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  • 誌上発表・査読有り：2012年

論　文（誌上発表・査読有り：2012年）

  • Fu SC., Huang HC., Horton P., Juan HF.,:"ValidNESs: a database of validated leucine-rich nuclear export signals.", Nucleic Acids Res. 41(Database issue):D338-43.(2012). headAbstract
  • Katoh K., Frith MC.,:"Adding unaligned sequences into an existing alignment using MAFFT and LAST.", Bioinformatics. 28(23):3144-6.(2012). headAbstract
  • Abe J., Nagai Y., Higashikuni R., Iida K., Hirokawa T., Nagai H, Kominato K, Tsuchida T, Hirata M, Inada M, Miyaura C, Nagasawa K.,:"Synthesis of vitamin D3 derivatives with nitrogen-linked substituents at A-ring C-2 and evaluation of their vitamin D receptor-mediated transcriptional activity.", Org Biomol Chem. 10(38):7826-39. doi: 10.1039/c2ob26017d.(2012). headAbstract
  • Aburatani, S., Fujibuchi, F.,:"Inference of Specific Gene Regulation by Environmental Chemicals in Human Embryonic Stem Cells." Journal of Molecular Biology Research, Canadian Center of Science and Education. 2(1): 56-64 (2012). headAbstract
  • Ono Y., Asai K., Hamada M.,:"PBSIM: PacBio reads simulator--toward accurate genome assembly.", Bioinformatics, 29(1):119-21. doi: 10.1093/bioinformatics/bts649.(2012). headAbstract
  • Sato K., Kato Y., Akutsu T., Asai K., Sakakibara Y.,:"DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.", Bioinformatics, 28(24):3218-24. doi: 10.1093/bioinformatics/bts612.(2012). headAbstract
  • Tsuji J., Frith MC., Tomii K., Horton P.,:"Mammalian NUMT insertion is non-random.", Nucleic Acids Res. 40(18):9073-88. doi: 10.1093/nar/gks424.(2012). headAbstract
  • Wang YB., Chen SH., Lin CY., Yu JK.,:"EST and transcriptome analysis of cephalochordate amphioxus--past, present and future.", Brief Funct Genomics, 11(2):96-106. doi: 10.1093/bfgp/els002.(2012). headAbstract
  • Wijaya E., Frith MC, Asai K., Horton P.,:"RecountDB: a database of mapped and count corrected transcribed sequences.", Nucleic Acids Res. 40(Database issue):D1089-92. doi: 10.1093/nar/gkr1172.(2012). headAbstract
  • Frith MC.,:"Gentle masking of low-complexity sequences improves homology search.", PLoS One. 6(12):e28819. doi: 10.1371/journal.pone.0028819.(2012). headAbstract
  • Hamada M., Wijaya E., Frith MC., Asai K.,:"Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection.", Bioinformatics, 27(22):3085-92. doi: 10.1093/bioinformatics/btr537.(2012). headAbstract
  • Gromiha M.M., Saranya N., Selvaraj S., Jayaram B., Fukui K.,:"Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes.", Proteome Sci. 9, Suppl 1:S13. doi: 10.1186/1477-5956-9-S1-S13.(2012). headAbstract
  • Aburatani S.,:"Network inference of pal-1 lineage-specific regulation in the C. elegans embryo by structural equation modeling.", Bioinformation, 8(14):652-7. doi: 10.6026/97320630008652.(2012). headAbstract
  • Ito J., Tabei Y., Shimizu K., Tomii K., Tsuda K.,:"PDB-scale analysis of known and putative ligand-binding sites with structural sketches.", Proteins, 80(3):747-63. doi: 10.1002/prot.23232.(2012). headAbstract
  • Miura K., Ishida K., Fujibuchi W., Ito A., Niikura H., Ogawa H., Sasaki I.,:"Differentiating rectal carcinoma by an immunohistological analysis of carcinomas of pelvic organs based on the NCBI Literature Survey and the Human Protein Atlas database.", Surg Today, 42(6):515-25. doi: 10.1007/s00595-012-0167-z.(2012). headAbstract
  • Ashida H., Asai K., Hamada M.,:"Shape-based alignment of genomic landscapes in multi-scale resolution.", Nucleic Acids Res. 40(14):6435-48. doi: 10.1093/nar/gks354.(2012). headAbstract
  • Kato Y., Sato K., Asai K., Akutsu T.,:"Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.", Nucleic Acids Res., 40(Web Server issue):W29-34. doi: 10.1093/nar/gks412.(2012). headAbstract
  • Hamada M., Asai K.,:"A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA).", J Comput Biol. 19(5):532-49. doi: 10.1089/cmb.2011.0197.(2012). headAbstract
  • Kiryu H., Asai K.,: "Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations.", Bioinformatics 28(8):1093-101. doi: 10.1093/bioinformatics/bts097.(2012). headAbstract
  • 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). headAbstract
  • 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) headAbstract
  • 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). headAbstract
  • 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). headAbstract
  • 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). headAbstract
  • 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). headAbstract
  • 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). headAbstract
  • 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). headAbstract
  • Priyadarzini TR, Selvin JF, Gromiha MM, Fukui K, Veluraja K.:"Theoretical Investigation on the Binding Specificity of Sialyldisaccharides with Hemagglutinins of Influenza A Virus by Molecular Dynamics Simulations", J Biol Chem.. 2012 Oct 5;287(41):34547-57. doi: 10.1074/jbc.M112.357061 (2012). headAbstract
  • Daiyasu H, Nemoto W, Toh H.:"Evolutionary analysis of functional divergence among chemokine receptors, decoy receptors and viral receptors.", Front Microbiol.. 2012;3:264. doi: 10.3389/fmicb.2012.00264.(2012). headAbstract
  • Yokobori T, Mimori K, Iwatsuki M, Ishii H, Tanaka F, Sato T, Toh H, Sudo T, Iwaya T, Tanaka Y, Onoyama I, Kuwano H, Nakayama KI, Mori M.:"Copy number loss of FBXW7 is related to gene expression and poor prognosis in esophageal squamous cell carcinoma.", Int J Oncol..2012 Jul;41(1):253-9. doi: 10.3892/ijo.2012.1436.(2012). headAbstract
  • Wataru Nemoto and Hiroyuki Toh: "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 doi:10.1186/1472-6807-12-11(2012). headAbstract
  • Martin C. Frith,Ryota Mori and Kiyoshi Asai:"A mostly-traditional approach improves alignment of bisulfite-converted DNA", Nucleic Acids Research. Volume 40, Issue 13:pp.e100.(2012). headAbstract
  • 根本 航:"生物物理学における情報科学的解析の未来", 生物物理. 52(2), pp.100-101.(2012).
  • Ito J, Tabei Y, Shimizu K, Tomii K, Tsuda K.:"PDB-scale analysis of known and putative ligand-binding sites with structural sketches.", Proteins.. 2012 Mar;80(3):747-63 (2012). headAbstract
  • Sayoko Yamamoto, Ying Zhang, Takumi Yamaguchi, Tomoshi Kameda and Koichi Kato: "Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations”,Chem Comm, 48(39), pp.4752-4754 (2012). headAbstract
  • M Michael Gromiha, K Harini, R Sowdhamini and Kazuhiko Fukui:"Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity", BMC Bioinformatics. 2012, 13(Suppl 7):S1 doi:10.1186/1471-2105-13-S7-S1 (2012). headAbstract
  • Muhammed Z, Arai S, Saijo S, Yamato I, Murata T, Suenaga A.:Calculating the Na+ translocating V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation.", J Mol Graph Model.. 2012 Jul;37:59-66. doi: 10.1016/j.jmgm.2012.03.006.(2012). headAbstract
  • Wan R, Anh VN, Asai K.:"Transformations for the compression of FASTQ quality scores of next-generation sequencing data.", Bioinformatics.. 2012 Mar 1;28(5):628-35. doi: 10.1093/bioinformatics/btr689.(2012). headAbstract
  • Fukui K, Takahashi K.:"Infrared multiple photon dissociation Spectroscopy and Computational Studies of O-Glycosylated Peptides", Anal Chem.. 2012 Mar 6;84(5):2188-94. doi: 10.1021/ac202379v. (2012). headAbstract
  • Satoshi Yamasaki, Shugo Nakamura, and Kazuhiko Fukui:"Prospects for Tertiary Structure Prediction of RNA Based on Secondary Structure Information.", J. Chem. Inf. Model.. 2012, 52 (2), pp.557-567 (2012). headAbstract
  • Watanabe M, Kobayashi T, Hirokawa T, Yoshida A, Ito Y, Yamada S, Orimoto N, Yamasaki Y, Arisawa M, Shuto S.:"Cyclopropane-based stereochemical diversity-oriented conformational restriction strategy: histamine H3 and/or H4 receptor ligands with the 2,3-methanobutane backbone.", Org Biomol Chem. 28;10(4):736-45.(2012). headAbstract
  • Ito J, Tabei Y, Shimizu K, Tsuda K, Tomii K.:"PoSSuM: a database of similar protein-ligand binding and putative pockets.", Nucleic Acids Res.. 2012 Jan;40(Database issue):D541-8.(2012). headAbstract
  • Hamada S, Satoh K, Fujibuchi W, Hirota M, Kanno A, Unno J, Masamune A, Kikuta K, Kume K, Shimosegawa T.:"MiR-126 acts as a tumor suppressor in pancreatic cancer cells via the regulation of ADAM9.", Mol Cancer Res.. 2012 Jan;10(1):3-10.(2012). headAbstract
  • Katsuhisa Horimoto:"On Two Issues of Molecular Network Models in Systems Biology - A Review", Proceedings, The Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), Dunhuang, China, August 28-31, 2011 pp.22-27 (2012). headFull Text
  • M. Michael Gromiha,R. Sowdhamini,K. Fukui:"Structure-Function Relationship in Olfactory Receptors", Bio-Inspired Computing and Applications Lecture Notes in Computer Science . Volume 6840, 2012, pp.618-623 (2012). headAbstract
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