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Suyama Mikita Last modified date:2022.01.05

Graduate School

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Academic Degree
Country of degree conferring institution (Overseas)
Field of Specialization
Bioinformatics, Comparative Genomics
Total Priod of education and research career in the foreign country
Outline Activities
We are mainly analyzing genomic sequences and epigenomic data to get much insight into gene regulation by computational biological approaches. The current research topics include,
(1) genome-wide identification of transcription factor binding sites.
(2) molecular evolutionary analysis of cis-elements for splicing.
(3) comparative genome analyses of gene duplications and genome rearrangements.
(4) genome informatics analysis of sex differences.
(5) development of tools for bioinformatics analyses.
Research Interests
  • Analysis of regulatory mechanisms for gene expression by comparative genomic approach.
    keyword : comparative genomics, bioinformatics
Academic Activities
1. Mikita Suyama, Mechanistic insights into mutually exclusive splicing in dynamin 1., Bioinformatics, 10.1093/bioinformatics/btt368, 29, 17, 2084-2087, 2013.06.
2. Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P., A network of conserved co-occurring motifs for the regulation of alternative splicing., Nucleic Acids Res., 10.1093/nar/gkq705, 38, 22, 7916-7926, 2010.08, Cis-acting short sequence motifs play important roles in alternative splicing. It is now possible to identify such sequence motifs as conserved sequence patterns in genome sequence alignments. Here, we report the systematic search for motifs in the neighboring introns of alternatively spliced exons by using comparative analysis of mammalian genome alignments. We identified 11 conserved sequence motifs that might be involved in the regulation of alternative splicing. These motifs are not only significantly overrepresented near alternatively spliced exons, but they also co-occur with each other, thus, forming a network of cis-elements, likely to be the basis for context-dependent regulation. Based on this finding, we applied the motif co-occurrence to predict alternatively skipped exons. We verified exon skipping in 29 cases out of 118 predictions (25%) by EST and mRNA sequences in the databases. For the predictions not verified by the database sequences, we confirmed exon skipping in 10 additional cases by using both RT-PCR experiments and the publicly available RNA-Seq data. These results indicate that even more alternative splicing events will be found with the progress of large-scale and high-throughput analyses for various tissue samples and developmental stages..
1. Mikita Suyama, Detection and interpretation of regulatory mutations, International Symposium on Frontiers in Bioinformatics, 2016.06.
2. Mikita Suyama, Exome sequencing, Computational Biology: Genomes to Systems (EMBO Practical Course), 2016.06.
3. T. Sato, M. Suyama, ChromContact: A Web Tool for Analyzing Spatial Contact of Chromosomes from Hi-C data, Annual Meeting of International Human Epigenome Consortium (IHEC) 2015, 2015.11.
4. Daisuke Saito, Mikita Suyama, Linkage analysis of Heterogeneity in methylation status of adjacent CpG sites, Annual Meeting of International Human Epigenome Consortium (IHEC) 2015, 2015.11.
5. Daisuke Saito, Mikita Suyama, Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation, The 25th Hot Spring Harbor International Symposium, 2015.11.
6. Mikita Suyama, Understanding genomic features from their structural aspects, The 25th Hot Spring Harbor International Symposium, 2015.11.
7. M. Yoshihara, L. Jiang, S. Akatsuka, S. Toyokuni, M. Suyama, Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus., The 4D Nucleome 2014, 2014.12.
Membership in Academic Society
  • Japanese Cancer Association
  • Japanese Society of Bioinformatics
Educational Activities
In the "Informatics for Genomic Medicine" course, I taught trends and future direction of genome analyses and their application in medicine.