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Genetics

D-Index
59
Citations
20870
World Ranking
3201
National Ranking
140

Overview

Toshimichi Ikemura is affiliated with the Nagahama Institute of Bio-Science and Technology in Japan. Their research spans multiple disciplines within the life sciences, focusing primarily on areas related to biochemistry, genetics, molecular biology, medicine, and agricultural and biological sciences.

Their work heavily involves subfields such as molecular biology, infectious diseases, plant science, animal science and zoology, and ecology. Within these fields, Ikemura has contributed to topics including genomics and phylogenetic studies, SARS-CoV-2 and COVID-19 research, viral gastroenteritis research and epidemiology, chromosomal and genetic variations, machine learning in bioinformatics, RNA and protein synthesis mechanisms, and animal virus infection studies.

Ikemura has published regularly in notable venues. Frequent publication outlets include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Research Square
  • Genes & Genetic Systems
  • BMC Microbiology
  • PLoS ONE

Collaborations have been significant throughout their career. Noteworthy coauthors consist of:

  • Yuki Iwasaki
  • Kennosuke Wada
  • Yoshiko Wada
  • Takashi Abe
  • Y Katsura

Representative recent papers authored or coauthored by Ikemura include:

  • "Time-series analyses of directional sequence changes in SARS-CoV-2 genomes and an efficient search method for candidates for advantageous mutations for growth in human cells," 2020, Gene
  • "Human cell-dependent, directional, time-dependent changes in the mono- and oligonucleotide compositions of SARS-CoV-2 genomes," 2021, BMC Microbiology
  • "Mb-level CpG and TFBS islands visualized by AI and their roles in the nuclear organization of the human genome," 2020, Genes & Genetic Systems
  • "Comparative genomics of Glandirana rugosa using unsupervised AI reveals a high CG frequency," 2021, Life Science Alliance
  • "Time-Series Trend of Pandemic SARS-CoV-2 Variants Visualized Using Batch-Learning Self-Organizing Map for Oligonucleotide Compositions," 2021, Data Science Journal

Their scientific output emphasizes the use of computational and artificial intelligence methods in genomics, particularly in visualizing genetic features and analyzing viral sequence evolution. This intersects with their broad interest in molecular mechanisms and pathogen genomics.

Best Publications

  • Codon usage and tRNA content in unicellular and multicellular organisms.

    T Ikemura

  • Correlation Between the Abundance of Escherichia Coli Transfer RNAs and the Occurrence of the Respective Codons in Its Protein Genes: A Proposal for a Synonymous Codon Choice That Is Optimal for the E. Coli Translational System

    Toshimichi Ikemura

  • Codon usage tabulated from international DNA sequence databases: status for the year 2000

    Yasukazu Nakamura;Takashi Gojobori;Toshimichi Ikemura

  • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes

    Toshimichi Ikemura

  • Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

    Hiroaki Sakai;Sung Shin Lee;Tsuyoshi Tanaka;Hisataka Numa

  • Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes: Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs

    Toshimichi Ikemura

  • Codon usage tabulated from the GenBank genetic sequence data.

    Shin-ichi Aota;Takashi Gojobori;Fumie Ishibashi;Takeo Maruyama

  • Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis.

    Shigehiko Kanaya;Yuko Yamada;Yoshihiro Kudo;Toshimichi Ikemura

  • Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes

    Taku Uchiyama;Takashi Abe;Toshimichi Ikemura;Kazuya Watanabe

  • Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis.

    Shigehiko Kanaya;Yuko Yamada;Makoto Kinouchi;Yoshihiro Kudo

  • Codon usage tabulated from the international DNA sequence databases

    Yasukazu Nakamura;Takashi Gojobori;Toshimichi Ikemura

  • Small Ribonucleic Acids of Escherichia coli I. CHARACTERIZATION BY POLYACRYLAMIDE GEL ELECTROPHORESIS AND FINGERPRINT ANALYSIS

    Toshimichi Ikemura;James E. Dahlberg

  • Informatics for Unveiling Hidden Genome Signatures

    Takashi Abe;Shigehiko Kanaya;Makoto Kinouchi;Yuta Ichiba

  • Three genes in the human MHC class III region near the junction with the class II: gene for receptor of advanced glycosylation end products, PBX2 homeobox gene and a notch homolog, human counterpart of mouse mammary tumor gene int-3.

    Kimihiko Sugaya;Tatsuo Fukagawa;Ken-ichi Matsumoto;Kazuei Mita

  • Specific Inactivation of 16S Ribosomal RNA Induced by Colicin E3 In Vivo

    C. M. Bowman;J. E. Dahlberg;T. Ikemura;J. Konisky

  • Diversity in G+C content at the third position of codons in vertebrate genes and its cause

    Shin-ichi Aota;Toshimichi Ikemura

  • Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome

    Shigehiko Kanaya;Makoto Kinouchi;Takashi Abe;Yoshihiro Kudo

  • Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region.

    Takashi Shiina;Gen Tamiya;Akira Oka;Nobusada Takishima

  • Chromosomal localization of the proteasome Z subunit gene reveals an ancient chromosomal duplication involving the major histocompatibility complex.

    Masanori Kasahara;Masaru Hayashi;Keiji Tanaka;Hidetoshi Inoko

  • Cordon usage tabulated from the Gen Bank genetic sequence data

    K. Wada;S. Aota;R. Tsuchiya;F. Ishibashi

Frequent Co-Authors

Shigehiko Kanaya
Shigehiko Kanaya Nara Institute of Science and Technology
Tatsuo Fukagawa
Tatsuo Fukagawa Osaka University
Hidetoshi Inoko
Hidetoshi Inoko Tokai University
Yasukazu Nakamura
Yasukazu Nakamura National Institute of Genetics
Takashi Gojobori
Takashi Gojobori King Abdullah University of Science and Technology
Hirotada Mori
Hirotada Mori Nara Institute of Science and Technology
Nobuhisa Mizuki
Nobuhisa Mizuki Yokohama City University
Ken Kurokawa
Ken Kurokawa National Institute of Genetics
Norihiro Okada
Norihiro Okada National Cheng Kung University

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