World's Best Scientists 2026 revealed!
Yuji Nagata

Yuji Nagata

D-Index & Metrics

Biology and Biochemistry

D-Index
55
Citations
8129
World Ranking
15296
National Ranking
1082

Overview

Yuji Nagata is affiliated with Tohoku University in Japan. Their research primarily spans the fields of Environmental Science and Biochemistry, Genetics and Molecular Biology. Within these fields, they have a significant focus on Molecular Biology, Ecology, Pollution, Genetics, and Health, Toxicology and Mutagenesis.

The scientist's research topics cover a variety of specialized areas including microbial bioremediation and biosurfactants, microbial community ecology and physiology, bacteriophages and microbial interactions, bacterial genetics and biotechnology, toxic organic pollutants impact, pesticide and herbicide environmental studies, and metal extraction and bioleaching.

Yuji Nagata has published in several academic venues, with frequent contributions to Bioscience Biotechnology and Biochemistry, Scientific Reports, Microbiology Spectrum, Research Square, and bioRxiv. Their recent notable papers include:

  • "Transcriptome Analysis of Zygotic Induction During Conjugative Transfer of Plasmid RP4," 2020, Frontiers in Microbiology
  • "Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria," 2023, Mobile DNA
  • "Reconstruction of a Soil Microbial Network Induced by Stress Temperature," 2022, Microbiology Spectrum
  • "Special Issue: Microbial Degradation of Xenobiotics," 2020, Microorganisms
  • "Long-term changes and effect of pterygium size on corneal topographic irregularity after recurrent pterygium surgery," 2020, Scientific Reports

Collaborations play a role in their research output, with frequent coauthors including Yoshiyuki Ohtsubo, Kouhei Kishida, Masataka Tsuda, Hiromi Kato, and Leonardo Stari.

Best Publications

  • Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes.

    Hiroshi Mori;Fumito Maruyama;Hiromi Kato;Atsushi Toyoda

  • Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate.

    Martina Pavlova;Martin Klvana;Zbynek Prokop;Radka Chaloupkova

  • GenomeMatcher: A graphical user interface for DNA sequence comparison

    Yoshiyuki Ohtsubo;Wakako Ikeda-Ohtsubo;Yuji Nagata;Masataka Tsuda

  • Aerobic degradation of lindane (γ-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis

    Yuji Nagata;Ryo Endo;Michihiro Ito;Yoshiyuki Ohtsubo

  • Cloning and sequencing of a dehalogenase gene encoding an enzyme with hydrolase activity involved in the degradation of gamma-hexachlorocyclohexane in Pseudomonas paucimobilis.

    Y Nagata;T Nariya;R Ohtomo;M Fukuda

  • Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel

    Radka Chaloupková;Jana Sýkorová;Zbyňek Prokop;Andrea Jesenská

  • Molecular cloning of a Pseudomonas paucimobilis gene encoding a 17-kilodalton polypeptide that eliminates HCl molecules from gamma-hexachlorocyclohexane.

    R Imai;Y Nagata;M Fukuda;M Takagi

  • Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26.

    Yuji Nagata;Keisuke Miyauchi;Jiri Damborsky;Katka Manova

  • Cloning and Sequencing of a Novel meta-Cleavage Dioxygenase Gene Whose Product Is Involved in Degradation of γ-Hexachlorocyclohexane in Sphingomonas paucimobilis

    Keisuke Miyauchi;Yugo Adachi;Yuji Nagata;Masamichi Takagi

  • Complete genome sequence of Acidovorax sp. strain KKS102, a polychlorinated-biphenyl degrader.

    Yoshiyuki Ohtsubo;Fumito Maruyama;Hisayuki Mitsui;Yuji Nagata

  • Cloning and Sequencing of a 2,5-Dichlorohydroquinone Reductive Dehalogenase Gene Whose Product Is Involved in Degradation of γ-Hexachlorocyclohexane by Sphingomonas paucimobilis

    Keisuke Miyauchi;Seug Kyo Suh;Yuji Nagata;Masamichi Takagi

  • Strategies for bioremediation of polychlorinated biphenyls

    Yoshiyuki Ohtsubo;Toshiaki Kudo;Masataka Tsuda;Yuji Nagata

  • Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

    Zbynek Prokop;Yukari Sato;Jan Brezovsky;Tomas Mozga

  • Catalytic mechanism of the haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26

    Zbyněk Prokop;Marta Monincová;Radka Chaloupková;Martin Klvaňa

  • Nucleotide sequence and functional analysis of the meta-cleavage pathway involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102.

    Y Kikuchi;Y Yasukochi;Y Nagata;M Fukuda

  • Crystal Structure of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 Å Resolution: Dynamics of Catalytic Residues

    Aaron J. Oakley;Martin Klvaňa;Michal Otyepka;Yuji Nagata

  • Two different types of dehalogenases, LinA and LinB, involved in γ- hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 are localized in the periplasmic space without molecular processing

    Yuji Nagata;Akiko Futamura;Keisuke Miyauchi;Masamichi Takagi

  • Isolation and characterization of naphthalene-catabolic genes and plasmids from oil-contaminated soil by using two cultivation-independent approaches

    Akira Ono;Ryo Miyazaki;Masahiro Sota;Masahiro Sota;Yoshiyuki Ohtsubo

  • Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities.

    Yukari Sato;Marta Monincova;Radka Chaloupkova;Zbynek Prokop

  • Cloning and sequencing of a 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase gene involved in the degradation of gamma-hexachlorocyclohexane in Pseudomonas paucimobilis.

    Y Nagata;R Ohtomo;K Miyauchi;M Fukuda

Frequent Co-Authors

Masataka Tsuda
Masataka Tsuda Tohoku University
Jiri Damborsky
Jiri Damborsky Masaryk University
Masamichi Takagi
Masamichi Takagi Niigata University of Pharmacy and Applied Life Sciences
Masao Fukuda
Masao Fukuda Chubu University
Masahiro Takagi
Masahiro Takagi Kyoto Sangyo University
Ryozo Imai
Ryozo Imai National Agriculture and Food Research Organization
Rebecca C. Wade
Rebecca C. Wade Heidelberg Institute for Theoretical Studies
Asao Fujiyama
Asao Fujiyama National Institute of Genetics
Kiwamu Minamisawa
Kiwamu Minamisawa Tohoku University
Michal Otyepka
Michal Otyepka Palacký University, Olomouc

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