Computational Biology Research Center[CBRC]

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2015/2/12

Biomolecular Informatics team: honored to give a talk on CAPRI round 30 at CASP11

2015/1/28

added "ScreenCap3" and "MitoFates" to our software list

2015/1/15

" Tokyo Workshop on Statistically Sound Data Mining" will be held on Feb. 16, presented by The University of Tokyo / CBRC

2014/11/27

Notice of blackout of CBRC

2014/11/19

Senior Researcher Kana Shimizu's presentation on privacy preserving database search at CSHL covered in GenomeWeb article

2014/10/1

We proudly welcome our new algorithm team leader Jun Sese

2014/9/2

GIW/InCoB 2015 will be held at Odaiba, on the Tokyo waterfront

2014/7/31

Notice about CBRC summer holiday

2014/7/18

A collaboration between CBRC and the AIST Research Center for Stem Cell Engineering published a research paper entitled "Methylome, transcriptome, and PPARγ cistrome analyses reveal two epigenetic transitions in fat cells" in "Epigenetics".

2014/4/30

BiWO2014 homepage opened.

2014/4/23

The C++ library of the lifted-ElGamal cryptosystem

2014/4/1

New "Computational Biology Research Center(CBRC)" started.

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RECENT PAPERS

Kazuhiro Sakamaki, Kouhei Shimizu, Hiroaki Iwata, Kenichiro Imai, Yutaka Satou, Noriko Funayama, Masami Nozaki, Mamiko Yajima, Osamu Nishimura, Mayura Higuchi, Kumiko Chiba, Michi Yoshimoto, Haruna Kimura, Andrew Y. Gracey, Takashi Shimizu, Kentaro Tomii, Osamu Goto, Koji Akasaka, Tatsuya Sawasaki and David J. Miller.: "The apoptotic initiator caspase-8: its functional ubiquity and genetic diversity during animal evolution", Molecular and Biology Evolution, 2014 Sep 3. [Online Ahead of Print]

Sheetlin SL, Park Y, Frith MC, Spouge JL.: "Frameshift alignment: statistics and post-genomic applications.", Bioinformatics, 2014 Aug 28. pii: btu576. [Epub ahead of print]

Szu-Chin Fu, Kenichiro Imai, Tatsuya Sawasaki and Kentaro Tomii (2014): "ScreenCap3: Improving prediction of caspase-3 cleavage sites using experimentally verified noncleavage sites", PROTEOMICS, Volume 14, Issue 17-18, pages 2042–2046, September 2014.

Marumo K, Nakada-Tsukui K, Tomii K, Nozaki T. (2014) "Ligand heterogeneity of the cysteine protease binding protein family in the parasitic protist Entamoeba histolytica. International Journal for Parasitology, 2014 Aug;44(9):625-35.

Myco Umemura, Nozomi Nagano, Hideaki Koike, Jin Kawano, Tomoko Ishii, Yuki Miyamura, Moto Kikuchi, Koichi Tamano, Jiujiang Yu, Kazuo Shin-ya, Masayuki Machida (2014) "Characterization of the biosynthetic gene cluster for the ribosomally synthesized cyclic peptide ustiloxin B in Aspergillus flavus." Fungal Genetics and Biology, in press.

Nagao C, Nagano N, Mizuguchi K (2014) "Prediction of detailed enzyme functions and identification of specificity determining residues by random forests." PLoS One, 9,e84623(2014)

Soichiro Kitazawa, Tomoshi Kameda, Ayumi Kumo, Maho Yagi-Utsumi, Nicola J. Baxter, Koichi Kato, Mike P. Williamson and Ryo Kitahara: "Close Identity between Alternatively Folded State N2 of Ubiquitin and the Conformation of the Protein Bound to the Ubiquitin-Activating Enzyme", Biochemistry 53 (3):447-449(2014)

Toda E, Terashima Y, Esaki K, Yoshinaga S, Sugihara M, Kofuku Y, Shimada I, Suwa M, Kanegasaki S, Terasawa H, Matsushima K.: "Identification of a binding element for the cytoplasmic regulator FROUNT in the membrane-proximal C-terminal region of chemokine receptors CCR2 and CCR5", Biochem J., 457(2):313-22. doi: 10.1042/BJ20130827 (2014)

Masayuki Sakurai, Hiroki Ueda, Takanori Yano, Shunpei Okada, Hideki Terajima, Toutai Mitsuyama, Atsushi oyoda, Asao Fujiyama, Hitomi Kawabata and Tsutomu Suzuki: ""4A biochemical landscape of A-to-I RNA editing in the human brain transcriptome", Genome Res., 3pp.522-534, doi: 10.1101/gr.162537.113 (2014).

Natsuhiro Ichinose, Tetsushi Yada, Osamu Gotoh: "Tetrahedral Gray Code for Visualization of Genome Information", PLOS ONE, 9 (1):e86133(2014)

Horton P.: "Next-generation Bioinformatics: connecting bases to genes, networks and disease", Brief Bioinform, 15 (2): 137 (2014)

S Aburatani and H Toh: "Network inference of AP pattern formation system in D. melanogaster by structural equation modeling", J. Phys.: Conf. Ser. 490 012145 doi:10.1088/1742-6596/490/1/012145 (2014)

Inoue, T., Takano, K., Watanabe, T., Kawahara, J., Yoshinaka, R., Kishimoto, A., Tsuda, K., Minato, S.-I., Hayashi, Y.: "Distribution Loss Minimization With Guaranteed Error Bound", IEEE Transactions on Smart Grid 5(1):102 - 111(2014)

Elahi M, Islam MM, Noguchi K, Yohda M, Toh H, Kuroda Y.: "Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3)", Biochim Biophys Acta., 1844 (3):585-92(2014).

Updated on Nov. 27, 2014