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T. Ikemura · SciRah

Researcher profile · Semantic Scholar

T. Ikemura

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T. Ikemura — researcher profile on SciRah

h-index: 44
Works: 171
Citations: 13K

Most-cited papers

Rice Annotation Project Database (RAP-DB): An Integrative and Interactive Database for Rice Genomics
H. Sakai, Sung-Shin Lee, Tsuyoshi Tanaka, H. Numa +13 more
2013Plant and Cell Physiology769 citations Open access
Semantic Scholar
Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes
T. Uchiyama, Takashi Abe, T. Ikemura, Kazuya Watanabe
2005Nature Biotechnology369 citations
Semantic Scholar
Informatics for unveiling hidden genome signatures.
Takashi Abe, S. Kanaya, M. Kinouchi, Yuta Ichiba +2 more
2003Genome Research268 citations Open access
Semantic Scholar
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, M. Kinouchi, Takashi Abe, Y. Kudo +4 more
2001Gene194 citations
Semantic Scholar
8-oxoguanine causes spontaneous de novo germline mutations in mice
M. Ohno, K. Sakumi, Ryutaro Fukumura, M. Furuichi +6 more
2014Scientific Reports159 citations Open access
Semantic Scholar
CENP-I is essential for centromere function in vertebrate cells.
A. Nishihashi, T. Haraguchi, Y. Hiraoka, T. Ikemura +4 more
2002Developmental Cell157 citations Open access
Semantic Scholar
Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions.
Yoshihisa Watanabe, A. Fujiyama, Yuta Ichiba, M. Hattori +3 more
2002Human Molecular Genetics136 citations Open access
Semantic Scholar
Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples.
Takashi Abe, H. Sugawara, M. Kinouchi, S. Kanaya +1 more
2005DNA Research133 citations Open access
Semantic Scholar
Bisulfite sequencing and dinucleotide content analysis of 15 imprinted mouse differentially methylated regions (DMRs): paternally methylated DMRs contain less CpGs than maternally methylated DMRs
H. Kobayashi, C. Suda, Takashi Abe, Yuji Kohara +2 more
2006Cytogenetic and Genome Research95 citations
Semantic Scholar
tRNADB-CE 2011: tRNA gene database curated manually by experts
Takashi Abe, T. Ikemura, Junichi Sugahara, A. Kanai +7 more
2010Nucleic Acids Res.93 citations Open access
Semantic Scholar
Triplex-forming DNAs in the human interphase nucleus visualized in situ by polypurine/polypyrimidine DNA probes and antitriplex antibodies
M. Ohno, T. Fukagawa, Jeremy S. Lee, T. Ikemura
2002Chromosoma93 citations
Semantic Scholar
Direct cloning of genes encoding novel xylanases from the human gut.
H. Hayashi, Takashi Abe, M. Sakamoto, Hiroki Ohara +3 more
2005Canadian Journal of Microbiology (print)61 citations
Semantic Scholar
Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis.
Atsushi Fukushima, T. Ikemura, M. Kinouchi, T. Oshima +3 more
2002Gene60 citations
Semantic Scholar
A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks
Ryo Nakao, Takashi Abe, A. Nijhof, Seigo Yamamoto +3 more
2014The ISME Journal58 citations Open access
Semantic Scholar
Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes.
Takashi Abe, H. Sugawara, S. Kanaya, M. Kinouchi +1 more
2006Gene56 citations
Semantic Scholar
tRNADB-CE: tRNA gene database well-timed in the era of big sequence data
Takashi Abe, H. Inokuchi, Yuko Yamada, A. Muto +2 more
2014Frontiers in Genetics54 citations Open access
Semantic Scholar
A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks
Ryo Nakao, Takashi Abe, A. Nijhof, Seigo Yamamoto +3 more
2013The ISME Journal54 citations Open access
Semantic Scholar
A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: self-organizing map of oligonucleotide frequency.
Takashi Abe, S. Kanaya, M. Kinouchi, Yuta Ichiba +2 more
2002Genome informatics. International Conference on Genome Informatics43 citations
Semantic Scholar
Dinucleosome DNA of human K562 cells: experimental and computational characterizations.
Megumi Kato, Y. Onishi, Y. Wada‐Kiyama, Takashi Abe +5 more
2003Journal of Molecular Biology37 citations
Semantic Scholar
tRNADB-CE: tRNA gene database curated manually by experts
Takashi Abe, T. Ikemura, Y. Ohara, H. Uehara +5 more
2008Nucleic Acids Res.36 citations Open access
Semantic Scholar
Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains
Y. Iwasaki, Takashi Abe, Y. Wada, K. Wada +1 more
2013BMC Infectious Diseases35 citations Open access
Semantic Scholar
Amplicons on human chromosome 11q are located in the early/late-switch regions of replication timing.
Yoshihisa Watanabe, T. Ikemura, H. Sugimura
2004Genomics34 citations
Semantic Scholar
A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental microbes
Takashi Abe, H. Sugawara, S. Kanaya, T. Ikemura
200623 citations
Semantic Scholar
Relationships between replication timing and GC content of cancer-related genes on human chromosomes 11q and 21q.
Yoshihisa Watanabe, Takashi Abe, T. Ikemura, M. Maekawa
2009Gene22 citations
Semantic Scholar
Sequences from Almost All Prokaryotic, Eukaryotic, and Viral Genomes Available Could be Classified According to Genomes on a Large-Scale Self-Organizing Map Constructed with the Earth Simulator
Takashi Abe, H. Sugawara, S. Kanaya, T. Ikemura
200621 citations
Semantic Scholar
Cloning of a new kinesin-related gene located at the centromeric end of the human MHC region
A. Ando, Y. Y. Kikuti, H. Kawata, Naoaki Okamoto +7 more
2004Immunogenetics21 citations
Semantic Scholar
Notable clustering of transcription-factor-binding motifs in human pericentric regions and its biological significance
Y. Iwasaki, K. Wada, Y. Wada, Takashi Abe +1 more
2013Chromosome Research18 citations Open access
Semantic Scholar
Systematization of the protein sequence diversity in enzymes related to secondary metabolic pathways in plants, in the context of big data biology inspired by the KNApSAcK motorcycle database.
Shun Ikeda, Takashi Abe, Yukiko Nakamura, Nelson K Kibinge +7 more
2013Plant and Cell Physiology18 citations Open access
Semantic Scholar
A Novel Bioinformatics Strategy for Function Prediction of Poorly-Characterized Protein Genes Obtained from Metagenome Analyses
Takashi Abe, S. Kanaya, H. Uehara, T. Ikemura
2009DNA Research18 citations Open access
Semantic Scholar
Prediction of Directional Changes of Influenza A Virus Genome Sequences with Emphasis on Pandemic H1N1/09 as a Model Case
Y. Iwasaki, Takashi Abe, K. Wada, M. Itoh +1 more
2011DNA Research17 citations Open access
Semantic Scholar
Extracellular matrix protein tenascin-like gene found in human MHC class III region
Ken-ichi Matsumoto, Nanayo Ishihara, A. Ando, H. Inoko +1 more
2004Immunogenetics17 citations
Semantic Scholar
GeneLook: a novel ab initio gene identification system suitable for automated annotation of prokaryotic sequences.
T. Nishi, T. Ikemura, S. Kanaya
2005Gene16 citations
Semantic Scholar
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
K. Wada, Y. Wada, T. Ikemura
2020bioRxiv15 citations Open access
Semantic Scholar
Directional and reoccurring sequence change in zoonotic RNA virus genomes visualized by time-series word count
Y. Wada, K. Wada, Y. Iwasaki, S. Kanaya +1 more
2016Scientific Reports15 citations Open access
Semantic Scholar
A novel bioinformatics strategy for searching industrially useful genome resources from metagenomic sequence libraries.
H. Uehara, Y. Iwasaki, C. Wada, T. Ikemura +1 more
2011Genes & Genetic Systems15 citations Open access
Semantic Scholar
Intra-Species Diversity between Seven Bifidobacterium adolescentis Strains Identified by Genome-Wide Tiling Array Analysis
Kazumasa Yasui, Mototsugu Tabata, Satoki Yamada, Takashi Abe +3 more
2009Bioscience, biotechnology and biochemistry15 citations Open access
Semantic Scholar
A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM)
Y. Iwasaki, Takashi Abe, K. Wada, Y. Wada +1 more
2013Microorganisms14 citations Open access
Semantic Scholar
Comparative genomics of Glandirana rugosa using unsupervised AI reveals a high CG frequency
Yukako Katsura, T. Ikemura, R. Kajitani, A. Toyoda +6 more
2021Life Science Alliance12 citations Open access
Semantic Scholar
Replication timing of extremely large genes on human chromosomes 11q and 21q.
Yoshihisa Watanabe, K. Shibata, T. Ikemura, M. Maekawa
2008Gene11 citations
Semantic Scholar
Detection of periodicity in eukaryotic genomes on the basis of power spectrum analysis.
Atsushi Fukushima, T. Ikemura, T. Oshima, H. Mori +1 more
2002Genome informatics. International Conference on Genome Informatics11 citations
Semantic Scholar
Mb-level CpG and TFBS islands visualized by AI and their roles in the nuclear organization of the human genome.
K. Wada, Y. Wada, T. Ikemura
2020Genes & Genetic Systems10 citations Open access
Semantic Scholar
Human cell-dependent, directional, time-dependent changes in the mono- and oligonucleotide compositions of SARS-CoV-2 genomes
Y. Iwasaki, Takashi Abe, T. Ikemura
2021bioRxiv9 citations Open access
Semantic Scholar
CG-containing oligonucleotides and transcription factor-binding motifs are enriched in human pericentric regions.
Y. Wada, Y. Iwasaki, Takashi Abe, K. Wada +2 more
2015Genes & Genetic Systems9 citations Open access
Semantic Scholar
Small Ribonucleic Acids of, Escherichia coli
T. Ikemura, J. E. Dahlberg
20029 citations Open access
Semantic Scholar
Novel bioinformatics for inter- and intraspecies comparison of genome signatures in plant genomes
Takashi Abe, K. Wada, Y. Iwasaki, T. Ikemura
20098 citations Open access
Semantic Scholar
Implication of a new function of human tDNAs in chromatin organization
Y. Iwasaki, T. Ikemura, Ken Kurokawa, N. Okada
2020Scientific Reports7 citations Open access
Semantic Scholar
Correlation Between Codon Usage and tRNA Content in Microorganisms
T. Ikemura
20187 citations
Semantic Scholar
Development of Self-Compressing BLSOM for Comprehensive Analysis of Big Sequence Data
Akihito Kikuchi, T. Ikemura, Takashi Abe
2015BioMed Research International7 citations Open access
Semantic Scholar
Evolutionary Changes in Vertebrate Genome Signatures with Special Focus on Coelacanth
Y. Iwasaki, Takashi Abe, N. Okada, K. Wada +2 more
2014DNA Research7 citations Open access
Semantic Scholar
Time-series trend of pandemic SARS-CoV-2 variants visualized using batch-learning self-organizing map for oligonucleotide compositions
Takashi Abe, Ryuki Furukawa, Y. Iwasaki, T. Ikemura
2021bioRxiv5 citations Open access
Semantic Scholar

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