2016 - Present
Anbo, H, Amagai, H. and Fukuchi, S. NeProc predicts binding segments in intrinsically disordered regions without learning binding region sequences. Biophysics and Physicobiology, https://doi.org/10.2142/biophysico.BSJ-202002, (2020)
Anbo, H., Sato, A., Okoshi, A., and Fukuchi, S. Functional segments on intrinsically disordered regions in disease-related proteins. Biomolecules, 9, 88, (2019)
Segawa, T., Fukuchi, S., Bodington, D., Tsuchida, S., Nguema, P. P. M., Mori, H., and Ushida, K. Genomic analyses of Bifidobacterium moukalabense reveal adaptations to frugivore/folivore feeding behavior. Microorganisms, 7(4), 99, (2019)
Homma, K., Anbo, H., Noguchi, T., and Fukuchi, S. Both intrinsically disordered regions and structural domains evolve rapidly in immune-related mammalian proteins. Int. J. Mol. Sci. 19, 3860 (2018)
Matsuo, N., Goda, N., Shimizu, K., Fukuchi, S., Ota, M. and Hiroaki, H. Discovery of cryoprotective activity in human genome-derived intrinsically disordered proteins. Int. J. Mol. Sci. 19, 401 (2018)
Uemura, E., Niwa, T., Minami, S., Takemoto, K., Fukuchi, S., Machida, K., Imataka, H., Ueda, T., Ota, M. and Taguchi, H. Large-scale aggregation analysis of eukaryotic proteins reveals an involvement of intrinsically disordered regions in protein folding. Scientific Repots. 8, article number 678 (2018)
Ota, H. Fukuchi, S. Sequence conservation of protein binding segments in intrinsically disordered regions. Biochemical and Biophysical Research Communications. 494, 602-607, (2017)
Subekti, D. R. G., Murata, A., Itoh, Y., Fukuchi, S., Takahashi, H., Kanbayashi, S., Takahashi, S., and Kamagata, K. The disordered linker in p53 participates in nonspecific binding to and one-dimensional sliding along DNA revealed by single-molecule fluorescence measurements. Biochemistry, 56, 4134 - 4144, (2017).
Homma, K., Noguchi, T., and Fukuchi, S. Codon usage is less optimized in eukaryotic gene segments encoding intrinsically disordered regions than in those encoding structural domains. Nucleic Acids Research, doi: 10.1093/nar/gkw899 (2016).
Ota, M., Gonja, H., Koike, R., Fukuchi, S. Multiple-Localization and Hub Proteins. PLoS ONE 11(6): e0156455. doi:10.1371/journal.pone.0156455 (2016).
2010 - 2015
Tomono, T., Kojima, H., Fukuchi, S., Tohsato, Y. and Ito, M. Investigation of glycan evolution based on a comprehensive analysis of glycosyltransferases using phylogenetic profiling. Biophysics and Physicobiology. 12, 57-68, (2015).
Maekawa, M. Iwayama, I., Ohnishi, T., Toyoshima, M., Shimamoto, C., Hisano, Y., Toyota, T., Balan, S., Matsuzaki, H., Iwata, Y., Takagai, S., Yamada, K., Ota, M., Fukuchi, S., Okada, Y., Akamatsu, W., Tsujii, M., Owada, Y., Okano, H., Mori, N., and Yoshikawa, T. Investigation of the fatty acid transporter-encoding genes SLC27A3 and SLC27A4 in Autism. Scientific Reports, 5, Article number:16239 (2015).
Goda, N., Matsuo, N., Tenno, T., Ishino, S., Ishino, Y., Fukuchi, S., Ota, M., and Hiroaki, H. An optimized Npro-based method for the expression and purification of intrinsically disordered proteins for an NMR study. Intrinsically Disordered Protein. DOI:10.1080/21690707.2015.1011004 (2015)
Balan S., Iwayama Y., Maekawa M., Toyota T., Ohnishi T., Toyoshima M., Shimamoto C., Esaki K., Yamada K., Iwata Y., Suzuki K., Ide M., Ota M., Fukuchi S., Tsujii M., Mori N., Shinkai Y., and Yoshikawa T. Exon resequencing of H3K9 methyltransferase complex genes, EHMT1, EHTM2 and WIZ in Japanese autism subjects. Mol. Autism 5, 49 (2014).
Fukuchi, S., Sakamoto, S., Nobe, Y., Murakami, D. S., Amemiya, T., Hosoda, K., Koike, R., Hiroaki, H., and Ota, M. IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners. Nucleic Acids Res. D1,D320 - D325 (2014).
Ota M., Koike R., Amemiya T., Tenno T., Romero R. P., Hiroaki H., Dunker K., and Fukuchi S. An assignment of intrinsically disordered regions of proteins based on NMR structures. J. Struct. Biol. 181, 29 - 36 (2013)
Ito M., Tohsato Y., Sugisawa H., Kohara S., Fukuchi S., Nishikawa I., and Nishikawa K. Intrinsically disordered proteins in human mitochondria. Genes Cells. 10, 817-825 (2012)
Fukuchi, S., Sakamoto, S., Nobe, Y., Murakami, D. S., Amemiya, T., Hosoda, K., Koike, R.,Hiroaki, H., and Ota, M. IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature. Nucleic Acids Res. 40(D1) D507-D511 (2012)
Homma K, Fukuchi S, Nishikawa K, Sakamoto S, Sugawara H. Intrinsically disordered regions have specific functions in mitochondrial and nuclear proteins. Mol. Biosyst. 8, 247-255 (2012).
Fukuchi, S., Hosoda, K. Homma, K., Gojobori, T. and Nishikawa, K. Binary classification of protein molecules into intrinsically disordered and ordered segments. BMC Structural Biology 11 29 (2011)
Nonomura, K., Eiguchi, M., Nakano, M., Takashima, K., Komeda, N., Fukuchi, S., Miyazaki, S., Miyano, A., Hirochika, H. and Kurata, N. A novel RNA-recognition-motif protein is required for premeiotic G1/S-phase transition in Rice. PLoS Genet. 7 e1001265 (2011)
Nishikawa, I., Nakajima, Y., Ito, M., Fukuchi, S., Homma K. and Nishikawa, K. Computational prediction of O-linked glycosylation sites that preferentially map on intrinsically disordered regions of extracellular proteins. Int. J.Mol. Sci. 11 4991-5008 (2010)
2005 - 2009
Fukuchi, S., Homma, K., Minezaki, Y., Gojobori, T. and Nishikawa, K. Development of an Accurate Classification system of Proteins into Structured and Unstructured Regions that Uncovers Novel Structural Domains: Its Application to Human Transcription Factors. BMC Structural Biology 9 26 (2009)
Fukuchi, S., Homma, K., Sakamoto, S., Sugawara, H., Tateno, Y., Gojobori, T. and Nishikawa, K. The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. Nucleic Acids Res. 37 D333-D337 (2009)
Sugawara, H., Ikeo, K., Fukuchi, S., Gojobori, T. and Tateno, Y. DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res. 37 D16-D18 (2009)
Genome Information Integration Project and H-Invitational 2. (176th in 183)The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res. 36, D793-D799 (2008).
You, D.J., Fukuchi, S., Nishikawa, K., Koga, Y., Takano, K. and Kanaya. S. Protein Thermostabilization Requires a Fine-tuned Placement of Surface-charged Residues. J Biochem (Tokyo) 142, 507-516 (2007).
Homma, K., Fukuchi, S., Nakamura, Y., Gojobori T. and Nishikawa, K. Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in Eight Species of {gamma}-Proteobacteria. Mol. Biol. Evol. 24,805-813 (2007) .
Fukuchi, S., Homma, K., Minezaki, Y. and Nishikawa, K. Intrinsically disordered loops inserted into the structural domains of human proteins. J. Mol. Biol. 355, 845-857 (2006).
Kosuge, T., Abe, T., Okido, T., Tanaka, N., Hirahata, M., Maruyama, Y., Mashima, J., Tomiki, A., Kurokawa, M., Himeno, R., Fukuchi, S., Miyazaki, S., Gojobori, T., Tateno, Y. and Sugawara, H. Exploration and Grading of Possible Genes from 183 Bacterial Strains by a Common Protocol to Identification of New Genes: Gene Trek in Prokaryote Space (GTPS). DNA Res. 13, 245-254 (2006).
Yamasaki, C., Koyanagi, KO., Fujii, Y., Itoh, T., Barrero, R., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., Takeda, J., Fukuchi, S., Miyazaki, S., Nomura, N., Sugano, S., Imanishi, T. and Gojobori, T. Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational database (H-InvDB). Gene 364, 99-107 (2005).
2000 - 2004
Fukuchi, S. and Nishikawa, K. Estimation of the number of authentic orphan genes in bacterial genomes. DNA Res. 11, 219?231 (2004).
Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan, C., Fukuchi, S., Gojobori, T., et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2, 856-875 (2004).
Fukuchi S., Yoshimune K., Wakayama M., Moriguchi M. and Nishikawa K. Unique amino acid composition of proteins in halophilic bacteria. J. Mol. Biol. 327, 347-357 (2003).
Nakashima, H., Fukuchi, S. and Nishikawa, K. Compositional changes of bacterial RNA, DNA and proteins for adaptation to higher/lower temperatures. J. Biochem. 133, 506-513 (2003).
Homma, K., Fukuchi, S., Kawabata, T., Ota, M. and Nishikawa, K. A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome. Gene 294, 25-33 (2002).
Kawabata, T., Fukuchi, S., Homma, K., Ota, M., Araki, J., Ito, T., Ichiyoshi, N. and Nishikawa, K. GTOP: a database of protein structures predicted from genome sequences. Nucleic Acids Res. 30, 294-298 (2002)
Terashima, H., Fukuchi, S., Nakai, K., Arisawa, M., Hamada, K., Yabuki, N. and Kitada, K. Sequence-based approach for identification of cell wall proteins in Saccharomyces cerevisiae. Curr. Genet. 40, 311-316 (2002).
Fukuchi, S. and Nishikawa, K. Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria. J. Mol. Biol. 309, 835-843 (2001).
Horimoto, K., Fukuchi, S. and Mori, K. Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes. Bioinformatics, 17 791-802 (2001).
Horimoto, K. and Fukuchi, S. Feasibility of gene-location distance in microbial genome analysis. INFORMATION, 3 263-269 (2000).
- 1999
Horimoto, K., Mori, K. and Fukuchi, S. Measures for circular genome comparison. INFORMATION 2, 83-90 (1999).
Hamada, K., Fukuchi, S., Arisawa, M., Baba, M. and Kitada, K. (1998) Screening for glycosylphosphatidylinositol(GPI)-dependent cell wall proteins in Saccharomyces cerevisiae. Mol. Gen. Genet. 33, 267-271 (1998).
Otsuka J., Fukuchi, S. and Kikuchi, N. (1997) A theoretical method for evaluating the relative importance of positive selection and neutral drift from observed base changes. J. Mol. Evol. 45, 178-192 (1997).
Fukuchi, S. and Otsuka, J. Evolution of the self-reproducing system to the biosynthesis of the membrane: an approach from the amino acid sequence similarity in proteins. J. Theor. Biol. 182, 117-136 (1996).
Fukuchi, S., Okayama, T. and Otsuka, J. Evolution of genetic information flow from the viewpoint of protein sequence similarity. J. Theor. Biol. 171, 179-195 (1994).
Fukuchi, S. and Otsuka, J. Evolution of metabolic pathways by chance assembly of enzyme proteins generated from sense and antisense strands of pre-existing genes. J. Theor. Biol. 158, 271-291 (1992).