Computational Biology Research Center[CBRC]

Advanced Industrial Science and Technology[AIST]

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Our research activities

Computational Biology Research Center (CBRC) performs
research activities to create a wide array of industrial technologies
using genomes and the other biological information to fulfill our mission.
The training of future specialists in the field is an additional
dimension of the CBRC's remit and in close coordination with
private enterprise and universities, we are engaged in programs
to cultivate human resources, those destined to be the architects
and builders of the next generation of bioinformatics technology.

NEWS>>>BackNumber

2013/05/30: Software "Spaln" has been added to our software list.
2013/05/16: NEWSLETTER No.42
2013/05/07: The Paper of Tomii Team Leader, Dr.Imai et al.:"Tam41 Is a CDP-Diacylglycerol Synthase Required for Cardiolipin Biosynthesis in Mitochondria." has been published in Cell Metabolism.
2013/03/21: Dr. Kazutaka Katoh's paper "MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability" is on the cover of Molecular Biology and Evolution(Volume 30, Issue 4).
2013/02/08: Dr. Sachiyo Aburatani received the best paper award at GLOBAL HEALTH 2012
2012/08/01: New Research Group "Comparative Genomics Research Group" started
2012/07/09: Tomii, K.(CBRC), et al."Convergent evolution in structural elements of proteins investigated using cross profile analysis", BMC Bioinformatics, 13:11,(2012). highly accessed.
2012/07/05: W. Nemoto(Tokyo Denki University) and H. Toh(CBRC) "Functional region prediction with a set of appropriate homologous sequences-an index for sequence selection by integrating structure and sequence information with spatial statistics", BMC Structural Biology, 12:11,(2012). highly accessed.
2012/06/28: Joint research by CBRC and the University of Tokyo on protein nuclear export "Prediction of leucine-rich nuclear export signal containing proteins with NESsential."（Nucleic Acids Res., 39(16), (2011）. rated as "must read" by the Faculty of 1000"

RECENT PAPERS

headmark Nishino T, Rago F, Hori T, Tomii K, Cheeseman IM, Fukagawa T.:"CENP-T provides a structural platform for outer kinetochore assembly.", The EMBO Journa, 6;32(3), pp.424-36.(2013). [Link]

headmark Kazutaka Katoh and Daron M. Standley; ”MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability”, Mol. Biol. Evol. 30(4), pp.772-780.(2013). [Link]

headmark Kimura M, Kose S, Okumura N, Imai K, Furuta M, Sakiyama N, Tomii K, Horton P, Takao T, Imamoto N.:"Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics.", Mol Cell Proteomics.,12(1), pp145-57(2013). [Link]

headmark Iwata H, Gotoh O.:"Benchmarking spliced alignment programs including an extended version of spaln (spaln2) that incorporates additional species-specific features", Nucleic Acids Res., 1;40(20):e161. doi: 10.1093/nar/gks708.(2012). [Link]

headmark Belinky F, Bahir I, Stelzer G, Zimmerman S, Rosen N, Nativ N, Dalah I, Iny Stein T, Rappaport N, Mituyama T, Safran M, Lancet D.:"Non-redundant compendium of human ncRNA genes in GeneCards.", Bioinformatics, (2012). (in press) [Link]

headmark Dmitry Nerukh, Noriaki Okimoto, Atsushi Suenaga, and Makoto Taiji:"Ligand diffusion on protein surface observed in molecular dynamics simulation", J. Phys. Chem. Lett.. 3 (23), pp.3476-3479 (2012). [Link]

headmark Krishnan Harini, Sankar Kannan, Wataru Nemoto, Kazuhiko Fukui, Ramanathan Sowdhamini:"Residue conservation and dimer-interface analysis of olfactory receptor molecular models", Journal of Molecular Biochemistry. 1, pp.161-170 (2012). [Link]

headmark Goro Terai, Hiroaki Okida, Kiyoshi Asai, Toutai Mituyama :"Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features", PLoS One.. PLoS ONE 7(9): e44314. doi:10.1371 (2012). [Link]

headmark Yamasaki S, Terada T, Kono H, Shimizu K, Sarai A.:"A new method for evaluating the specificity of indirect readout in protein-DNA recognition", Nucleic Acids Res.. 1;40(17):e129 (2012). [Link]

headmark Akiyama S, Suenaga A, Kobayashi T, Kamioka T, Taiji M, Kuroda Y.:"Experimental identification and theoretical analysis of a thermally stabilized green fluorescent protein variant", Biochemistry.. 9;51(40):7974-82. doi: 10.1021/bi300580j.(2012). [Link]

headmark Suenaga A, Okimoto N, Hirano Y, Fukui K.:"An efficient computational method for calculating ligand binding affinities", PLoS One.. ;7(8):e42846. doi: 10.1371(2012). [Link]

Updated on Feb. 12, 2013

CBRC Introduction movie (in Japanese)

Software & Database : CBRC's literary property (software tools and databases) can be used.

Developers -The road to our research success.-

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