Riu Yamashita - researchr alias

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Viewing Publication 1 - 14 from 14

2025

SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics dataShunsuke 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. ploscb, 21(2):1012854, 2025. [doi]

2015

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation dataAyako Suzuki, Hiroyuki Wakaguri, Riu Yamashita, Shin Kawano, Katsuya Tsuchihara, Sumio Sugano, Yutaka Suzuki, Kenta Nakai. nar, 43(Database-Issue):87-91, 2015. [doi]

2012

DBTSS: DataBase of Transcriptional Start Sites progress report in 2012Riu Yamashita, Sumio Sugano, Yutaka Suzuki, Kenta Nakai. nar, 40(Database-Issue):150-154, 2012. [doi]

2011

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applicationsToshiaki 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 J. P. Bonnal, José M. Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd 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 Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi. biomedsem, 2:4, 2011. [doi]

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applicationsToshiaki 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 J. P. Bonnal, José M. 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 Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi. biomedsem, 2:4, 2011. [doi]

2010

DBTSS provides a tissue specific dynamic view of Transcription Start SitesRiu Yamashita, Hiroyuki Wakaguri, Sumio Sugano, Yutaka Suzuki, Kenta Nakai. nar, 38(Database-Issue):98-104, 2010. [doi]

2008

DBTSS: database of transcription start sites, progress report 2008Hiroyuki Wakaguri, Riu Yamashita, Yutaka Suzuki, Sumio Sugano, Kenta Nakai. nar, 36(Database-Issue):97-101, 2008. [doi]

2007

Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regionsToshiyuki Okumura, Hiroki Makiguchi, Yuko Makita, Riu Yamashita, Kenta Nakai. nar, 35(Web-Server-Issue):227-231, 2007. [doi]

2006

DBTGR: a database of tunicate promoters and their regulatory elementsNicolas Sierro, Takehiro Kusakabe, Keun-Joon Park, Riu Yamashita, Kengo Kinoshita, Kenta Nakai. nar, 34(Database-Issue):552-555, 2006. [doi]

DBTSS: DataBase of Human Transcription Start Sites, progress report 2006Riu Yamashita, Yutaka Suzuki, Hiroyuki Wakaguri, Katsuki Tsuritani, Kenta Nakai, Sumio Sugano. nar, 34(Database-Issue):86-89, 2006. [doi]

2005

Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissuesKikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai. nar, 33(Database-Issue):533-536, 2005. [doi]

2004

2002

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAsYutaka Suzuki, Riu Yamashita, Kenta Nakai, Sumio Sugano. nar, 30(1):328-331, 2002.

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