SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data. - Sakai, Shunsuke A.; Nomura, Ryosuke; Nagasawa, Satoi; Chi, Sunggi; Suzuki, Ayako; Suzuki, Yutaka; Imai, Mitsuho; Nakamura, Yoshiaki; Yoshino, Takayuki; Ishikawa, Shumpei; Tsuchihara, Katsuya; Kageyama, Shun-Ichiro; et al. (PLoS Comput. Biol., 2025)

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data. - Suzuki, Ayako; Wakaguri, Hiroyuki; Yamashita, Riu; Kawano, Shin; Tsuchihara, Katsuya; Sugano, Sumio; Suzuki, Yutaka; Nakai, Kenta (Nucleic Acids Res., 2015)

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012. - Yamashita, Riu; Sugano, Sumio; Suzuki, Yutaka; Nakai, Kenta (Nucleic Acids Res., 2012)

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. - Katayama, Toshiaki; Wilkinson, Mark D.; Vos, Rutger A.; Kawashima, Takeshi; Kawashima, Shuichi; Nakao, Mitsuteru; Yamamoto, Yasunori; Chun, Hong-Woo; Yamaguchi, Atsuko; Kawano, Shin; Aerts, Jan; Aoki-Kinoshita, Kiyoko F.; et al. (J. Biomed. Semant., 2011)

DBTSS provides a tissue specific dynamic view of Transcription Start Sites. - Yamashita, Riu; Wakaguri, Hiroyuki; Sugano, Sumio; Suzuki, Yutaka; Nakai, Kenta (Nucleic Acids Res., 2010)

DBTSS: database of transcription start sites, progress report 2008. - Wakaguri, Hiroyuki; Yamashita, Riu; Suzuki, Yutaka; Sugano, Sumio; Nakai, Kenta (Nucleic Acids Res., 2008)

Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. - Okumura, Toshiyuki; Makiguchi, Hiroki; Makita, Yuko; Yamashita, Riu; Nakai, Kenta (Nucleic Acids Res., 2007)

DBTSS: DataBase of Human Transcription Start Sites, progress report 2006. - Yamashita, Riu; Suzuki, Yutaka; Wakaguri, Hiroyuki; Tsuritani, Katsuki; Nakai, Kenta; Sugano, Sumio (Nucleic Acids Res., 2006)

DBTGR: a database of tunicate promoters and their regulatory elements. - Sierro, Nicolas; Kusakabe, Takehiro; Park, Keun-Joon; Yamashita, Riu; Kinoshita, Kengo; Nakai, Kenta (Nucleic Acids Res., 2006)

Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. - Kato, Kikuya; Yamashita, Riu; Matoba, Ryo; Monden, Morito; Noguchi, Shinzaburo; Takagi, Toshihisa; Nakai, Kenta (Nucleic Acids Res., 2005)

Large-scale collection and characterization of promoters of human and mouse genes. - Suzuki, Yutaka; Yamashita, Riu; Shirota, Matsuyuki; Sakakibara, Yuta; Chiba, Joe; Mizushima-Sugano, Junko; Kel, Alexander E.; Arakawa, Takahiro; Carninci, Piero; Kawai, Jun; Hayashizaki, Yoshihide; Takagi, Toshihisa; et al. (Silico Biol., 2004)

BTSS, DataBase of Transcriptional Start Sites: progress report 2004. - Suzuki, Yutaka; Yamashita, Riu; Sugano, Sumio; Nakai, Kenta (Nucleic Acids Res., 2004)

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. - Suzuki, Yutaka; Yamashita, Riu; Nakai, Kenta; Sugano, Sumio (Nucleic Acids Res., 2002)