Haruka Murakami, Naoko Shibata, Masahiro Ando, Takahiro Nagatake, Kana Konishi, Harumi Ohno, Kumpei Tanisawa, Attayeb Mohsen, Yi-An Chen, Hitoshi Kawashima, Yayoi Natsume-Kitatani, Yoshimasa Oka, Hidenori Shimizu, Mari Furuta, Yoko Tojima, Kento Sawane, Azusa Saika, Saki Kondo, Yasunori Yonejima, Haruko Takeyama, Akira Matsutani, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa

Nature Communications　Vol. 13　No. 1　p. 4477-4477　2022/08/18　Research paper (scientific journal)

TargetMine 2022: A new vision into drug target analysis.

Yi-An Chen, Rodolfo S Allendes Osorio, Kenji Mizuguchi

Bioinformatics (Oxford, England)　2022/07/27　Research paper (scientific journal)

Integrative Network Modeling Highlights the Crucial Roles of Rho-GDI Signaling Pathway in the Progression of Non-Small Cell Lung Cancer.

Saransh Gupta, Haswanth Vundavilli, Rodolfo S Allendes Osorio, Mari N Itoh, Attayeb Mohsen, Aniruddha Datta, Kenji Mizuguchi, Lokesh P Tripathi

IEEE journal of biomedical and health informatics　Vol. PP　2022/07/12　Research paper (scientific journal)

Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2

Attayeb Mohsen, Yi-An Chen, Rodolfo S. Allendes Osorio, Chihiro Higuchi, Kenji Mizuguchi

Frontiers in Bioinformatics　Vol. 2　p. 893933-893933　2022/07/01　Research paper (scientific journal)

Dietary Vitamin B1 Intake Influences Gut Microbial Community and the Consequent Production of Short-Chain Fatty Acids.

Jonguk Park, Koji Hosomi, Hitoshi Kawashima, Yi-An Chen, Attayeb Mohsen, Harumi Ohno, Kana Konishi, Kumpei Tanisawa, Masako Kifushi, Masato Kogawa, Haruko Takeyama, Haruka Murakami, Tetsuya Kubota, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi

Nutrients　Vol. 14　No. 10　2022/05/16　Research paper (scientific journal)

Co-expression analysis to identify key modules and hub genes associated with COVID-19 in platelets

Ahmed B. Alarabi, Attayeb Mohsen, Kenji Mizuguchi, Fatima Z. Alshbool, Fadi T. Khasawneh

BMC Medical Genomics　Vol. 15　No. 1　2022/04　Research paper (scientific journal)

Altered gut microbiota and its association with inflammation in patients with chronic thromboembolic pulmonary hypertension: a single-center observational study in Japan

Yumiko Ikubo, Takayuki Jujo Sanada, Koji Hosomi, Jonguk Park, Akira Naito, Hiroki Shoji, Tomoko Misawa, Rika Suda, Ayumi Sekine, Toshihiko Sugiura, Ayako Shigeta, Hinako Nanri, Seiichiro Sakao, Nobuhiro Tanabe, Kenji Mizuguchi, Jun Kunisawa, Takuji Suzuki, Koichiro Tatsumi

BMC Pulmonary Medicine　Vol. 22　No. 1　2022/04　Research paper (scientific journal)

Classification of the Occurrence of Dyslipidemia Based on Gut Bacteria Related to Barley Intake

Satoko Maruyama, Tsubasa Matsuoka, Koji Hosomi, Jonguk Park, Mao Nishimura, Haruka Murakami, Kana Konishi, Motohiko Miyachi, Hitoshi Kawashima, Kenji Mizuguchi, Toshiki Kobayashi, Tadao Ooka, Zentaro Yamagata, Jun Kunisawa

Frontiers in Nutrition　Vol. 9　2022/03/24　Research paper (scientific journal)

α-Amino acid and peptide synthesis using catalytic cross-dehydrogenative coupling

Taro Tsuji, Kayoko Hashiguchi, Mana Yoshida, Tetsu Ikeda, Yunosuke Koga, Yusaku Honda, Tsukushi Tanaka, Suyong Re, Kenji Mizuguchi, Daisuke Takahashi, Ryo Yazaki, Takashi Ohshima

Nature Synthesis　Vol. 1　No. 4　p. 304-312　2022/03/14　Research paper (scientific journal)

Temporal dynamics from phosphoproteomics using endoscopic biopsy specimens provides new therapeutic targets in stage IV gastric cancer

Hidekazu Hirano, Yuichi Abe, Yosui Nojima, Masahiko Aoki, Hirokazu Shoji, Junko Isoyama, Kazufumi Honda, Narikazu Boku, Kenji Mizuguchi, Takeshi Tomonaga, Jun Adachi

Scientific Reports　Vol. 12　No. 1　2022/03　Research paper (scientific journal)

Relationships between barley consumption and gut microbiome characteristics in a healthy Japanese population: a cross-sectional study

Tsubasa Matsuoka, Koji Hosomi, Jonguk Park, Yuka Goto, Mao Nishimura, Satoko Maruyama, Haruka Murakami, Kana Konishi, Motohiko Miyachi, Hitoshi Kawashima, Kenji Mizuguchi, Toshiki Kobayashi, Hiroshi Yokomichi, Jun Kunisawa, Zentaro Yamagata

BMC Nutrition　Vol. 8　No. 1　p. 23-23　2022/03　Research paper (scientific journal)

The Gut Microbiome as a Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma

TAKEHIRO OTOSHI, TATSUYA NAGANO, JONGUK PARK, KOJI HOSOMI, TOMOYA YAMASHITA, MOTOKO TACHIHARA, TOKIKO TABATA, REINA SEKIYA, YUGO TANAKA, KAZUYUKI KOBAYASHI, KENJI MIZUGUCHI, TOMOO ITOH, YOSHIMASA MANIWA, JUN KUNISAWA, YOSHIHIRO NISHIMURA

Anticancer Research　Vol. 42　No. 3　p. 1589-1598　2022/03　Research paper (scientific journal)

Group IIA secreted phospholipase A2 controls skin carcinogenesis and psoriasis by shaping the gut microbiota

Yoshimi Miki, Yoshitaka Taketomi, Yuh Kidoguchi, Kei Yamamoto, Kazuaki Muramatsu, Yasumasa Nishito, Jonguk Park, Koji Hosomi, Kenji Mizuguchi, Jun Kunisawa, Tomoyoshi Soga, Eric Boilard, Siddabasave Gowda B. Gowda, Kazutaka Ikeda, Makoto Arita, Makoto Murakami

JCI Insight　Vol. 7　No. 2　2022/01/25　Research paper (scientific journal)

Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide

Daiki Yamane, Satsuki Onitsuka, Suyong Re, Hikaru Isogai, Rui Hamada, Tadanari Hiramoto, Eiji Kawanishi, Kenji Mizuguchi, Naoya Shindo, Akio Ojida

Chemical Science　Vol. 13　No. 10　p. 3027-3034　2022　Research paper (scientific journal)

Flavivirus recruits the valosin-containing protein (VCP)/NPL4 complex to induce stress granule disassembly for efficient viral genome replication

Masashi Arakawa, Keisuke Tabata, Kotaro Ishida, Makiko Kobayashi, Arisa Arai, Tomohiro Ishikawa, Ryosuke Suzuki, Hiroaki Takeuchi, Lokesh P. Tripathi, Kenji Mizuguchi, Eiji Morita

Journal of Biological Chemistry　p. 101597-101597　2022/01　Research paper (scientific journal)

Effects of Malted Rice Amazake on Constipation Symptoms and Gut Microbiota in Children and Adults with Severe Motor and Intellectual Disabilities: A Pilot Study

Suzumi Kageyama, Rikako Inoue, Koji Hosomi, Jonguk Park, Hitomi Yumioka, Tomo Suka, Yoshihiro Kurohashi, Kazuaki Teramoto, A. Yasmin Syauki, Miki Doi, Haruka Sakaue, Kenji Mizuguchi, Jun Kunisawa, Yasuyuki Irie

Nutrients　Vol. 13　No. 12　p. 4466-4466　2021/12/14　Research paper (scientific journal)

Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts

Jonguk Park, Kumiko Kato, Haruka Murakami, Koji Hosomi, Kumpei Tanisawa, Takashi Nakagata, Harumi Ohno, Kana Konishi, Hitoshi Kawashima, Yi-An Chen, Attayeb Mohsen, Jin-zhong Xiao, Toshitaka Odamaki, Jun Kunisawa, Kenji Mizuguchi, Motohiko Miyachi

BMC Microbiology　Vol. 21　No. 1　p. 151-151　2021/12　Research paper (scientific journal)

Categorization of the Ocular Microbiome in Japanese Stevens–Johnson Syndrome Patients With Severe Ocular Complications

Mayumi Ueta, Koji Hosomi, Jonguk Park, Kenji Mizuguchi, Chie Sotozono, Shigeru Kinoshita, Jun Kunisawa

Frontiers in Cellular and Infection Microbiology　Vol. 11　p. 741654-741654　2021/11/19　Research paper (scientific journal)

Deep Learning Prediction of Adverse Drug Reactions in Drug Discovery Using Open TG–GATEs and FAERS Databases

Attayeb Mohsen, Lokesh P. Tripathi, Kenji Mizuguchi

Frontiers in Drug Discovery　Vol. 1　2021/10/27　Research paper (scientific journal)

Relationship between Human Gut Microbiota and Nutrition Intake in Hypertensive Discordant Monozygotic Twins

Rie Tomizawa, Jonguk Park, Natsuko Matsumoto, Koji Hosomi, Hitoshi Kawashima, Kenji Mizuguchi, Jun Kunisawa, Chika Honda

Journal of Hypertension: Open Access　Vol. 10　No. 8　2021/08　Research paper (scientific journal)

Distinct Age-Specific miRegulome Profiling of Isolated Small and Large Intestinal Epithelial Cells in Mice

Juneyoung Lee, Attayeb Mohsen, Anik Banerjee, Louise D. McCullough, Kenji Mizuguchi, Motomu Shimaoka, Hiroshi Kiyono, Eun Jeong Park

International Journal of Molecular Sciences　Vol. 22　No. 7　p. 3544-3544　2021/03/29　Research paper (scientific journal)

Relationship between Nutrient Intake and Human Gut Microbiota in Monozygotic Twins

Natsuko Matsumoto, Jonguk Park, Rie Tomizawa, Hitoshi Kawashima, Koji Hosomi, Kenji Mizuguchi, Chika Honda, Ritsuko Ozaki, Yoshinori Iwatani, Mikio Watanabe, Jun Kunisawa

Medicina　Vol. 57　No. 3　p. 275-275　2021/03/16　Research paper (scientific journal)

Network Modeling and Inference of Peroxisome Proliferator-Activated Receptor Pathway in High fat diet-linked Obesity.

Haswanth Vundavilli, Lokesh P.Tripathi, Aniruddha Datta, Kenji Mizuguchi

Journal of theoretical biology　p. 110647-110647　2021/02/25　Research paper (scientific journal)

Development of an In Silico Prediction Model for P-glycoprotein Efflux Potential in Brain Capillary Endothelial Cells toward the Prediction of Brain Penetration

Reiko Watanabe, Tsuyoshi Esaki, Rikiya Ohashi, Masataka Kuroda, Hitoshi Kawashima, Hiroshi Komura, Yayoi Natsume-Kitatani, Kenji Mizuguchi

Journal of Medicinal Chemistry　2021/02/23　Research paper (scientific journal)

Glycan Cluster Shielding and Antibody Epitopes on Lassa Virus Envelop Protein

Suyong Re, Kenji Mizuguchi

The Journal of Physical Chemistry B　Vol. 125　No. 8　p. 2089-2097　2021/02/19　Research paper (scientific journal)

Proteomics of serum extracellular vesicles identifies a novel COPD biomarker, fibulin-3 from elastic fibres

Taro Koba, Yoshito Takeda, Ryohei Narumi, Takashi Shiromizu, Yosui Nojima, Mari Ito, Muneyoshi Kuroyama, Yu Futami, Takayuki Takimoto, Takanori Matsuki, Ryuya Edahiro, Satoshi Nojima, Yoshitomo Hayama, Kiyoharu Fukushima, Haruhiko Hirata, Shohei Koyama, Kota Iwahori, Izumi Nagatomo, Mayumi Suzuki, Yuya Shirai, Teruaki Murakami, Kaori Nakanishi, Takeshi Nakatani, Yasuhiko Suga, Kotaro Miyake, Takayuki Shiroyama, Hiroshi Kida, Takako Sasaki, Koji Ueda, Kenji Mizuguchi, Jun Adachi, Takeshi Tomonaga, Atsushi Kumanogoh

ERJ Open Research　Vol. 7　No. 1　p. 00658-2020　2021/01　Research paper (scientific journal)

Integrative Analysis Reveals Common and Unique Roles of Tetraspanins in Fibrosis and Emphysema

Lokesh P. Tripathi, Mari N. Itoh, Yoshito Takeda, Kazuyuki Tsujino, Yasushi Kondo, Atsushi Kumanogoh, Kenji Mizuguchi

Frontiers in Genetics　Vol. 11　p. 585998-585998　2020/12/10　Research paper (scientific journal)

MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data

Yi-An Chen, Jonguk Park, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Attayeb Mohsen, Koji Hosomi, Kumpei Tanisawa, Harumi Ohno, Kana Konishi, Haruka Murakami, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi

PLOS ONE　Vol. 15　No. 12　p. e0243609-e0243609　2020/12/04　Research paper (scientific journal)

Developing a Kinase-Specific Target Selection Method Using a Structure-Based Machine Learning Approach

Arina Afanasyeva, Chioko Nagao, Kenji Mizuguchi

Advances and Applications in Bioinformatics and Chemistry　Vol. Volume 13　p. 27-40　2020/12　Research paper (scientific journal)

Metabolomic analysis of fibrotic mice combined with public RNA-Seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis.

Yosui Nojima, Yoshito Takeda, Yohei Maeda, Takeshi Bamba, Eiichiro Fukusaki, Mari N Itoh, Kenji Mizuguchi, Atsushi Kumanogoh

FEBS open bio　Vol. 10　No. 11　p. 2427-2436　2020/09/22　Research paper (scientific journal)

Panomicon: A web-based environment for interactive, visual analysis of multi-omics data.

Rodolfo S Allendes Osorio, Johan T Nyström-Persson, Yosui Nojima, Yuji Kosugi, Kenji Mizuguchi, Yayoi Natsume-Kitatani

Heliyon　Vol. 6　No. 8　p. e04618-e04618　2020/08　Research paper (scientific journal)

Update of the GRIP web service.

Akira Saito, Daiki Tsuchiya, Seiji Sato, Atsushi Okamoto, Yoichi Murakami, Kenji Mizuguchi, Hiroyuki Toh, Wataru Nemoto

Journal of receptor and signal transduction research　Vol. 40　No. 4　p. 348-356　2020/08　Research paper (scientific journal)

Gut microbial composition in patients with atrial fibrillation: effects of diet and drugs.

Tokiko Tabata, Tomoya Yamashita, Koji Hosomi, Jonguk Park, Tomohiro Hayashi, Naofumi Yoshida, Yoshihiro Saito, Koji Fukuzawa, Kana Konishi, Haruka Murakami, Hitoshi Kawashima, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa, Ken-Ichi Hirata

Heart and vessels　Vol. 36　No. 1　p. 105-114　2020/07/18　Research paper (scientific journal)

Gut microbiota modification suppresses the development of pulmonary arterial hypertension in an SU5416/hypoxia rat model

Takayuki J. Sanada, Koji Hosomi, Hiroki Shoji, Jonguk Park, Akira Naito, Yumiko Ikubo, Asako Yanagisawa, Takayuki Kobayashi, Hideki Miwa, Rika Suda, Seiichiro Sakao, Kenji Mizuguchi, Jun Kunisawa, Nobuhiro Tanabe, Koichiro Tatsumi

Pulmonary Circulation　Vol. 10　No. 3　p. 204589402092914-204589402092914　2020/07　Research paper (scientific journal)

Novel anti-flavivirus drugs targeting the nucleolar distribution of core protein.

Makoto Tokunaga, Yoichi Miyamoto, Tatsuya Suzuki, Mayumi Otani, Shinsuke Inuki, Tsuyoshi Esaki, Chioko Nagao, Kenji Mizuguchi, Hiroaki Ohno, Yoshihiro Yoneda, Toru Okamoto, Masahiro Oka, Yoshiharu Matsuura

Virology　Vol. 541　p. 41-51　2020/02　Research paper (scientific journal)

Actin Cytoskeletal Reorganization Function of JRAB/MICAL-L2 Is Fine-tuned by Intramolecular Interaction between First LIM Zinc Finger and C-terminal Coiled-coil Domains

Miyake K, Sakane A, Tsuchiya Y, Sagawa I, Tomida Y, Kasahara J, Imoto I, Watanabe S, Higo D, Mizuguchi K, Sasaki T

Scientific Reports　Vol. 9　No. 1　p. 12794-12794　2019/12　Research paper (scientific journal)

A prospective compound screening contest identified broader inhibitors for Sirtuin 1

Shuntaro Chiba, Masahito Ohue, Anastasiia Gryniukova, Petro Borysko, Sergey Zozulya, Nobuaki Yasuo, Ryunosuke Yoshino, Kazuyoshi Ikeda, Woong-Hee Shin, Daisuke Kihara, Mitsuo Iwadate, Hideaki Umeyama, Takaaki Ichikawa, Reiji Teramoto, Kun-Yi Hsin, Vipul Gupta, Hiroaki Kitano, Mika Sakamoto, Akiko Higuchi, Nobuaki Miura, Kei Yura, Masahiro Mochizuki, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, M. Michael Gromiha, Itsuo Nakane, Nanako Uchida, Hayase Hakariya, Modong Tan, Hironori K. Nakamura, Shogo D. Suzuki, Tomoki Ito, Masahiro Kawatani, Kentaroh Kudoh, Sakurako Takashina, Kazuki Z. Yamamoto, Yoshitaka Moriwaki, Keita Oda, Daisuke Kobayashi, Tatsuya Okuno, Shintaro Minami, George Chikenji, Philip Prathipati, Chioko Nagao, Attayeb Mohsen, Mari Ito, Kenji Mizuguchi, Teruki Honma, Takashi Ishida, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima

Scientific Reports　Vol. 9　No. 1　2019/12　Research paper (scientific journal)

Development of an in silico prediction system of human renal excretion and clearance from chemical structure information incorporating fraction unbound in plasma as a descriptor

Watanabe R, Ohashi R, Esaki T, Kawashima H, Natsume-Kitatani Y, Nagao C, Mizuguchi K

Scientific Reports　Vol. 9　No. 1　p. 18782-18782　2019/12　Research paper (scientific journal)

Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks

Mohsen A, Park J, Chen YA, Kawashima H, Mizuguchi K

BMC Bioinformatics　Vol. 20　No. 1　2019/12　Research paper (scientific journal)

CLINE: a web-tool for the comparison of biological dendrogram structures

Allendes Osorio RS, Tripathi LP, Mizuguchi K

BMC Bioinformatics　Vol. 20　No. 1　2019/12　Research paper (scientific journal)

The TargetMine Data Warehouse: Enhancement and Updates

Chen YA, Tripathi LP, Fujiwara T, Kameyama T, Itoh MN, Mizuguchi K

Frontiers in Genetics　Vol. 10　2019/10　Research paper (scientific journal)

B cell-intrinsic MyD88 signaling controls IFN-γ-mediated early IgG2c class switching in mice in response to a particulate adjuvant

Michelle Sue Jann Lee, Yayoi Natsume-Kitatani, Burcu Temizoz, Yukiko Fujita, Aki Konishi, Kyoko Matsuda, Yoshikatsu Igari, Toshihiro Tsukui, Kouji Kobiyama, Etsushi Kuroda, Motoyasu Onishi, Thomas Marichal, Wataru Ise, Takeshi Inoue, Tomohiro Kurosaki, Kenji Mizuguchi, Shizuo Akira, Ken J. Ishii, Cevayir Coban

European Journal of Immunology　Vol. 49　No. 9　p. 1433-1440　2019/09/01　Research paper (scientific journal)

Constructing an in silico three-class predictor of human intestinal absorption with Caco-2 permeability and dried-DMSO solubility

Esaki T, Ohashi R, Watanabe R, Natsume-Kitatani Y, Kawashima H, Nagao C, Komura H, Mizuguchi K

Journal of Pharmaceutical Sciences　Vol. 108　No. 11　p. 3630-3639　2019/07　Research paper (scientific journal)

Computational Model To Predict the Fraction of Unbound Drug in the Brain

Tsuyoshi Esaki, Rikiya Ohashi, Reiko Watanabe, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Chioko Nagao, Kenji Mizuguchi

Journal of Chemical Information and Modeling　Vol. 59　No. 7　p. 3251-3261　2019/07　Research paper (scientific journal)

Development of Simplified in Vitro P-Glycoprotein Substrate Assay and in Silico Prediction Models To Evaluate Transport Potential of P-Glycoprotein

Rikiya Ohashi, Reiko Watanabe, Tsuyoshi Esaki, Tomomi Taniguchi, Nao Torimoto-Katori, Tomoko Watanabe, Yuko Ogasawara, Tsuyoshi Takahashi, Mikiko Tsukimoto, Kenji Mizuguchi

Molecular Pharmaceutics　Vol. 16　No. 5　p. 1851-1863　2019/04　Research paper (scientific journal)

High-Contrast Facile Imaging with Target-Directing Fluorescent Molecular Rotors, the N3-Modified Thioflavin T Derivatives

Yuka Kataoka, Hiroto Fujita, Arina Afanaseva, Chioko Nagao, Kenji Mizuguchi, Yuuya Kasahara, Satoshi Obika, Masayasu Kuwahara

Biochemistry　Vol. 58　No. 6　p. 493-498　2019/02　Research paper (scientific journal)

Assessing drug target suitability using TargetMine

Yi-An Chen, Erika Yogo, Naoko Kurihara, Tomoshige Ohno, Chihiro Higuchi, Masatomo Rokushima, Kenji Mizuguchi

F1000Research　Vol. 8　p. 233-233　2019/02　Research paper (scientific journal)

Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing

Yasuharu Takahashi, Jonguk Park, Koji Hosomi, Tomonori Yamada, Ayaka Kobayashi, Yuji Yamaguchi, Susumu Iketani, Jun Kunisawa, Kenji Mizuguchi, Nobuko Maeda, Tomoko Ohshima

Journal of Oral Biosciences　Vol. 61　No. 2　p. 120-128　2019/01/01　Research paper (scientific journal)

Prediction of the secondary structure of short DNA aptamers

Arina Afanasyeva, Chioko Nagao, Kenji Mizuguchi

Biophysics and Physicobiology　Vol. 16　No. 0　p. 287-294　2019　Research paper (scientific journal)

Data Curation can Improve the Prediction Accuracy of Metabolic Intrinsic Clearance.

Esaki T, Watanabe R, Kawashima H, Ohashi R, Natsume-Kitatani Y, Nagao C, Mizuguchi K

Molecular informatics　Vol. 38　No. 1-2　2018/09　Research paper (scientific journal)

Predicting Fraction Unbound in Human Plasma from Chemical Structure: Improved Accuracy in the Low Value Ranges.

Watanabe R, Esaki T, Kawashima H, Natsume-Kitatani Y, Nagao C, Ohashi R, Mizuguchi K

Molecular pharmaceutics　Vol. 15　No. 11　p. 5302-5311　2018/09　Research paper (scientific journal)

Double deletion of tetraspanins CD9 and CD81 in mice leads to a syndrome resembling accelerated aging.

Yingji Jin, Yoshito Takeda, Yasushi Kondo, Lokesh P Tripathi, Sujin Kang, Hikari Takeshita, Hanako Kuhara, Yohei Maeda, Masayoshi Higashiguchi, Kotaro Miyake, Osamu Morimura, Taro Koba, Yoshitomo Hayama, Shohei Koyama, Kaori Nakanishi, Takeo Iwasaki, Satoshi Tetsumoto, Kazuyuki Tsujino, Muneyoshi Kuroyama, Kota Iwahori, Haruhiko Hirata, Takayuki Takimoto, Mayumi Suzuki, Izumi Nagatomo, Ken Sugimoto, Yuta Fujii, Hiroshi Kida, Kenji Mizuguchi, Mari Ito, Takashi Kijima, Hiromi Rakugi, Eisuke Mekada, Isao Tachibana, Atsushi Kumanogoh

Scientific reports　Vol. 8　No. 1　p. 5145-5145　2018/03/23　Research paper (scientific journal)

An Antigen-Free, Plasmacytoid Dendritic Cell-Targeting Immunotherapy To Bolster Memory CD8+ T Cells in Nonhuman Primates.

Yuji Masuta, Takuya Yamamoto, Yayoi Natsume-Kitatani, Tomohiro Kanuma, Eiko Moriishi, Kouji Kobiyama, Kenji Mizuguchi, Yasuhiro Yasutomi, Ken J Ishii

Journal of immunology (Baltimore, Md. : 1950)　Vol. 200　No. 6　p. 2067-2075　2018/03/15　Research paper (scientific journal)

PSOPIA: Toward more reliable protein-protein interaction prediction from sequence information

Yoichi Murakami, Kenji Mizuguchi

ICIIBMS 2017 - 2nd International Conference on Intelligent Informatics and Biomedical Sciences　Vol. 2018-　p. 255-261　2018/02/02　Research paper (international conference proceedings)

Essential role of CARD14 in murine experimental psoriasis

Mayuri Tanaka, Kouji Kobiyama, Tetsuya Honda, Kozue Uchio-Yamada, Yayoi Natsume-Kitatani, Kenji Mizuguchi, Kenji Kabashima, Ken J. Ishii

Journal of Immunology　Vol. 200　No. 1　p. 71-81　2018/01/01　Research paper (scientific journal)

Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism

Shandar Ahmad, Philip Prathipati, Lokesh P. Tripathi, Yi-An Chen, Ajay Arya, Yoichi Murakami, Kenji Mizuguchi

Nucleic Acids Research　Vol. 46　No. 1　p. 54-70　2018　Research paper (scientific journal)

Quantifying the relative immune cell activation from whole tissue/organ-derived differentially expressed gene data

Edward Wijaya, Yoshinobu Igarashi, Noriyuki Nakatsu, Yasunari Haseda, Joel Billaud, Yi-An Chen, Kenji Mizuguchi, Hiroshi Yamada, Ken Ishii, Taiki Aoshi

SCIENTIFIC REPORTS　Vol. 7　No. 1　2017/10　Research paper (scientific journal)

Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity.

Koji Hosomi, Harumi Ohno, Haruka Murakami, Yayoi Natsume-Kitatani, Kumpei Tanisawa, Soichiro Hirata, Hidehiko Suzuki, Takahiro Nagatake, Tomomi Nishino, Kenji Mizuguchi, Motohiko Miyachi, Jun Kunisawa

Scientific reports　Vol. 7　No. 1　p. 4339-4339　2017/06/28　Research paper (scientific journal)

Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences

Munazah Andrabi, Andrew Paul Hutchins, Diego Miranda-Saavedra, Hidetoshi Kono, Ruth Nussinov, Kenji Mizuguchi, Shandar Ahmad

SCIENTIFIC REPORTS　Vol. 7　No. 1　2017/06　Research paper (scientific journal)

Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates

Johan Nystroem-Persson, Yayoi Natsume-Kitatani, Yoshinobu Igarashi, Daisuke Satoh, Kenji Mizuguchi

SCIENTIFIC REPORTS　Vol. 7　No. 1　2017/05　Research paper (scientific journal)

A-kinase anchoring protein BIG3 coordinates oestrogen signalling in breast cancer cells

Tetsuro Yoshimaru, Masaya Ono, Yoshimi Bando, Yi-An Chen, Kenji Mizuguchi, Hiroshi Shima, Masato Komatsu, Issei Imoto, Keisuke Izumi, Junko Honda, Yasuo Miyoshi, Mitsunori Sasa, Toyomasa Katagiri

NATURE COMMUNICATIONS　Vol. 8　2017/05　Research paper (scientific journal)

Classification of idiopathic interstitial pneumonias using anti-myxovirus resistance-protein 1 autoantibody

Yoshimasa Hamano, Hiroshi Kida, Shoichi Ihara, Akihiro Murakami, Masahiro Yanagawa, Ken Ueda, Osamu Honda, Lokesh P. Tripathi, Toru Arai, Masaki Hirose, Toshimitsu Hamasaki, Yukihiro Yano, Tetsuya Kimura, Yasuhiro Kato, Hyota Takamatsu, Tomoyuki Otsuka, Toshiyuki Minami, Haruhiko Hirata, Koji Inoue, Izumi Nagatomo, Yoshito Takeda, Masahide Mori, Hiroyoshi Nishikawa, Kenji Mizuguchi, Takashi Kijima, Masanori Kitaichi, Noriyuki Tomiyama, Yoshikazu Inoue, Atsushi Kumanogoh

SCIENTIFIC REPORTS　Vol. 7　2017/02　Research paper (scientific journal)

Syndecan-4 as a biomarker to predict clinical outcome for glioblastoma multiforme treated with WT1 peptide vaccine.

Satoshi Takashima, Yoshihiro Oka, Fumihiro Fujiki, Soyoko Morimoto, Hiroko Nakajima, Yoshiki Nakae, Jun Nakata, Sumiyuki Nishida, Naoki Hosen, Naoya Tatsumi, Kenji Mizuguchi, Naoya Hashimoto, Yusuke Oji, Akihiro Tsuboi, Atsushi Kumanogoh, Haruo Sugiyama

Future science OA　Vol. 2　No. 4　2016/12　Research paper (scientific journal)

Conformational plasticity of JRAB/MICAL-L2 provides "law and order" in collective cell migration

Ayuko Sakane, Shin Yoshizawa, Masaomi Nishimura, Yuko Tsuchiya, Natsuki Matsushita, Kazuhisa Miyake, Kazuki Horikawa, Issei Imoto, Chiharu Mizuguchi, Hiroyuki Saito, Takato Ueno, Sachi Matsushita, Hisashi Haga, Shinji Deguchi, Kenji Mizuguchi, Hideo Yokota, Takuya Sasaki

MOLECULAR BIOLOGY OF THE CELL　Vol. 27　No. 20　p. 3095-3108　2016/10　Research paper (scientific journal)

Improved pose and affinity predictions using different protocols tailored on the basis of data availability

Philip Prathipati, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN　Vol. 30　No. 9　p. 817-828　2016/09　Research paper (scientific journal)

Ligand-induced Ordering of the C-terminal Tail Primes STING for Phosphorylation by TBK1

Yuko Tsuchiya, Nao Jounai, Fumihiko Takeshita, Ken J. Ishii, Kenji Mizuguchi

EBIOMEDICINE　Vol. 9　p. 87-96　2016/07　Research paper (scientific journal)

Integration of Ligand and Structure Based Approaches for CSAR-2014

Philip Prathipati, Kenji Mizuguchi

JOURNAL OF CHEMICAL INFORMATION AND MODELING　Vol. 56　No. 6　p. 974-987　2016/06　Research paper (scientific journal)

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops

Yuko Tsuchiya, Kenji Mizuguchi

PROTEIN SCIENCE　Vol. 25　No. 4　p. 815-825　2016/04　Research paper (scientific journal)

An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework

Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION　Vol. 2016　2016/03　Research paper (scientific journal)

Retinoblastoma-binding Protein 4-regulated Classical Nuclear Transport Is Involved in Cellular Senescence

Akira Tsujii, Yoichi Miyamoto, Tetsuji Moriyama, Yuko Tsuchiya, Chikashi Obuse, Kenji Mizuguchi, Masahiro Oka, Yoshihiro Yoneda

JOURNAL OF BIOLOGICAL CHEMISTRY　Vol. 290　No. 49　p. 29375-29388　2015/12　Research paper (scientific journal)

Profiles of microRNA networks in intestinal epithelial cells in a mouse model of colitis

Juneyoung Lee, Eun Jeong Park, Yoshikazu Yuki, Shandar Ahmad, Kenji Mizuguchi, Ken J. Ishii, Motomu Shimaoka, Hiroshi Kiyono

SCIENTIFIC REPORTS　Vol. 5　2015/12　Research paper (scientific journal)

Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target

Shuntaro Chiba, Kazuyoshi Ikeda, Takashi Ishida, M. Michael Gromiha, Y-h. Taguchi, Mitsuo Iwadate, Hideaki Umeyama, Kun-Yi Hsin, Hiroaki Kitano, Kazuki Yamamoto, Nobuyoshi Sugaya, Koya Kato, Tatsuya Okuno, George Chikenji, Masahiro Mochizuki, Nobuaki Yasuo, Ryunosuke Yoshino, Keisuke Yanagisawa, Tomohiro Ban, Reiji Teramoto, Chandrasekaran Ramakrishnan, A. Mary Thangakani, D. Velmurugan, Philip Prathipati, Junichi Ito, Yuko Tsuchiya, Kenji Mizuguchi, Teruki Honma, Takatsugu Hirokawa, Yutaka Akiyama, Masakazu Sekijima

SCIENTIFIC REPORTS　Vol. 5　2015/11　Research paper (scientific journal)

Two distinct effector memory cell populations of WT1 (Wilms' tumor gene 1)-specific cytotoxic T lymphocytes in acute myeloid leukemia patients

Yoshiki Nakae, Yoshihiro Oka, Fumihiro Fujiki, Soyoko Morimoto, Toshio Kamiya, Satoshi Takashima, Jun Nakata, Sumiyuki Nishida, Hiroko Nakajima, Naoki Hosen, Akihiro Tsuboi, Taiichi Kyo, Yusuke Oji, Kenji Mizuguchi, Atsushi Kumanogoh, Haruo Sugiyama

CANCER IMMUNOLOGY IMMUNOTHERAPY　Vol. 64　No. 7　p. 791-804　2015/07　Research paper (scientific journal)

BIG3 Inhibits the Estrogen-Dependent Nuclear Translocation of PHB2 via Multiple Karyopherin-Alpha Proteins in Breast Cancer Cells

Nam-Hee Kim, Tetsuro Yoshimaru, Yi-An Chen, Taisuke Matsuo, Masato Komatsu, Yasuo Miyoshi, Eiji Tanaka, Mitsunori Sasa, Kenji Mizuguchi, Toyomasa Katagiri

PLOS ONE　Vol. 10　No. 6　2015/06　Research paper (scientific journal)

Pathway-Based Analysis of Genome-Wide siRNA Screens Reveals the Regulatory Landscape of App Processing (10, e0115369, 2015)

Luiz Miguel Camargo, Xiaohua Douglas Zhang, Patrick Loerch, Ramon Miguel Caceres, Shane D. Marine, Paolo Uva, Marc Ferrer, Emanuele de Rinaldis, David J. Stone, John Majercak, William J. Ray, Chen Yi-An, Mark S. Shearman, Kenji Mizuguchi

PLOS ONE　Vol. 10　No. 6　2015/06

Pathway-Based Analysis of Genome-Wide siRNA Screens Reveals the Regulatory Landscape of App Processing

Luiz Miguel Camargo, Xiaohua Douglas Zhang, Patrick Loerch, Ramon Miguel Caceres, Shane D. Marine, Paolo Uva, Marc Ferrer, Emanuele de Rinaldis, David J. Stone, John Majercak, William J. Ray, Chen Yi-An, Mark S. Shearman, Kenji Mizuguchi

PLOS ONE　Vol. 10　No. 2　2015/02　Research paper (scientific journal)

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs

Jun-ichi Ito, Kazuyoshi Ikeda, Kazunori Yamada, Kenji Mizuguchi, Kentaro Tomii

NUCLEIC ACIDS RESEARCH　Vol. 43　No. D1　p. D392-D398　2015/01　Research paper (scientific journal)

Altered Actions of Memantine and NMDA-Induced Currents in a New Grid2-Deleted Mouse Line

Ayako Kumagai, Akira Fujita, Tomoki Yokoyama, Yuki Nonobe, Yasuhiro Hasaba, Tsutomu Sasaki, Yumi Itoh, Minako Koura, Osamu Suzuki, Shigeki Adachi, Haruko Ryo, Arihiro Kohara, Lokesh P. Tripathi, Masato Sanosaka, Toshiki Fukushima, Hiroyuki Takahashi, Kazuo Kitagawa, Yasuo Nagaoka, Hidehisa Kawahara, Kenji Mizuguchi, Taisei Nomura, Junichiro Matsuda, Toshihide Tabata, Hiroshi Takemori

Genes　Vol. 5　No. 4　p. 1095-1114　2014/12　Research paper (scientific journal)

Dextran sulfate-resistant A/Puerto Rico/8/34 influenza virus is associated with the emergence of specific mutations in the neuraminidase glycoprotein

Hiroshi Yamada, Chioko Nagao, Ahmad M. Haredy, Yasuko Mori, Kenji Mizuguchi, Koichi Yamanishi, Shigefumi Okamoto

ANTIVIRAL RESEARCH　Vol. 111　p. 69-77　2014/11　Research paper (scientific journal)

High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations

Hiroki Shirai, Kazuyoshi Ikeda, Kazuo Yamashita, Yuko Tsuchiya, Jamica Sarmiento, Shide Liang, Tatsuaki Morokata, Kenji Mizuguchi, Junichi Higo, Daron M. Standley, Haruki Nakamura

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 82　No. 8　p. 1624-1635　2014/08　Research paper (scientific journal)

Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type -helical structure

Yi-An Chen, Yoichi Murakami, Shandar Ahmad, Tetsuro Yoshimaru, Toyomasa Katagiri, Kenji Mizuguchi

BMC Research Notes　Vol. 7　No. 1　2014/07/06　Research paper (scientific journal)

Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators

Yoichi Murakami, Kenji Mizuguchi

BMC BIOINFORMATICS　Vol. 15　No. 1　2014/06　Research paper (scientific journal)

Integrated Pathway Clusters with Coherent Biological Themes for Target Prioritisation

Yi-An Chen, Lokesh P. Tripathi, Benoit H. Dessailly, Johan Nystroem-Persson, Shandar Ahmad, Kenji Mizuguchi

PLOS ONE　Vol. 9　No. 6　2014/06　Research paper (scientific journal)

Crystal structure of FtsA from Staphylococcus aureus

Junso Fujita, Yoko Maeda, Chioko Nagao, Yuko Tsuchiya, Yuma Miyazaki, Mika Hirose, Eiichi Mizohata, Yoshimi Matsumoto, Tsuyoshi Inoue, Kenji Mizuguchi, Hiroyoshi Matsumura

FEBS LETTERS　Vol. 588　No. 10　p. 1879-1885　2014/05　Research paper (scientific journal)

Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability

Munazah Andrabi, Kenji Mizuguchi, Shandar Ahmad

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 82　No. 5　p. 841-857　2014/05　Research paper (scientific journal)

Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome

Naoki Takemura, Takumi Kawasaki, Jun Kunisawa, Shintaro Sato, Aayam Lamichhane, Kouji Kobiyama, Taiki Aoshi, Junichi Ito, Kenji Mizuguchi, Thangaraj Karuppuchamy, Kouta Matsunaga, Shoichiro Miyatake, Nobuko Mori, Tohru Tsujimura, Takashi Satoh, Yutaro Kumagai, Taro Kawai, Daron M. Standley, Ken J. Ishii, Hiroshi Kiyono, Shizuo Akira, Satoshi Uematsu

NATURE COMMUNICATIONS　Vol. 5　2014/03　Research paper (scientific journal)

Prediction of Detailed Enzyme Functions and Identification of Specificity Determining Residues by Random Forests

Chioko Nagao, Nozomi Nagano, Kenji Mizuguchi

PLOS ONE　Vol. 9　No. 1　2014/01　Research paper (scientific journal)

Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform

Johan Nystroem-Persson, Yoshinobu Igarashi, Maori Ito, Mizuki Morita, Noriyuki Nakatsu, Hiroshi Yamada, Kenji Mizuguchi

BIOINFORMATICS　Vol. 29　No. 23　p. 3080-3086　2013/12　Research paper (scientific journal)

Expression, purification, crystallization and preliminary crystallographic study of FtsA from methicillin-resistant Staphylococcus aureus

Junso Fujita, Yuma Miyazaki, Mika Hirose, Chioko Nagao, Eiichi Mizohata, Yoshimi Matsumoto, Kenji Mizuguchi, Tsuyoshi Inoue, Hiroyoshi Matsumura

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS　Vol. 69　No. 8　p. 895-898　2013/08　Research paper (scientific journal)

Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter

Prabha Tiwari, Lokesh P. Tripathi, Teppei Nishikawa-Matsumura, Shandar Ahmad, Soken-Nakazawa J. Song, Tomoyasu Isobe, Kenji Mizuguchi, Kazuyuki Yoshizaki

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS　Vol. 1830　No. 6　p. 3650-3655　2013/06　Research paper (scientific journal)

Understanding the Biological Context of NS5A-Host Interactions in HCV Infection: A Network-Based Approach

Lokesh P. Tripathi, Hiroto Kambara, Yi-An Chen, Yorihiro Nishimura, Kohji Moriishi, Toru Okamoto, Eiji Morita, Takayuki Abe, Yoshio Mori, Yoshiharu Matsuura, Kenji Mizuguchi

JOURNAL OF PROTEOME RESEARCH　Vol. 12　No. 6　p. 2537-2551　2013/06　Research paper (scientific journal)

Functional site plasticity in domain superfamilies

Benoit H. Dessailly, Natalie L. Dawson, Kenji Mizuguchi, Christine A. Orengo

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS　Vol. 1834　No. 5　p. 874-889　2013/05　Research paper (scientific journal)

The Chemotherapeutic Agent DMXAA as a Unique IRF3-Dependent Type-2 Vaccine Adjuvant

Choon Kit Tang, Taiki Aoshi, Nao Jounai, Junichi Ito, Keiichi Ohata, Kouji Kobiyama, Benoit H. Dessailly, Etsushi Kuroda, Shizuo Akira, Kenji Mizuguchi, Cevayir Coban, Ken J. Ishii

PLOS ONE　Vol. 8　No. 3　2013/03　Research paper (scientific journal)

Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells.

Tetsuro Yoshimaru, Masato Komatsu, Taisuke Matsuo, Yi-An Chen, Yoichi Murakami, Kenji Mizuguchi, Eiichi Mizohata, Tsuyoshi Inoue, Miki Akiyama, Rui Yamaguchi, Seiya Imoto, Satoru Miyano, Yasuo Miyoshi, Mitsunori Sasa, Yusuke Nakamura, Toyomasa Katagiri

Nature communications　Vol. 4　p. 2443-2443　2013　Research paper (scientific journal)

Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions

Chioko Nagao, Nozomi Izako, Shinji Soga, Samia Haseeb Khan, Shigeki Kawabata, Hiroki Shirai, Kenji Mizuguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 80　No. 10　p. 2426-2436　2012/10　Research paper (scientific journal)

Proteomic Analysis of Hepatitis C Virus (HCV) Core Protein Transfection and Host Regulator PA28 gamma Knockout in HCV Pathogenesis: A Network-Based Study

Lokesh P. Tripathi, Hiroto Kambara, Kohji Moriishi, Eiji Morita, Takayuki Abe, Yoshio Mori, Yi-An Chen, Yoshiharu Matsuura, Kenji Mizuguchi

JOURNAL OF PROTEOME RESEARCH　Vol. 11　No. 7　p. 3664-3679　2012/07　Research paper (scientific journal)

Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes

Tim R. Blower, Francesca L. Short, Feng Rao, Kenji Mizuguchi, Xue Y. Pei, Peter C. Fineran, Ben F. Luisi, George P. C. Salmond

NUCLEIC ACIDS RESEARCH　Vol. 40　No. 13　p. 6158-6173　2012/07　Research paper (scientific journal)

Inhibitory Roles of Signal Transducer and Activator of Transcription 3 in Antitumor Immunity during Carcinogen-Induced Lung Tumorigenesis

Shoichi Ihara, Hiroshi Kida, Hisashi Arase, Lokesh P. Tripathi, Yi-An Chen, Tetsuya Kimura, Mitsuhiro Yoshida, Yozo Kashiwa, Haruhiko Hirata, Reiko Fukamizu, Ruriko Inoue, Kana Hasegawa, Sho Goya, Ryo Takahashi, Toshiyuki Minami, Kazuyuki Tsujino, Mayumi Suzuki, Satoshi Kohmo, Koji Inoue, Izumi Nagatomo, Yoshito Takeda, Takashi Kijima, Kenji Mizuguchi, Isao Tachibana, Atsushi Kumanogoh

CANCER RESEARCH　Vol. 72　No. 12　p. 2990-2999　2012/06　Research paper (scientific journal)

Sagace: A web-based search engine for biomedical databases in Japan

Mizuki Morita, Yoshinobu Igarashi, Maori Ito, Yi-An Chen, Chioko Nagao, Yuki Sakaguchi, Ryuichi Sakate, Tohru Masui, Kenji Mizuguchi

BMC Research Notes　Vol. 5　2012　Research paper (scientific journal)

Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

Mizuki Morita, AVSK M. Katta, Shandar Ahmad, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi

BMC Biophysics　Vol. 4　No. 1　2011/12/14　Research paper (scientific journal)

Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data

Shandar Ahmad, Kenji Mizuguchi

PLOS ONE　Vol. 6　No. 12　2011/12　Research paper (scientific journal)

Prediction of dinucleotide-specific RNA-binding sites in proteins

Michael Fernandez, Yutaro Kumagai, Daron M. Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad

BMC BIOINFORMATICS　Vol. 12　No. S-13　2011/11　Research paper (scientific journal)

Using Knowledge of Protein Structural Constraints to Predict the Evolution of HIV-1

Simon G. Williams, Rachit Madan, Matthew G. S. Norris, John Archer, Kenji Mizuguchi, David L. Robertson, Simon C. Lovell

JOURNAL OF MOLECULAR BIOLOGY　Vol. 410　No. 5　p. 1023-1034　2011/07　Research paper (scientific journal)

Identification of novel functional organic anion-transporting polypeptide 1B3 polymorphisms and assessment of substrate specificity

Ute I. Schwarz, Henriette E. Meyer Zu Schwabedissen, Rommel G. Tirona, Atsuko Suzuki, Brenda F. Leake, Younes Mokrab, Kenji Mizuguchi, Richard H. Ho, Richard B. Kim

PHARMACOGENETICS AND GENOMICS　Vol. 21　No. 3　p. 103-114　2011/03　Research paper (scientific journal)

TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery

Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi

PLOS ONE　Vol. 6　No. 3　2011/03　Research paper (scientific journal)

A structural dissection of amino acid substitutions in helical transmembrane proteins

Younes Mokrab, Tim J. Stevens, Kenji Mizuguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 78　No. 14　p. 2895-2907　2010/11　Research paper (scientific journal)

Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores

Sukanta Mondal, Chioko Nagao, Kenji Mizuguchi

PROTEIN ENGINEERING DESIGN & SELECTION　Vol. 23　No. 11　p. 859-869　2010/11　Research paper (scientific journal)

Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins

Shandar Ahmad, Yumlembam Hemajit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi

BMC BIOINFORMATICS　Vol. 11　2010/10　Research paper (scientific journal)

On nucleotide solvent accessibility in RNA structure

Yumlembam H. Singh, Munazah Andrabi, Bratati Kahali, Tapash Chandra Ghosh, Kenji Mizuguchi, Alex V. Kochetov, Shandar Ahmad

GENE　Vol. 463　No. 1-2　p. 41-48　2010/09　Research paper (scientific journal)

Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies

Chioko Nagao, Nozomi Nagano, Kenji Mizuguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 78　No. 10　p. 2369-2384　2010/08　Research paper (scientific journal)

CCRXP: exploring clusters of conserved residues in protein structures

Shandar Ahmad, Ozlem Keskin, Kenji Mizuguchi, Akinori Sarai, Ruth Nussinov

NUCLEIC ACIDS RESEARCH　Vol. 38　No. SUPPL. 2　p. W398-W401　2010/07　Research paper (scientific journal)

Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein–protein interaction sites

Yoichi Murakami, Kenji Mizuguchi

Bioinformatics　Vol. 26　No. 15　p. 1841-1848　2010/06/06　Research paper (scientific journal)

Creation of lysine-deficient mutant lymphotoxin-alpha with receptor selectivity by using a phage display system

Yasuo Yoshioka, Hikaru Watanabe, Tomohiro Morishige, Xinglei Yao, Shinji Ikemizu, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi, Shin-ichi Tsunoda, Yasuo Tsutsumi, Yohei Mukai, Naoki Okada, Shinsaku Nakagawa

BIOMATERIALS　Vol. 31　No. 7　p. 1935-1943　2010/03　Research paper (scientific journal)

Network based analysis of hepatitis C virus Core and NS4B protein interactions

Lokesh P. Tripathi, Chikako Kataoka, Shuhei Taguwa, Kohji Moriishi, Yoshio Mori, Yoshiharu Matsuura, Kenji Mizuguchi

MOLECULAR BIOSYSTEMS　Vol. 6　No. 12　p. 2539-2553　2010　Research paper (scientific journal)

Structural insights into the enzyme mechanism of a new family of d-2-hydroxyacid dehydrogenases, a close homolog of 2-ketopantoate reductase.

Mondal S, Mizuguchi K

Genome informatics. International Conference on Genome Informatics　Vol. 23　No. 1　p. 98-105　2009/10/01　Research paper (scientific journal)

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai, Shandar Ahmad

BMC STRUCTURAL BIOLOGY　Vol. 9　2009/05　Research paper (scientific journal)

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

Munazah Andrabi, Kenji Mizuguchi, Akinori Sarai, Shandar Ahmad

BMC Structural Biology　Vol. 9　2009　Research paper (scientific journal)

Molecular Basis for SUMOylation-dependent Regulation of DNA Binding Activity of Heat Shock Factor 2

Yukihiro Tateishi, Mariko Ariyoshi, Ryuji Igarashi, Hideyuki Hara, Kenji Mizuguchi, Azusa Seto, Akira Nakai, Tetsuro Kokubo, Hidehito Tochio, Masahiro Shirakawa

JOURNAL OF BIOLOGICAL CHEMISTRY　Vol. 284　No. 4　p. 2435-2447　2009/01　Research paper (scientific journal)

Lipophobicity and the residue environments of the transmembrane alpha-helical bundle

Younes Mokrab, Thn J. Stevens, Kenji Mizuguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 74　No. 1　p. 32-49　2009/01　Research paper (scientific journal)

Docking of cytochrome c(6) and plastocyanin to the aa(3)-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum

Sarah E. Hart, Christopher J. Howe, Kenji Mizuguchi, Juan Fernandez-Recio

PROTEIN ENGINEERING DESIGN & SELECTION　Vol. 21　No. 12　p. 689-698　2008/12　Research paper (scientific journal)

Drosophila Neurotrophins Reveal a Common Mechanism for Nervous System Formation

Bangfu Zhu, Jenny A. Pennack, Peter McQuilton, Manuel G. Forero, Kenji Mizuguchi, Ben Sutcliffe, Chun-Jing Gu, Janine C. Fenton, Alicia Hidalgo

PLOS BIOLOGY　Vol. 6　No. 11　p. 2476-2495　2008/11　Research paper (scientific journal)

A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins

Xavier Bailly, Stefano Vanin, Christine Chabasse, Kenji Mizuguchi, Serge N. Vinogradov

BMC EVOLUTIONARY BIOLOGY　Vol. 8　No. 1　2008/09

Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor

Younes Mokrab, Vassiliy N. Bavro, Kenji Mizuguchi, N. P. Todorov, Ian L. Martin, Susan M. J. Dunn, S. L. Chan, P. -L. Chau

JOURNAL OF MOLECULAR GRAPHICS & MODELLING　Vol. 26　No. 4　p. 760-774　2007/11　Research paper (scientific journal)

A model of globin evolution

Serge N. Vinogradov, David Hoogewijs, Xavier Bailly, Kenji Mizuguchi, Sylvia Dewilde, Luc Moens, Jacques R. Vanfleteren

GENE　Vol. 398　No. 1-2　p. 132-142　2007/08　Research paper (scientific journal)

Environment specific substitution tables for thermophilic proteins

K. Mizuguchi, M. Sele, M. V. Cubellis

BMC BIOINFORMATICS　Vol. 8　2007　Research paper (scientific journal)

Disrupted in schizophrenia 1 interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia

L. M. Camargo, V. Collura, J-C Rain, K. Mizuguchi, H. Hermjakob, S. Kerrien, T. P. Bonnert, P. J. Whiting, N. J. Brandon

MOLECULAR PSYCHIATRY　Vol. 12　No. 1　p. 74-86　2007/01　Research paper (scientific journal)

FlyMine: an integrated database for Drosophila and Anopheles genomics

Rachel Lyne, Richard Smith, Kim Rutherford, Matthew Wakeling, Andrew Varley, Francois Guillier, Hilde Janssens, Wenyan Ji, Peter Mclaren, Philip North, Debashis Rana, Tom Riley, Julie Sullivan, Xavier Watkins, Mark Woodbridge, Kathryn Lilley, Steve Russell, Michael Ashburner, Kenji Mizuguchi, Gos Micklem

GENOME BIOLOGY　Vol. 8　No. 7　2007　Research paper (scientific journal)

The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97

Kumiko Shiozawa, Natsuko Goda, Toshiyuki Shimizu, Kenji Mizuguchi, Naomi Kondo, Nobuyuki Shimozawa, Masahiro Shirakawa, Hidekazu Hiroaki

FEBS JOURNAL　Vol. 273　No. 21　p. 4959-4971　2006/11　Research paper (scientific journal)

The guanidino-group modifying enzymes: Structural basis for their diversity and commonality

Hiroki Shirai, Younes Mokrab, Kenji Mizuguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 64　No. 4　p. 1010-1023　2006/09　Research paper (scientific journal)

A novel mechanism of allosteric regulation of archaeal phosphoenolpyruvate carboxylase: a combined approach to structure-based alignment and model assessment

Hiroyoshi Matsumura, Katsura Izui, Kenji Mizuguchi

PROTEIN ENGINEERING DESIGN & SELECTION　Vol. 19　No. 9　p. 409-419　2006/09　Research paper (scientific journal)

Organic anion transporting polypeptides of the OATP/SLCO superfamily: Identification of new members in nonmammalian species, comparative modeling and a potential transport mode

F Meier-Abt, Y Mokrab, K Mizuguchi

JOURNAL OF MEMBRANE BIOLOGY　Vol. 208　No. 3　p. 213-227　2006/04/20　Research paper (scientific journal)

Functional restraints on the patterns of amino acid substitutions: Application to sequence-structure homology recognition

Chelliah, V, T Blundell, K Mizuguchi

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS　Vol. 61　No. 4　p. 722-731　2005/12　Research paper (scientific journal)

Amino-acid substitutions in membrane proteins: Applications to homology recognition and comparative modelling

Younes Mokrab, Kenji Mizuguchi

BMC BIOINFORMATICS　Vol. 6　No. S-3　2005/09

A model of a transmembrane drug-efflux pump from Gram-negative bacteria

J Fernandez-Recio, F Walas, L Federici, JV Pratap, VN Bavro, RN Miguel, K Mizuguchi, B Luisi

FEBS LETTERS　Vol. 578　No. 1-2　p. 5-9　2004/12　Research paper (scientific journal)

Distinct protein interfaces in transmembrane domains suggest an in vivo folding model

TJ Stevens, K Mizuguchi, IT Arkin

PROTEIN SCIENCE　Vol. 13　No. 11　p. 3028-3037　2004/11　Research paper (scientific journal)

HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database

LA Stebbings, K Mizuguchi

NUCLEIC ACIDS RESEARCH　Vol. 32　No. Database-Issue　p. D203-D207　2004/01　Research paper (scientific journal)

Prediction of the structure and function of AstA and AstB, the first two enzymes of the arginine succinyltransferase pathway of arginine catabolism

H Shirai, K Mizuguchi

FEBS LETTERS　Vol. 555　No. 3　p. 505-510　2003/12　Research paper (scientific journal)

The export of coat protein from enteroaggregative Escherichia coli by a specific ATP-binding cassette transporter system

J Nishi, J Sheikh, K Mizuguchi, B Luisi, Burland, V, A Boutin, DJ Rose, FR Blattner, JP Nataro

JOURNAL OF BIOLOGICAL CHEMISTRY　Vol. 278　No. 46　p. 45680-45689　2003/11　Research paper (scientific journal)

Structure of the periplasmic domain of Pseudomonas aeruginosa TolA: evidence for an evolutionary relationship with the TonB transporter protein

M Witty, C Sanz, A Shah, JG Grossmann, K Mizuguchi, RN Perham, B Luisi

EMBO JOURNAL　Vol. 21　No. 16　p. 4207-4218　2002/08　Research paper (scientific journal)

The SWIB and the MDM2 domains are homologous and share a common fold

R Bennett-Lovsey, SE Hart, H Shirai, K Mizuguchi

BIOINFORMATICS　Vol. 18　No. 4　p. 626-630　2002/04　Research paper (scientific journal)

A family of proteins related to Spatzle, the toll receptor ligand, are encoded in the Drosophila genome

JS Parker, K Mizuguchi, NJ Gay

PROTEINS-STRUCTURE FUNCTION AND GENETICS　Vol. 45　No. 1　p. 71-80　2001/10　Research paper (scientific journal)

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families

PIW de Bakker, A Bateman, DF Burke, RN Miguel, K Mizuguchi, J Shi, H Shirai, TL Blundell

BIOINFORMATICS　Vol. 17　No. 8　p. 748-749　2001/08　Research paper (scientific journal)

A novel superfamily of enzymes that catalyze the modification of guanidino groups

H Shirai, TL Blundell, K Mizuguchi

TRENDS IN BIOCHEMICAL SCIENCES　Vol. 26　No. 8　p. 465-468　2001/08　Research paper (scientific journal)

FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties

JY Shi, TL Blundell, K Mizuguchi

JOURNAL OF MOLECULAR BIOLOGY　Vol. 310　No. 1　p. 243-257　2001/06　Research paper (scientific journal)

Sequence-structure homology recognition by iterative alignment refinement and comparative modeling

MG Williams, H Shirai, J Shi, HG Nagendra, J Mueller, K Mizuguchi, RN Miguel, SC Lovell, CA Innis, CM Deane, L Chen, N Campillo, DF Burke, TL Blundell, PIW de Bakker

PROTEINS-STRUCTURE FUNCTION AND GENETICS　Vol. 45　No. SUPPL. 5　p. 92-97　2001　Research paper (scientific journal)

Analysis of conservation and substitutions of secondary structure elements within protein superfamilies

K Mizuguchi, TL Blundell

BIOINFORMATICS　Vol. 16　No. 12　p. 1111-1119　2000/12　Research paper (scientific journal)

beta 3: An additional auxiliary subunit of the voltage-sensitive sodium channel that modulates channel gating with distinct kinetics

K Morgan, EB Stevens, B Shah, PJ Cox, AK Dixon, K Lee, RD Pinnock, J Hughes, PJ Richardson, K Mizuguchi, AP Jackson

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　Vol. 97　No. 5　p. 2308-2313　2000/02　Research paper (scientific journal)

Characterisation of the gene for Drosophila amphiphysin

A Razzaq, Y Su, JE Mehren, K Mizuguchi, AP Jackson, NJ Gay, CJ O'Kane

GENE　Vol. 241　No. 1　p. 167-174　2000/01　Research paper (scientific journal)

A six-stranded double-psi beta barrel is shared by several protein superfamilies

RM Castillo, K Mizuguchi, Dhanaraj, V, A Albert, TL Blundell, AG Murzin

STRUCTURE WITH FOLDING & DESIGN　Vol. 7　No. 2　p. 227-236　1999/02　Research paper (scientific journal)

An iterative structure-assisted approach to sequence alignment and comparative modeling

DF Burke, CM Deane, HA Nagarajaram, N Campillo, M Martin-Martinez, J Mendes, F Molina, J Perry, BVB Reddy, CM Soares, RE Steward, M Williams, MA Carrondo, TL Blundell, K Mizuguchi

PROTEINS-STRUCTURE FUNCTION AND GENETICS　Vol. 37　p. 55-60　1999　Research paper (scientific journal)

A third fibronectin type III domain in the extracellular region of the insulin receptor family

C Marino-Buslje, K Mizuguchi, K Siddle, TL Blundell

FEBS LETTERS　Vol. 441　No. 2　p. 331-336　1998/12　Research paper (scientific journal)

Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

R Sowdhamini, DF Burke, C Deane, JF Huang, K Mizuguchi, HA Nagarajaram, JP Overington, N Srinivasan, RE Steward, TL Blundell

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY　Vol. 54　p. 1168-1177　1998/11　Research paper (scientific journal)

CAMPASS: a database of structurally aligned protein superfamilies

R Sowdhamini, DF Burke, JF Huang, K Mizuguchi, HA Nagarajaram, N Srinivasan, RE Steward, TL Blundell

STRUCTURE WITH FOLDING & DESIGN　Vol. 6　No. 9　p. 1087-1094　1998/09　Research paper (scientific journal)

Getting knotted: a model for the structure and activation of Spatzle

K Mizuguchi, JS Parker, TL Blundell, NJ Gay

TRENDS IN BIOCHEMICAL SCIENCES　Vol. 23　No. 7　p. 239-242　1998/07　Research paper (scientific journal)

HOMSTRAD: A database of protein structure alignments for homologous families

Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, John, P. Overington

Protein Science　Vol. 7　p. 2469-2471　1998/01/01　Research paper (scientific journal)

Erratum: Getting knotted: A model for the structure and activation of Spatzle (TIBS 23 (239-242))

K. Mizuguchi

Trends in Biochemical Sciences　Vol. 23　No. 9　p. 361-361　1998/01/01　Research paper (scientific journal)

JOY: protein sequence-structure representation and analysis

K Mizuguchi, CM Deane, TL Blundell, MS Johnson, JP Overingon

BIOINFORMATICS　Vol. 14　No. 7　p. 617-623　1998　Research paper (scientific journal)

Crystal structure of glutathione synthetase at optimal pH: Domain architecture and structural similarity with other proteins

K Matsuda, K Mizuguchi, T Nishioka, H Kato, N Go, J Oda

PROTEIN ENGINEERING　Vol. 9　No. 12　p. 1083-1092　1996/12　Research paper (scientific journal)

Comparison of spatial arrangements of secondary structural elements in proteins

K. Mizuguchi, N. Go

Protein Engineering　Vol. 8　No. 4　p. 353-362　1995　Research paper (scientific journal)

Collective motions in proteins investigated by X‐ray diffuse scattering

K MIZUGUCHI, A KIDERA, N GO

PROTEINS-STRUCTURE FUNCTION AND GENETICS　Vol. 18　No. 1　p. 34-48　1994/01　Research paper (scientific journal)