Graph-based clustering for finding distant relationships in a large set of protein sequences. - Hideya Kawaji; Yoichi Takenaka; Hideo Matsuda (Bioinform., 2004)

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. - Hideya Kawaji; Takeya Kasukawa; Shiro Fukuda; Shintaro Katayama; Chikatoshi Kai; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki (Nucleic Acids Res., 2006)

SDRF2GRAPH - a visualization tool of a spreadsheet-based description of experimental processes. - Hideya Kawaji; Yoshihide Hayashizaki; Carsten O. Daub (BMC Bioinform., 2009)

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. - Hideya Kawaji; Jessica Severin; Marina Lizio; Alistair R. R. Forrest; Erik van Nimwegen; Michael Rehli; Kate Schroder; Katharine M. Irvine; Harukazu Suzuki; Piero Carninci; Yoshihide Hayashizaki; Carsten O. Daub (Nucleic Acids Res., 2011)

The RIKEN integrated database of mammals. - Hiroshi Masuya; Yuko Makita; Norio Kobayashi; Koro Nishikata; Yuko Yoshida; Yoshiki Mochizuki; Koji Doi; Terue Takatsuki; Kazunori Waki; Nobuhiko Tanaka; Manabu Ishii; Akihiro Matsushima; et al. (Nucleic Acids Res., 2011)

CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments. - Emmanuel Dimont; Oliver Hofmann 001; Shannan J. Ho Sui; Alistair R. R. Forrest; Hideya Kawaji; Winston Hide (Bioinform., 2014)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

The BioMart community portal: an innovative alternative to large, centralized data repositories. - Damian Smedley; Syed Haider; Steffen Durinck; Luca Pandini; Paolo Provero; James E. Allen; Olivier Arnaiz; Mohammad Hamza Awedh; Richard A. Baldock; Giulia Barbiera; Philippe Bardou; Tim Beck; et al. (Nucleic Acids Res., 2015)

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response. - Stuart Aitken; Shigeyuki Magi; Ahmad M. N. Alhendi; Masayoshi Itoh; Hideya Kawaji; Timo Lassmann; Carsten O. Daub; Erik Arner; Piero Carninci; Alistair R. R. Forrest; Yoshihide Hayashizaki; Levon M. Khachigian; et al. (PLoS Comput. Biol., 2015)

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. - Imad Abugessaisa; Hisashi Shimoji; Serkan Sahin; Atsushi Kondo; Jayson Harshbarger; Marina Lizio; Yoshihide Hayashizaki; Piero Carninci; Alistair R. R. Forrest; Takeya Kasukawa; Hideya Kawaji (Database J. Biol. Databases Curation, 2016)

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. - Hans Ienasescu; Kang Li; Robin Andersson; Morana Vitezic; Sarah Rennie; Yun Chen; Kristoffer Vitting-Seerup; Emil Lagoni; Mette Boyd; Jette Bornholdt; Michiel J. L. de Hoon; Hideya Kawaji; et al. (Database J. Biol. Databases Curation, 2016)

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. - David J. Arenillas; Alistair R. R. Forrest; Hideya Kawaji; Timo Lassmann; Wyeth W. Wasserman; Anthony Mathelier (Bioinform., 2016)

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. - Marina Lizio; Jayson Harshbarger; Imad Abugessaisa; Shuei Noguchi; Atsushi Kondo; Jessica Severin; Chris Mungall; David J. Arenillas; Anthony Mathelier; Yulia A. Medvedeva; Andreas Lennartsson; Finn Drabløs; et al. (Nucleic Acids Res., 2017)

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. - J. Kenneth Baillie; Andrew Bretherick; Christopher S. Haley; Sara Clohisey; Alan Gray; Lucile P. A. Neyton; Jeffrey Barrett; Eli A. Stahl; Albert Tenesa; Robin Andersson; J. Ben Brown; Geoffrey J. Faulkner; et al. (PLoS Comput. Biol., 2018)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. - Marina Lizio; Imad Abugessaisa; Shuhei Noguchi; Atsushi Kondo; Akira Hasegawa; Chung-Chau Hon; Michiel J. L. de Hoon; Jessica Severin; Shinya Oki; Yoshihide Hayashizaki; Piero Carninci; Takeya Kasukawa; et al. (Nucleic Acids Res., 2019)

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; et al. (Nucleic Acids Res., 2021)