kenta nakai

中井 謙太|Kenta Nakai








Moesa H. A., Wakabayashi S., Nakai K. and Patil A.
Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification.
Mol. Biosystems, 8, 3262-3273,2012.
Morita S., Takahashi R., Yamashita R., Toyoda A., Horii T., Kimura M., Fujiyama A., Nakai K., Tajima S., Matoba R., Ochiya R. and Hatada I.
Genome-wide analysis of DNA methylation and expression of microRNAs in breast cancer cells.
Int. J. Mol. Sci., 13(7), 8259-8272, 2012.
Kraut D., Israeli E., Shrader E., Patil A., Nakai K., Nanavati D., Inobe T. and Matouschek A.
Sequence- and species-dependence of proteasomal processivity.
ACS Chemical Biology,7(8), 1444-1453, 2012.
Kimura K., Koike A. and Nakai K.
A Bit-parallel dynamic programming algorithm suitable for DNA sequence alignment.
J. Bioinformatics and Computational Biology,10(4),1250002, 2012.
Yamashita R., Sugano S., Suzuki Y. and Nakai K.
DBTSS: database of transcriptional start sites progress report in 2012.
Nucl. Acids Res., 40(Database Issue), D150-154, 2012.
Patil A., Teraguchi S., Dinh H., Nakai K. and Standley D. M.
Functional annotation of intrinsically disordered domains by their amino acid content using IDD Navigator.
Pacific Symposium on Biocomputing 17, 164-175, 2012.
Patil A., Nakai K. and Kinoshita K.
Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks.
BMC Genomics 12(Suppl. 3), S19, 2011.
Okamura K., Yamashita R., Takimoto N., Nishitsuji K., Suzuki Y., Kusakabe T. G. and Nakai K.
Profiling ascidian promoters as the primordial type of vertebrate promoter.
BMC Genomics 12(Suppl. 3), S7, 2011.
Kimura K., Koike A. and Nakai K.
Seed-set construction by equi-entropy partitioning for efficient and sensitive short-read mapping.
Algorithms in Bioinformatics in T.M.Przytycka and M.-F. Sagot ed.)Lecture Notes in Computer Science, 6833, 151-162, 2011.
Ohshima D., Qin J., Konnno H., Hirosawa A., Shiraishi T., Yanai H., Shimo Y., Akiyama N., Yamashita R., Nakai K. and Inoue J.
RANK signaling induces interferon-stimulated genes in the fetal thymic stroma.
Biochem. Biophys. Res. Comm., 408(4), 530-536, 2011.
Irie T., Park S. J., Yamashita R., Seki M., Yada T., Sugano S., Nakai K. and Suzuki Y.
Predicting promoter activities of primary human DNA sequences.
Nucl. Acids Res., 39(11), e75, 2011.
Yamashita R., Sathira N. P., Kanai A., Tanimoto K., Arauchi T., Tanaka Y., Hashimoto S., Sugano S., Nakai K. and Suzuki Y.
Genome-wide characterization of transcription start sites in humans by integrative transcriptome analysis.
Genome Res., 21(5), 775-789, 2011.
Khare P., Mortimer S. I., Cleto C. L., Okamura K., Suzuki Y., Kusakabe T., Nakai K., Meedel T. H. and Hastings K. E. M.
Cross-validated methods for promoter/transcription start site mapping in SL trans-spliced genes, established using the Ciona intestinalis troponin I gene.
Nucleic Acids Res., 39(7), 2638-2648, 2011.
Park S. J. and Nakai K.
A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns.
BMC Bioinformatics, 12(Suppl 1), S50, 2011.
Patil A., Nakai K. and Nakamura H.
HitPredict: a database of quality assessed protein-protein interactions in nine species.
Nucl. Acids Res., 39, D744-D799, 2011.
Ranganathan S., Schönbach C., Nakai K. and Tan T. W.
Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics(InCoB 2010).
BMC Genomics, 11(Suppl 4), S1, 2010.
Imai K. and Nakai K.
Prediction of subcellular location of proteins: where to proceed?
Proteomics, 10(22), 3970-3983, 2010.
Satoh T., Takeuchi O., Vandenbon A., Yasuda K., Tanaka Y., Kumagai Y., Miyake T., Matsushita K., Okazaki T., Saitoh T., Honma K., Matsuyama T., Yui K., Tsujimura T., Standley D.M., Nakanishi K., Nakai K. and Akira S.
The JMJD3-IRF4 axis regulates M2 macrophage polarization and host responses against helminth infection.
Nature Immunol., 11(10), 936-944, 2010.
Okamura K., Matsumoto K. A. and Nakai K.
Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution.
BMC Bioinformatics, 11(Suppl 7), S2, 2010.
Schönbach C., Nakai K., Tan T. W. and Ranganathan S.
InCoB2010 -- 9th Internatonal Conference on Bioinformatics at Tokyo, Japan September 26-28, 2010.
BMC Bioinformatics, 11(Suppl 7), S1, 2010.
Kawaki H., Kubota S., Aoyama E., Fujita N., Hanagata H., Miyauchi A., Nakai K. and Takigawa M.
Design and utility of CCN2 anchor peptide aptamers.
Biochemie, 92(8), 1010-1015, 2010.
Tanaka Y., Yamashita R., Suzuki Y. and Nakai K.
Effects of Alu elements on global nucleosome positioning in the human genome.
BMC Genomics, 11, 309, 2010.
Kubo A., Suzuki N., Yuan X., Nakai K., Satoh N., S. Imai K. and Satou Y.
Genomic cis-regulatory networks in the Ciona intestinalis embryo.
Development, 137(10), 1613-1623, 2010.
Tanaka Y., Yoshimura I. and Nakai K.
Positional variations among heterogeneous nucleosome maps give dynamical information on chromatin.
Chromosoma, 119(4), 391-404, 2010.
Sathira N., Yamashita R., Tanimoto K., Kanai A., Arauchi T., Kanematsu S., Nakai K., Suzuki Y. and Sugano S.
Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer.
DNA Res., 17(3), 169-183, 2010
Yamashita R., Wakaguri H., Sugano S., Suzuki Y. and Nakai K.
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.
Nucl. Acids Res., 38, D98-D104, 2010.
Vandenbon A. and Nakai K.
Modeling tissue-specific structural patterns in human and mouse promoters.
Nucl. Acids Res., 38(1), 17-25, 2010