Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases

Kosuke Hashimoto, Igor B. Rogozin, Anna R. Panchenko

HUMAN MUTATION　Vol. 33　No. 11　p. 1566-1575　2012/11　Research paper (scientific journal)

Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization.

Kosuke Hashimoto, Hafumi Nishi, Stephen Bryant, Anna R Panchenko

Physical biology　Vol. 8　No. 3　p. 035007-035007　2011/06　Research paper (scientific journal)

Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states

Kosuke Hashimoto, Anna R. Panchenko

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA　Vol. 107　No. 47　p. 20352-20357　2010/11　Research paper (scientific journal)

Functional States of Homooligomers: Insights from the Evolution of Glycosyltransferases

Kosuke Hashimoto, Thomas Madej, Stephen H. Bryant, Anna R. Panchenko

JOURNAL OF MOLECULAR BIOLOGY　Vol. 399　No. 1　p. 196-206　2010/05　Research paper (scientific journal)

Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans

Kosuke Hashimoto, Toshiaki Tokimatsu, Shin Kawano, Akiyasu C. Yoshizawa, Shujiro Okuda, Susumu Goto, Minoru Kanehisa

CARBOHYDRATE RESEARCH　Vol. 344　No. 7　p. 881-887　2009/05　Research paper (scientific journal)

Mining significant tree patterns in carbohydrate sugar chains

Kosuke Hashimoto, Ichigaku Takigawa, Motoki Shiga, Minoru Kanehisa, Hiroshi Mamitsuka

BIOINFORMATICS　Vol. 24　No. 16　p. I167-I173　2008/08　Research paper (scientific journal)

The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes

Kosuke Hashimoto, Akiyasu C. Yoshizawa, Shujiro Okuda, Keiichi Kuma, Susumu Goto, Minoru Kanehisa

JOURNAL OF LIPID RESEARCH　Vol. 49　No. 1　p. 183-191　2008/01　Research paper (scientific journal)

KEGG as a glycome informatics resource

Kosuke Hashimoto, Susumu Goto, Shin Kawano, Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Masami Hamajima, Toshisuke Kawasaki, Minoru Kanehisa

Glycobiology　Vol. 16　No. 5　p. 63R-70R　2006/05/01　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)

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)

PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment

Junichiro Takano, Shinsuke Ito, Yixing Dong, Jafar Sharif, Yaeko Nakajima-Takagi, Taichi Umeyama, Yong-Woon Han, Kyoichi Isono, Takashi Kondo, Yusuke Iizuka, Tomohiro Miyai, Yoko Koseki, Mika Ikegaya, Mizuki Sakihara, Manabu Nakayama, Osamu Ohara, Yoshinori Hasegawa, Kosuke Hashimoto, Erik Arner, Robert J. Klose, Atsushi Iwama, Haruhiko Koseki, Tomokatsu Ikawa

Nature Communications　Vol. 13　No. 1　p. 7159-7159　2022/11/28　Research paper (scientific journal)

Recombination of repeat elements generates somatic complexity in human genomes.

Giovanni Pascarella, Chung Chau Hon, Kosuke Hashimoto, Annika Busch, Joachim Luginbühl, Callum Parr, Wing Hin Yip, Kazumi Abe, Anton Kratz, Alessandro Bonetti, Federico Agostini, Jessica Severin, Shigeo Murayama, Yutaka Suzuki, Stefano Gustincich, Martin Frith, Piero Carninci

Cell　Vol. 185　No. 16　p. 3025-3040　2022/08/04　Research paper (scientific journal)

DUX4 is a multifunctional factor priming human embryonic genome activation.

Sanna Vuoristo, Shruti Bhagat, Christel Hydén-Granskog, Masahito Yoshihara, Lisa Gawriyski, Eeva-Mari Jouhilahti, Vipin Ranga, Mahlet Tamirat, Mikko Huhtala, Ida Kirjanov, Sonja Nykänen, Kaarel Krjutškov, Anastassius Damdimopoulos, Jere Weltner, Kosuke Hashimoto, Gaëlle Recher, Sini Ezer, Priit Paluoja, Pauliina Paloviita, Yujiro Takegami, Ai Kanemaru, Karolina Lundin, Tomi T Airenne, Timo Otonkoski, Juha S Tapanainen, Hideya Kawaji, Yasuhiro Murakawa, Thomas R Bürglin, Markku Varjosalo, Mark S Johnson, Timo Tuuri, Shintaro Katayama, Juha Kere

iScience　Vol. 25　No. 4　p. 104137-104137　2022/04/15　Research paper (scientific journal)

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.

Imad Abugessaisa, Jordan A Ramilowski, Marina Lizio, Jesicca Severin, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Shuhei Noguchi, Chi Wai Yip, Jasmine Li Ching Ooi, Michihira Tagami, Fumi Hori, Saumya Agrawal, Chung Chau Hon, Melissa Cardon, Shuya Ikeda, Hiromasa Ono, Hidemasa Bono, Masaki Kato, Kosuke Hashimoto, Alessandro Bonetti, Masaki Kato, Norio Kobayashi, Jay Shin, Michiel de Hoon, Yoshihide Hayashizaki, Piero Carninci, Hideya Kawaji, Takeya Kasukawa

Nucleic acids research　Vol. 49　No. D1　2021/01/08　Research paper (scientific journal)

Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene.

Daniela Kajihara, Chung-Chau Hon, Aimi Naim Abdullah, João Wosniak Jr, Ana Iochabel S Moretti, Joice F Poloni, Diego Bonatto, Kosuke Hashimoto, Piero Carninci, Francisco R M Laurindo

BMC genomics　Vol. 21　No. 1　p. 766-766　2020/11/04　Research paper (scientific journal)

Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages.

Ayumi Taguchi, Kazunori Nagasaka, Charles Plessy, Hiroe Nakamura, Yoshiko Kawata, Sachi Kato, Kosuke Hashimoto, Takeshi Nagamatsu, Katsutoshi Oda, Iwao Kukimoto, Kei Kawana, Piero Carninci, Yutaka Osuga, Tomoyuki Fujii

Scientific reports　Vol. 10　No. 1　p. 17991-17991　2020/10/22　Research paper (scientific journal)

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Jordan A Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, Ivan V Kulakovskiy, Mickaël Mendez, Jasmine Li Ching Ooi, John F Ouyang, Nick Parkinson, Andreas Petri, Leonie Roos, Jessica Severin, Kayoko Yasuzawa, Imad Abugessaisa, Altuna Akalin, Ivan V Antonov, Erik Arner, Alessandro Bonetti, Hidemasa Bono, Beatrice Borsari, Frank Brombacher, Christopher JF Cameron, Carlo Vittorio Cannistraci, Ryan Cardenas, Melissa Cardon, Howard Chang, Josée Dostie, Luca Ducoli, Alexander Favorov, Alexandre Fort, Diego Garrido, Noa Gil, Juliette Gimenez, Reto Guler, Lusy Handoko, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Kosuke Hashimoto, Norihito Hayatsu, Peter Heutink, Tetsuro Hirose, Eddie L Imada, Masayoshi Itoh, Bogumil Kaczkowski, Aditi Kanhere, Emily Kawabata, Hideya Kawaji, Tsugumi Kawashima, S Thomas Kelly, Miki Kojima, Naoto Kondo, Haruhiko Koseki, Tsukasa Kouno, Anton Kratz, Mariola Kurowska-Stolarska, Andrew Tae Jun Kwon, Jeffrey Leek, Andreas Lennartsson, Marina Lizio, Fernando López-Redondo, Joachim Luginbühl, Shiori Maeda, Vsevolod J Makeev, Luigi Marchionni, Yulia A Medvedeva, Aki Minoda, Ferenc Müller, Manuel Muñoz-Aguirre, Mitsuyoshi Murata, Hiromi Nishiyori, Kazuhiro R Nitta, Shuhei Noguchi, Yukihiko Noro, Ramil Nurtdinov, Yasushi Okazaki, Valerio Orlando, Denis Paquette, Callum J C Parr, Owen J L Rackham, Patrizia Rizzu, Diego Fernando Sánchez Martinez, Albin Sandelin, Pillay Sanjana, Colin A M Semple, Youtaro Shibayama, Divya M Sivaraman, Takahiro Suzuki, Suzannah C Szumowski, Michihira Tagami, Martin S Taylor, Chikashi Terao, Malte Thodberg, Supat Thongjuea, Vidisha Tripathi, Igor Ulitsky, Roberto Verardo, Ilya E Vorontsov, Chinatsu Yamamoto, Robert S Young, J Kenneth Baillie, Alistair R R Forrest, Roderic Guigó, Michael M Hoffman, Chung Chau Hon, Takeya Kasukawa, Sakari Kauppinen, Juha Kere, Boris Lenhard, Claudio Schneider, Harukazu Suzuki, Ken Yagi, Michiel J L de Hoon, Jay W Shin, Piero Carninci

Genome research　Vol. 30　No. 7　p. 1060-1072　2020/07　Research paper (scientific journal)

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.

Alessandro Bonetti, Federico Agostini, Ana Maria Suzuki, Kosuke Hashimoto, Giovanni Pascarella, Juliette Gimenez, Leonie Roos, Alex J Nash, Marco Ghilotti, Christopher J F Cameron, Matthew Valentine, Yulia A Medvedeva, Shuhei Noguchi, Eneritz Agirre, Kaori Kashi, Samudyata, Joachim Luginbühl, Riccardo Cazzoli, Saumya Agrawal, Nicholas M Luscombe, Mathieu Blanchette, Takeya Kasukawa, Michiel de Hoon, Erik Arner, Boris Lenhard, Charles Plessy, Gonçalo Castelo-Branco, Valerio Orlando, Piero Carninci

Nature communications　Vol. 11　No. 1　p. 1018-1018　2020/02/24　Research paper (scientific journal)

Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation.

Soichiro Yamanaka, Hidenori Nishihara, Hidehiro Toh, Luis Augusto Eijy Nagai, Kosuke Hashimoto, Sung-Joon Park, Aoi Shibuya, Ana Maria Suzuki, Yujiro Tanaka, Kenta Nakai, Piero Carninci, Hiroyuki Sasaki, Haruhiko Siomi

Developmental cell　Vol. 51　No. 1　p. 21-34　2019/10/07　Research paper (scientific journal)

Multi-year whole-blood transcriptome data for the study of onset and progression of Parkinson's Disease.

Matthew N Z Valentine, Kosuke Hashimoto, Takeshi Fukuhara, Shinji Saiki, Kei-Ichi Ishikawa, Nobutaka Hattori, Piero Carninci

Scientific data　Vol. 6　No. 1　p. 20-20　2019/04/05　Research paper (scientific journal)

OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances cell-state reprogramming towards epithelial lineages.

Watanabe K, Liu Y, Noguchi S, Murray M, Chang JC, Kishima M, Nishimura H, Hashimoto K, Minoda A, Suzuki H

Scientific reports　Vol. 9　No. 1　2019/04　Research paper (scientific journal)

Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development.

Michal Pawlak, Katarzyna Z Kedzierska, Maciej Migdal, Karim Abu Nahia, Jordan A Ramilowski, Lukasz Bugajski, Kosuke Hashimoto, Aleksandra Marconi, Katarzyna Piwocka, Piero Carninci, Cecilia L Winata

Genome research　Vol. 29　No. 3　p. 506-519　2019/03　Research paper (scientific journal)

Prevention of hepatocellular carcinoma by targeting MYCN-positive liver cancer stem cells with acyclic retinoid.

Xian-Yang Qin, Harukazu Suzuki, Masao Honda, Hikari Okada, Shuichi Kaneko, Ikuyo Inoue, Etsuko Ebisui, Kosuke Hashimoto, Piero Carninci, Keita Kanki, Hideki Tatsukawa, Naoto Ishibashi, Takahiro Masaki, Tomokazu Matsuura, Hiroyuki Kagechika, Kan Toriguchi, Etsuro Hatano, Yohei Shirakami, Goshi Shiota, Masahito Shimizu, Hisataka Moriwaki, Soichi Kojima

Proceedings of the National Academy of Sciences of the United States of America　Vol. 115　No. 19　p. 4969-4974　2018/05/08　Research paper (scientific journal)

An integrated expression atlas of miRNAs and their promoters in human and mouse

Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Astrom, Magda Babina, Nicolas Bertin, A. Maxwell Burroughs, Ailsa J. Carlisle, Carsten O. Daub, Michael Detmar, Ruslan Deviatiiarov, Alexandre Fort, Claudia Gebhard, Daniel Goldowitz, Sven Guhl, Thomas J. Ha, Jayson Harshbarger, Akira Hasegawa, Kosuke Hashimoto, Meenhard Herlyn, Peter Heutink, Kelly J. Hitchens, Chung Chau Hon, Edward Huang, Yuri Ishizu, Chieko Kai, Takeya Kasukawa, Peter Klinken, Timo Lassmann, Charles-Henri Lecellier, Weonju Lee, Marina Lizio, Vsevolod Makeev, Anthony Mathelier, Yulia A. Medvedeva, Niklas Mejhert, Christopher J. Mungall, Shohei Noma, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Helena Persson, Patrizia Rizzu, Filip Roudnicky, Pal Saetrom, Hiroki Sato, Jessica Severin, Jay W. Shin, Rolf K. Swoboda, Hiroshi Tarui, Hiroo Toyoda, Kristoffer Vitting-Seerup, Louise Winteringham, Yoko Yamaguchi, Kayoko Yasuzawa, Misako Yoneda, Noriko Yumoto, Susan Zabierowski, Peter G. Zhang, Christine A. Wells, Kim M. Summers, Hideya Kawaji, Albin Sandelin, Michael Rehli, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Michiel J. L. de Hoon

NATURE BIOTECHNOLOGY　Vol. 35　No. 9　p. 872-+　2017/09　Research paper (scientific journal)

Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress

Ali Tebbi, Florence Levillayer, Gregory Jouvion, Laurence Fiette, Guillaume Soubigou, Hugo Varet, Nesrine Boudjadja, Stefano Cairo, Kosuke Hashimoto, Ana Maria Suzuki, Piero Carninci, Annamaria Carissimo, Diego di Bernardo, Yu Wei

CARCINOGENESIS　Vol. 37　No. 1　p. 39-48　2016/01　Research paper (scientific journal)

STAP cells are derived from ES cells

Daijiro Konno, Takeya Kasukawa, Kosuke Hashimoto, Takehiko Itoh, Taeko Suetsugu, Ikuo Miura, Shigeharu Wakana, Piero Carninci, Fumio Matsuzaki

NATURE　Vol. 525　No. 7570　p. E4-+　2015/09　Research paper (scientific journal)

Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming

Alexandre Fort, Daisuke Yamada, Kosuke Hashimoto, Haruhiko Koseki, Piero Carninci

CELL CYCLE　Vol. 14　No. 8　p. 1148-1155　2015/04　Research paper (scientific journal)

Characterization of novel transcripts of human papillomavirus type 16 using cap analysis gene expression technology.

Ayumi Taguchi, Kazunori Nagasaka, Kei Kawana, Kosuke Hashimoto, Rika Kusumoto-Matsuo, Charles Plessy, Miranda Thomas, Hiroe Nakamura, Alessandro Bonetti, Katsutoshi Oda, Iwao Kukimoto, Piero Carninci, Lawrence Banks, Yutaka Osuga, Tomoyuki Fujii

Journal of virology　Vol. 89　No. 4　p. 2448-52　2015/02　Research paper (scientific journal)

Evolutionary, Physicochemical, and Functional Mechanisms of Protein Homooligomerization

Hafumi Nishi, Kosuke Hashimoto, Thomas Madej, Anna R. Panchenko

OLIGOMERIZATION IN HEALTH AND DISEASE　Vol. 117　p. 3-24　2013　Part of collection (book)

Cancer missense mutations alter binding properties of proteins and their interaction networks.

Hafumi Nishi, Manoj Tyagi, Shaolei Teng, Benjamin A Shoemaker, Kosuke Hashimoto, Emil Alexov, Stefan Wuchty, Anna R Panchenko

PloS one　Vol. 8　No. 6　2013

Mutations that reduce its specific DNA binding inhibit high NaCl-induced nuclear localization of the osmoprotective transcription factor NFAT5

Yuichiro Izumi, Jinxi Li, Courtney Villers, Kosuke Hashimoto, Maurice B. Burg, Joan D. Ferraris

AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY　Vol. 303　No. 10　p. C1061-C1069　2012/11　Research paper (scientific journal)

Large-scale mapping of human protein interactome using structural complexes

Manoj Tyagi, Kosuke Hashimoto, Benjamin A. Shoemaker, Stefan Wuchty, Anna R. Panchenko

EMBO REPORTS　Vol. 13　No. 3　p. 266-271　2012/03　Research paper (scientific journal)

Phosphorylation in Protein-Protein Binding: Effect on Stability and Function

Hafumi Nishi, Kosuke Hashimoto, Anna R. Panchenko

STRUCTURE　Vol. 19　No. 12　p. 1807-1815　2011/12　Research paper (scientific journal)

KEGG GLYCAN for integrated analysis of pathways, genes, and glycan structures

Kosuke Hashimoto, Minoru Kanehisa

Handbook of Glycomics　p. 197-210　2010　Part of collection (book)

The Global Picture of Glycosyltransferase Families in Eukaryotes

Kosuke Hashimoto, Toshiaki Tokimatsu, Susumu Goto, Minoru Kanehisa

GLYCOBIOLOGY　Vol. 18　No. 11　p. 968-968　2008/11

A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology

Kosuke Hashimoto, Kiyoko Flora Aoki-Kinoshita, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka

ACM Transactions on Knowledge Discovery from Data　Vol. 2　No. 1　2008/03/01　Research paper (scientific journal)

An improved scoring scheme for predicting glycan structures from gene expression data

Akitsugu Suga, Yoshihiro Yamanishi, Kosuke Hashimoto, Susumu Goto, Minoru Kanehisa

GENOME INFORMATICS 2007, VOL 18　Vol. 18　p. 237-246　2007　Research paper (international conference proceedings)

A new efficient probabilistic model for mining labeled ordered trees

Kosuke Hashimoto, Kiyoko F. Aqki-Kinoshita, Nobuhisa Ueda, Minoru Kanehisa, Hiroshi Mamitsuka

Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining　Vol. 2006　p. 177-186　2006　Research paper (international conference proceedings)

The repertoire of desaturases for unsaturated fatty acid synthesis in 397 genomes.

Hashimoto K, Yoshizawa AC, Saito K, Yamada T, Kanehisa M

Genome informatics. International Conference on Genome Informatics　Vol. 17　No. 1　p. 173-183　2006

Prediction of glycan structures from gene expression data based on glycosyltransferase reactions

S Kawano, K Hashimoto, T Miyama, S Goto, M Kanehisa

BIOINFORMATICS　Vol. 21　No. 21　p. 3976-3982　2005/11　Research paper (scientific journal)

A global representation of the carbohydrate structures: a tool for the analysis of glycan.

Hashimoto K, Kawano S, Goto S, Aoki-Kinoshita KF, Kawashima M, Kanehisa M

Genome informatics. International Conference on Genome Informatics　Vol. 16　No. 1　p. 214-222　2005

Extraction of species-specific glycan substructures.

Hizukuri Y, Yamanishi Y, Hashimoto K, Kanehisa M

Genome informatics. International Conference on Genome Informatics　Vol. 15　No. 1　p. 69-81　2004

GLYCAN: The Database of Carbohydrate Structures

Hashimoto Kosuke, Hamajima Masami, Goto Susumu, Masumoto Shigekazu, Kawasima Masayuki, Kanehisa Minoru

GI　Vol. 14　p. 649-650　2003

Prediction of Glycan Structures from Glycosyltransferase Expression Profiles

Kawano Shin, Okuno Yasushi, Hashimoto Kosuke, Yamamoto Harumi, Takematsu Hiromu, Kozutsumi Yasunori, Goto Susumu, Kanehisa Minoru

GI　Vol. 14　p. 304-305　2003