Riu Yamashita

13 papers Journal 13
YearRankTypeTitle / Venue / Authors
2025 J jnl
SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data.
PLoS Comput. Biol.
Shunsuke A. Sakai, Ryosuke Nomura, Satoi Nagasawa, Sunggi Chi, Ayako Suzuki, Yutaka Suzuki, Mitsuho Imai, Yoshiaki Nakamura, Takayuki Yoshino, Shumpei Ishikawa, Katsuya Tsuchihara, Shun-Ichiro Kageyama, Riu Yamashita
2015 J jnl
DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
Nucleic Acids Res.
Ayako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, Kenta Nakai
2012 J jnl
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012.
Nucleic Acids Res.
Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai
2011 J jnl
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.
J. Biomed. Semant.
Toshiaki Katayama, Mark D. Wilkinson, Rutger A. Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F. Aoki-Kinoshita, Kazuharu Arakawa, Bruno Aranda, Raoul Jean Pierre Bonnal, José María Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd W. Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, E. Luke McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas H. Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi
2010 J jnl
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.
Nucleic Acids Res.
Riu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, Kenta Nakai
2008 J jnl
DBTSS: database of transcription start sites, progress report 2008.
Nucleic Acids Res.
Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai
2007 J jnl
Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.
Nucleic Acids Res.
Toshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, Kenta Nakai
2006 J jnl
DBTGR: a database of tunicate promoters and their regulatory elements.
Nucleic Acids Res.
Nicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai
2006 J jnl
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006.
Nucleic Acids Res.
Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano
2005 J jnl
Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues.
Nucleic Acids Res.
Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai
2004 J jnl
BTSS, DataBase of Transcriptional Start Sites: progress report 2004.
Nucleic Acids Res.
Yutaka Suzuki, Riu Yamashita, Sumio Sugano, Kenta Nakai
2004 J jnl
Large-scale collection and characterization of promoters of human and mouse genes.
Silico Biol.
Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Alexander E. Kel, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Toshihisa Takagi, Kenta Nakai, Sumio Sugano
2002 J jnl
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.
Nucleic Acids Res.
Yutaka Suzuki, Riu Yamashita, Kenta Nakai, Sumio Sugano