Sakaki Yoshiyuki

Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns (2009)

Kawaura Kanako, Mochida Keiichi, Enju Akiko, Totoki Yasushi, Toyoda Atsushi, Sakaki Yoshiyuki, ...

Abstract Background Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs) for wheat is becoming particularly important for...

The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family (2009)

Goto Hiroki, Watanabe Kazunori, Araragi Naozumi, Kageyama Rui, Tanaka Kunika, Kuroki Yoko, ...

Abstract Background The glutamate receptors (GluRs) play a vital role in the mediation of excitatory synaptic transmission in the central nervous system. To clarify the evolutionary dynamics and...

Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili (2008)

Futamura Norihiro, Totoki Yasushi, Toyoda Atsushi, Igasaki Tomohiro, Nanjo Tokihiko, Seki Motoaki, ...

Abstract Background Cryptomeria japonica D. Don is one of the most commercially important conifers in Japan. However, the allergic disease caused by its pollen is a severe public health problem in...

Absolute quantification of the budding yeast transcriptome by means of competitive PCR between genomic and complementary DNAs (2008)

Miura Fumihito, Kawaguchi Noriko, Yoshida Mikio, Uematsu Chihiro, Kito Keiji, Sakaki Yoshiyuki, ...

Abstract Background An ideal format to describe transcriptome would be its composition measured on the scale of absolute numbers of individual mRNAs per cell. It would help not only to precisely...

Large-scale collection and annotation of full-length enriched cDNAs from a model halophyte, Thellungiella halophila (2008)

Taji Teruaki, Sakurai Tetsuya, Mochida Keiichi, Ishiwata Atsushi, Kurotani Atsushi, Totoki Yasushi, ...

Abstract Background Thellungiella halophila (also known as Thellungiella salsuginea) is a model halophyte with a small plant size, short life cycle, and small genome. It easily undergoes genetic...

Identification and classification of genes regulated by phosphatidylinositol 3-kinase- and TRKB-mediated signalling pathways during neuronal differentiation in two subtypes of the human neuroblastoma cell line SH-SY5Y (2008)

Nishida Yuichiro, Adati Naoki, Ozawa Ritsuko, Maeda Aasami, Sakaki Yoshiyuki, Takeda Tadayuki

Abstract Background SH-SY5Y cells exhibit a neuronal phenotype when treated with all-trans retinoic acid (RA), but the molecular mechanism of activation in the signalling pathway mediated by...

An integrative in silico approach for discovering candidates for drug-targetable protein-protein interactions in interactome data (2007)

Sugaya Nobuyoshi, Ikeda Kazuyoshi, Tashiro Toshiyuki, Takeda Shizu, Otomo Jun, Ishida Yoshiko, ...

Abstract Background Protein-protein interactions (PPIs) are challenging but attractive targets for small chemical drugs. Whole PPIs, called the 'interactome', have been emerged in several organisms,...

Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones (2007)

Nanjo Tokihiko, Sakurai Tetsuya, Totoki Yasushi, Toyoda Atsushi, Nishiguchi Mitsuru, Kado Tomoyuki, ...

Abstract Background Populus is one of favorable model plants because of its small genome. Structural genomics of Populus has reached a breakpoint as nucleotides of the entire genome have been...

Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response (2007)

Sakurai Tetsuya, Plata Germán, Rodríguez-Zapata Fausto, Seki Motoaki, Salcedo Andrés, Toyoda Atsushi, ...

Abstract Background Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial...

Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression (2004)

Murakami Katsuhiko, Kojima Toshio, Sakaki Yoshiyuki

Abstract Background Gene expression is regulated mainly by transcription factors (TFs) that interact with regulatory cis-elements on DNA sequences. To identify functional regulatory elements,...

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)

Imanishi Tadashi, Itoh Takeshi, Suzuki Yutaka, O'Donovan Claire, Fukuchi Satoshi, Koyanagi Kanako O, ...

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...