NISHIDA Hiromi

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Name
NISHIDA Hiromi
Affiliation
Toyama Prefectural University
Section
Biotechnology Research Center and Department of Biotechnology
Job title
Professor
Degree
Ph. D.(University of Tokyo)

Research Interests

 
 

Research Areas

 
 

Published Papers

 
Morita Y, Nishida H*
Open Bioinformatics Journal   11 252-258   Nov 2018   [Refereed]
Nishino K, Morita Y, Takahashi S, Okumura M, Shiratani S, Umemura K, Narumi I, Kondo C, Ochiai R, Oshima T, Nishida H*
Microbiology   164 1361-1371   Oct 2018   [Refereed]
Morita Y, Narumi I, Nishida H
Bulletin of Toyama Prefectural University   28 41-43   Mar 2018
Nakazawa M, Nishida H*
Jacobs Journal of Biotechnology and Bioengineering   3 014   Nov 2017   [Refereed]
Terasaki M, Fukuyama A, Takahashi Y, Yamada M, Nishida H*
Current Microbiology   74 1432-1437   Nov 2017   [Refereed]
Nishino K, Nishida H*
Journal of General and Applied Microbiology   63 203-206   Jul 2017   [Refereed]
Nakamiya H, Ijima S, Nishida H*
AIMS Microbiology   3 136-142   Mar 2017   [Refereed]
Shimizu T, Yin L, Yoshida A, Yokooji Y, Hachisuka S-I, Sato T, Tomita T, Nishida H, Atomi H, Kuzuyama T, Nishiyama M*
Biochemical Journal   474 105-122   Mar 2017   [Refereed]
Nakazawa M, Nishida H*
Journal of General and Applied Microbiology   63 58-61   Mar 2017   [Refereed]
Nishida H*, Oshima T
Journal of General and Applied Microbiology   63 28-35   Mar 2017   [Refereed]
Takahashi S, Takayanagi A, Takahashi Y, Oshima T, Nishida H*
AIMS Microbiology   2(2) 152-189   May 2016   [Refereed]
Takahashi S, Nishida H
Bulletin of Toyama Prefectural University   26 27-30   Mar 2016
Yamauchi K, Kondo S, Hamamoto M, Suzuki Y, Nishida H*
AIMS Microbiology   2 69-91   Mar 2016   [Refereed]
Takayanagi A, Takahashi S, Nishida H*
Journal of General and Applied Microbiology   62(1) 14-17   Feb 2016   [Refereed]
Takahashi S, Nishida H*
Journal of General and Applied Microbiology   61(6) 262-265   Jan 2016   [Refereed]
Yamauchi K, Kondo S*, Hamamoto M, Takahashi Y, Ogura Y, Hayashi T, Nishida H*
Genome Announcements   3(3) e00220-15   May 2015   [Refereed]
Nishida H
Journal of General and Applied Microbiology   61(1) 24-26   Mar 2015   [Refereed]
Takahashi Y, Shintani M, Takase N, Kazo Y, Kawamura F, Hara H, Nishida H, Okada K, Yamane H, Nojiri H*
Environmental Microbiology   17 134-155   Jan 2015   [Refereed]
Nishida H
Recent Advances in DNA & Gene Sequences   8(1) 10-14   Oct 2014   [Refereed]
Nishida H*, Matsumoto T, Kondo S, Hamamoto M, Yoshikawa H
Journal of General and Applied Microbiology   60(1) 7-12   Feb 2014   [Refereed]
Nishida H*, Katayama T, Suzuki Y, Kondo S, Horiuchi H
Gene   525(1) 5-10   Aug 2013   [Refereed]
Ouchi T, Tomita T, Horie A, Yoshida A, Takahashi K, Nishida H, Lassak K, Taka H, Mineki R, Fujimura T, Kosono S, Nishiyama C, Masui R, Kuramitsu S, Albers S-V, Kuzuyama T, Nishiyama M*
Nature Chemical Biology   9(4) 277-283   Mar 2013   [Refereed]
Nishida H
Report of the Noda Institute for Scientific Research   57 38-39   2013   [Invited]
Nishida H
Current Issues in Molecular Biology   15 19-24   2013   [Refereed]
Nishida H
Frontiers in Microbiology   3 Art. no. 420   Nov 2012   [Refereed]
Nishida H
ISRN Molecular Biology   2012 Art. ID 245706   Sep 2012   [Refereed]
Nishida H*, Kondo S, Matsumoto T, Suzuki Y, Yoshikawa H, Taylor TD, Sugiyama J
Open Biology   2 Art. ID 120043   2012   [Refereed]
Ueda K*, Nishida H, Beppu T
International Journal of Evolutionary Biology   2012 Art. ID 324549   2012   [Refereed]
Nishida H*, Nishiyama M
International Journal of Evolutionary Biology   2012 Art. ID 745931   2012   [Refereed]
Nishida H
International Journal of Evolutionary Biology   2012 Art. ID 342482   2012   [Refereed]
Nishida H
The Scientific World Journal   2012 Art. ID 298174   2012   [Refereed]
Nishida H
International Journal of Evolutionary Biology   2012 Art. ID 254941   2012   [Refereed]
Nishida H*, Abe R, Nagayama T, Yano K
International Journal of Evolutionary Biology   2012 Art. ID 205274   2012   [Refereed]
Nishida H*, Beppu T, Ueda K
Genomics   98(5) 370-375   Nov 2011   [Refereed]
Shintani M, Tokumaru H, Takahashi Y, Miyakoshi M, Yamane H, Nishida H, Nojiri H*
Plasmid   66(2) 85-92   Jul 2011   [Refereed]
Nishida H*, Yun CS
Mobile Genetic Elements   1(1) 78-79   May 2011   [Refereed][Invited]
Yun CS, Nishida H*
PLoS ONE   6 Art. ID e16548   Jan 2011   [Refereed]
Matsumoto T, Yun CS, Yoshikawa H, Nishida H*
PLoS ONE   6 Art. ID e16372   Jan 2011   [Refereed]
Nishida H*, Hamamoto M, Sugiyama J
Journal of General and Applied Microbiology   57(4) 243-246   2011   [Refereed]
Nishida H, Kondo S, Nojiri H, Noma K, Oshima K
International Journal of Evolutionary Biology   2011 Art. ID 319479   2011   [Invited]
Nishida H*, Nagatsuka Y, Sugiyama J
Journal of General and Applied Microbiology   57(1) 63-67   2011   [Refereed]
Nishida H*, Yun CS
International Journal of Evolutionary Biology   2011 Art. ID 634505   Dec 2010   [Refereed]
Oshima K, Ueda K, Beppu T, Nishida H*
International Journal of Evolutionary Biology   2011 Art. ID 376831   Dec 2010   [Refereed]
Yun CS, Suzuki C, Naito K, Takeda T, Takahashi Y, Sai F, Terabayashi T, Miyakoshi M, Shintani M, Nishida H, Yamane H, Nojiri H*
Journal of Bacteriology   192(18) 4720-4731   Sep 2010   [Refereed]
Shintani M, Takahashi Y, Tokumaru H, Kadota K, Hara H, Miyakoshi M, Naito K, Yamane H, Nishida H, Nojiri H*
Environmental Microbiology   12(6) 1413-1426   Jun 2010   [Refereed]
Nishida H*, Motoyama T, Suzuki Y, Yamamoto S, Aburatani H, Osada H
PLoS ONE   5 Art. ID e9916   Mar 2010   [Refereed]
Oshima K, Hoshi A, Ishii Y, Kakizawa S, Kawanishi T, Kojima N, Sugawara K, Ishii Y, Nishida H, Namba S
Japanese Journal of Mycoplasmology   36 74-77   Mar 2010   [Invited]
Gene transfer, synthetic organisms, and the origins of life
Nishida H
Journal of Cosmology   8 6   2010   [Refereed][Invited]
High adaptability of bacteria for extreme environments
Nishida H
Journal of Cosmology   13 3625-3627   2010   [Refereed][Invited]
Nishida H*, Motoyama T, Yamamoto S, Aburatani H, Osada H
Bioinformatics   25(18) 2295-2297   Sep 2009   [Refereed]
Miyakoshi M, Nishida H, Shintani M, Yamane H, Nojiri H*
BMC Genomics   10 Art. no. 12   Jan 2009   [Refereed]
Nishida H, Beppu T, Ueda K*
Journal of Molecular Evolution   68(1) 90-96   Jan 2009   [Refereed]
Nishida H
Comparative and Functional Genomics   2009 Art. ID 379317   2009   [Refereed]
Nishida H
Open Systems Biology Journal   2 1-7   2009   [Refereed]
Nishida H*, Kondo S, Suzuki T, Tsujimura Y, Komatsu S, Wakayama T, Hayashizaki Y
Mammalian Genome   19(10-12) 667-674   Oct 2008   [Refereed]
Oshima K, Nishida H*
Journal of Molecular Evolution   66(5) 529-532   May 2008   [Refereed]
Oshima K, Nishida H*
Journal of Molecular Evolution   65(3) 249-258   Sep 2007   [Refereed]
Nishida H*, Ohnishi Y, Beppu T, Horinouchi S
Environmental Microbiology   9(8) 1986-1994   Aug 2007   [Refereed]
Nishida H*, Narumi I
Bioscience, Biotechnology, and Biochemistry   71(4) 1015-1020   Apr 2007   [Refereed]
Nishida H
Bioscience, Biotechnology, and Biochemistry   70(11) 2646-2652   Nov 2006   [Refereed]
Nishida H*, Suzuki T, Kondo S, Miura H, Fujimura Y, Hayashizaki Y*
Chromosome Research   14(2) 203-211   2006   [Refereed]
Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P*, Hayashizaki Y*, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engström PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C*
Science   309(5740) 1564-1566   Sep 2005   [Refereed]
Nishida H*, Suzuki T, Ookawa H, Tomaru Y, Hayashizaki Y
BMC Genomics   6 Art. no. 108   Aug 2005   [Refereed]
Nishida H*, Tomaru Y, Oho Y, Hayashizaki Y
BMC Genetics   6 Art. no. 23   May 2005   [Refereed]
Nishida H*, Suzuki T, Tomaru Y, Hayashizaki Y
BMC Genetics   6 Art. no. 10   Feb 2005   [Refereed]
Lutzoni F*, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B, Padamsee M, Hibbett D, James TY, Baloch E, Grube M, Reeb V, Hofstetter V, Schoch C, Arnold AE, Miadlikowska J, Spatafora J, Johnson D, Hambleton S, Crockett M, Shoemaker R, Sung GH, Lücking R, Lumbsch T, O'Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim YW, Matheny B, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R
American Journal of Botany   91 1446-1480   Oct 2004   [Refereed]
An KD, Nishida H*, Miura Y, Yokota A
BMC Evolutionary Biology   3 Art. no. 9   May 2003   [Refereed]
Sobajima H, Takeda M, Sugimori M, Kobashi N, Kiribuchi K, Cho EM, Akimoto C, Yamaguchi T, Minami E, Shibuya N, Schaller F, Weiler EW, Yoshihara T, Nishida H, Nojiri H, Omori T, Nishiyama M, Yamane H*
Planta   216(4) 692-698   Feb 2003   [Refereed]
Nishida H*, Narumi I
Microbiology   148(9) 2911-2914   Sep 2002   [Refereed]
Sjamsuridzal W, Nishida H*, Yokota A
Journal of General and Applied Microbiology   48(2) 121-123   Apr 2002   [Refereed]
An KD, Nishida H*, Miura Y, Yokota A
BMC Evolutionary Biology   2 Art. no. 6   Apr 2002   [Refereed]
Nishida H
Bioinformatics   17(12) 1224-1225   2001   [Refereed]
Ohno M, Shiratori H, Park MJ, Saitoh Y, Kumon Y, Yamashita N, Hirata A, Nishida H, Ueda K, Beppu T*
International Journal of Systematic and Evolutionary Microbiology   50(5) 1829-1832   Sep 2000   [Refereed]
Nishida H*, Ogura A, Yokota A, Yamaguchi I, Sugiyama J
Bioscience, Biotechnology, and Biochemistry   64(3) 606-609   Mar 2000   [Refereed]
Nishida H*, Nishiyama M
Journal of Molecular Evolution   51(3) 299-302   2000   [Refereed]
Nishida H, Nishiyama M*, Kobashi N, Kosuge T, Hoshino T, Yamane H
Genome Research   9(12) 1175-1183   Dec 1999   [Refereed]
Sjamsuridzal W, Nishida H, Ogawa H, Kakishima M, Sugiyama J*
Mycoscience   40(1) 21-27   1999   [Refereed]
Nishida H, Tajiri Y, Sugiyama J*
Journal of Molecular Evolution   46(4) 442-448   Apr 1998   [Refereed]
Sjamsuridzal W, Tajiri Y, Nishida H, Thuan TB, Kawasaki H, Hirata A, Yokota A, Sugiyama J*
Mycoscience   38(3) 267-280   1997   [Refereed]
Nishida H, Sugiyama J*
Molecular Biology and Evolution   12(5) 883-886   Sep 1995   [Refereed]
Nishida H, Ando K, Ando Y, Hirata A, Sugiyama J*
Canadian Journal of Botany   73(Suppl.) S660-S666   1995   [Refereed]
Nishida H, Sugiyama J*
Mycoscience   35(4) 361-366   1994   [Refereed]
Ohkuma M, Hwang CW, Masuda Y, Nishida H, Sugiyama J, Ohta A, Takagi M*
Bioscience, Biotechnology, and Biochemistry   57(10) 1793-1794   Oct 1993   [Refereed]
Nishida H, Blanz PA, Sugiyama J*
Journal of Molecular Evolution   37(1) 25-28   Jul 1993   [Refereed]
Nishida H, Sugiyama J*
Molecular Biology and Evolution   10(2) 431-436   Mar 1993   [Refereed]

Books etc

 
DNA traffic in the environment
Nishida H, Oshima T (Part:Editor)
Springer   Mar 2019   
Dickinson M, Hodgetts J (eds) Phytoplasma: Methods and Protocols. Methods in Molecular Biology, vol. 938
Nishida H (pp. 319-327) (Part:Contributor, Phylogenetic analyses of phytoplasmas based on whole-genome comparison)
Humana Press   2013   
Nishida H, Kondo S, Nojiri H, Noma K, Oshima K (eds) Special Issue on Evolutionary Mechanisms of Microbial Genomes 2012, International Journal of Evolutionary Biology
Hindawi Publishing Corporation   2012   
Nishida H, Kondo S, Nojiri H, Noma K, Oshima K (eds) Special Issue on Evolutionary Mechanisms of Microbial Genomes, International Journal of Evolutionary Biology
SAGE-Hindawi Access to Research   2011   
Kurtzman CP, Fell JW, Boekhout T (eds) The Yeasts, a taxonomic study, 5th ed.
Nishida H, Robert V, Sugiyama J (pp. 1499-1502) (Part:Contributor, Mixia C.L. Kramer emend. H. Nishida, K. Ando, Y. Ando, Hirata & Sugiyama)
Elsevier, Amsterdam   2011   
Colwell RR, Simidu U, Ohwada K (eds) Microbial diversity in time and space
Sugiyama J, Nagahama T, Nishida H (pp. 41-51) (Part:Contributor, Fungal diversity and phylogeny with emphasis on 18S ribosomal DNA sequence divergence)
Plenum Press, New York   1996   
Arai R, Kato M, Doi Y (eds) Biodiversity and Evolution
Sugiyama J, Nishida H (pp. 177-195) (Part:Contributor, The higher fungi: their evolutionary relationships and implications for fungal systematics)
National Science Museum Foundation, Tokyo, Japan   1995   
Reynolds DR, Taylor JW (eds) The Fungal Holomorph: mitotic, meiotic and pleomorphic speciation in fungal systematics
Sugiyama J, Nishida H, Suh S-O (pp. 261-269) (Part:Contributor, The paradigm of fungal diagnoses and descriptions in the era of molecular systematics: Saitoella complicata as an example)
CAB International, Wallingford, UK   1993   

Conference Activities & Talks

 
DNA sequence bias between exonic and intronic regions causes nucleosome density difference in the filamentous ascomycetes Aspergillus [Invited]
Hiromi Nishida
1st International Caparica Conference in Splicing, Splicing 2016   13 Sep 2016   
Comparative studies of fungal nucleosome positioning [Invited]
Nishida H
15th Fungal Genetics and Biology Conference of the Microbiological Society of Korea   Jan 2012   
Comparison of nucleosome positions in promoters of orthologous genes between Aspergillus fumigatus and Sacchromyces cerevisiae
Nishida H
4th International Conference on Environmental, Industrial and Applied Microbiology   Sep 2011   
Nucleosomal DNA length and nucleosome positioning [Invited]
Nishida H
2nd World DNA and Genome Day   Apr 2011   
Genome-wide maps of nucleosomes of TSA-treated and untreated cells of Aspergillus fumigatus
Nishida H, Motoyama T, Suzuki Y, Yamamoto S, Aburatani H, Osada H
9th International Mycological Congress, Symposium "Fungal epigenetics"   Aug 2010   
Genome-wide map of fungal nucleosomes by the massively parallel DNA sequencing [Invited]
Nishida H
Seminar, Center for Informational Biology, Ochanomizu University   May 2010   
Exhaustive analysis of RNA expression in the cells containing of a genome combining the Synechocystis genome and the Bacillus genome [Invited]
Nishida H, Itaya M
The University of Tokyo International Symposium, Frontier of Microbial and Plant Biotechnology in Environmental and Life Sciences   Dec 2007   
What is characteristic of fungal lysine synthesis through the aminoadipic acid pathway? [Invited]
Nishida H
Annual Meeting, 2000, of The Japan Society for Microbial Systematics - Microbial Systematics, Today and Tomorrow   Oct 2000   
A prokaryotic gene cluster involved in synthesis of lysine through the aminoadipate pathway
Nishida H, Nishiyama M, Kobashi N, Kosuge T, Hoshino T, Yamane H, Yokota A
International Symposium "Evolution 2000" - Biodiversity in Network of Bioinformation from the Standpoint of Devo-Evo View   Mar 2000   
Evolution in the Archiascomycetes [Invited]
Nishida H, Sugiyama J
XVI International Botanical Congress   Aug 1999   
Molecular phylogeny and evolution of the urediniomycetes including Mixia and basidiomycetous yeasts [Invited]
Nishida H, Sjamusuridzal W, Bauer R, Oberwinkler F, Kakishima M, Sugiyama J
Sixth International Symposium of the Mycological Society of Japan - Joint Symposium of MSJ/BMS (British Mycological Society)   Nov 1998   
A major lineage, which connects the ascomycetes with the basidiomycetes, inferred from the molecular approaches: Taphrina, Protomyces, Saitoella, and related taxa [Invited]
Nishida H, Sugiyama J
XV International Botanical Congress   Aug 1993   
Horizontal transfer of the higher fungus Protomyces group I introns
Nishida H, Sugiyama J
First Annual Society for Molecular Biology and Evolution Conference   Jul 1993