PhD, 1995, Biotechnology, University of Tokyo
BS, 1990, University of Tokyo
Professional Experience
2022.04– , Professor, Department of Food and Life Sciences, Toyo University
2013.04–2022.03, Professor, Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University
2005.11–2013.03, Associate Professor, Graduate School of Agricultural and Life Sciences, University of Tokyo
2003.07–2005.10, Research Scientist, Genome Science Center, RIKEN
1997.04–2003.06, Research Associate, Institute of Molecular and Cellular Biosciences, University of Tokyo
1996.04–1997.03, Postdoctoral Fellow, RIKEN
1995.04–1996.03, Postdoctoral Fellow, Japan Society for the Promotion of Science
1994.04–1995.03, Fellow, Japan Society for the Promotion of Science
Editorial Works
2025–, Editorial Board (microbiology), Scientific Reports
2024, Editor, Special Issue on Applied and Fundamental Studies of Yeast in Fermented Foods and Beverages, Fermentation
2022, Editor, Research Topic on Microorganisms and Their Metabolism Affecting Quality, Safety and Functionality of Agricultural Products, Frontiers in Microbiology
2021, Editor, Special Issue on Microbial Components and Function in Fermented Alcoholic Drink and Production Process, Microorganisms
2021, Editor, Special Issue on Microbioinformatics, International Journal of Molecular Sciences
2020, Editor, Special Issue on Bacterial Plasma Membrane Dynamics, International Journal of Molecular Sciences
2019–, Editorial Board (cell physiology and cell signaling), Microbial Cell
2019, Editor, Special Issue on Bacterial Cell Surface, AIMS Microbiology
2019, Editor, DNA Traffic in the Environment, Springer
2017–2021, Editorial Board, Open Bioinformatics Journal
2014–2017, Editor, Journal of General and Applied Microbiology [2017–, Advisory Board]
2013, Editor, Research Topic on Evolution and function of bacterial and archaeal genome sequences, Frontiers in Microbiology
2012, Editor, Special Issue on Evolutionary Mechanisms of Microbial Genomes 2012, International Journal of Evolutionary Biology
2011, Editor, Special Issue on Evolutionary Mechanisms of Microbial Genomes, International Journal of Evolutionary Biology
2008–2021, Editorial Board, Advances and Applications in Bioinformatics and Chemistry
Other Sites
Publications in English (*Corresponding author)
[122] Book chapter
Nishida H (2024) Microbiology of sake. Tamang JP (ed). Microbiology and Health Benefits of Traditional Alcoholic Beverages, pp. 295-309, Elsevier
[121] Peer-reviewed review paper
Nishida H (2024) Kuratsuki bacteria interactions with sake yeast and effect on taste. Applied Microbiology 4, 1309-1319 DOI: 10.3390/applmicrobiol4030090
[120] Peer-reviewed full paper
Kobayashi K, Nishida H* (2024) Transcriptome analysis of sake yeast in co-culture with kuratsuki Kocuria. Fermentation 10, 249 DOI: 10.3390/fermentation10050249 [selected as an editor's choice article]
[119] Peer-reviewed full paper
Kobayashi K, Nishida H* (2024) Effect of kuratsuki Bacillus and Priestia on taste of sake. Applied Microbiology 4, 147-161 DOI: 10.3390/applmicrobiol4010011
[118] Peer-reviewed minireview paper
Nishida H (2024) Kuratsuki bacteria and sake making. Bioscience, Biotechnology, and Biochemistry 88, 249-253 DOI: 10.1093/bbb/zbad147
[117] Peer-reviewed short paper
Yazaki A, Nishida H* (2023) Effect of kuratsuki Kocuria on sake's taste varies depending on the sake yeast strain used in sake brewing. Archives of Microbiology 205, 290 DOI: 10.1007/s00203-023-03625-6
[116] Peer-reviewed short paper
Saito M, Nishida H* (2023) Molecular hydrogen treatment of sake yeast and kuratsuki bacteria affects sake taste. Fermentation 9, 516 DOI: 10.3390/fermentation9060516
[115] Editorial
Kimura M*, Nishida H, Kato M, Goto M, Nakagawa T (2023) Editorial: Microorganisms and Their Metabolism Affecting Quality, Safety and Functionality of Agricultural Products. Frontiers in Microbiology 14, 1215112 DOI: 10.3389/fmicb.2023.1215112
[114] Peer-reviewed review paper
Nishida H* (2023) Approaches for introducing large DNA molecules into bacterial cells. Journal of Applied Microbiology 134, lxad059 DOI: 10.1093/jambio/lxad059 [picked up in the microbiologist]
[113] Peer-reviewed full paper
Yazaki A, Nishida H* (2023) Effect of kuratsuki Kocuria on sake brewing in different koji conditions. FEMS Microbiology Letters 370, fnad020 DOI: 10.1093/femsle/fnad020
[112] Peer-reviewed full paper
Takahashi S, Nishida H* (2022) Effects of heterologous genome microinjection on the enlargement of Enterococcus faecalis protoplasts. Current Research in Microbial Sciences 3, 100104 DOI: 10.1016/j.crmicr.2022.100104
[111] Peer-reviewed short paper
Kanamoto E, Terashima K, Shiraki Y, Nishida H* (2021) Diversity of Bacillus isolates from the sake brewing process at a sake brewery. Microorganisms 9, 1760 DOI: 10.3390/microorganisms9081760
[110] Peer-reviewed full paper
Terasaki M, Inoue A, Kanamoto E, Yoshida S, Yamada M, Toda H, Nishida H* (2021) Co-cultivation of sake yeast and Kocuria isolates from the sake brewing process. FEMS Microbiology Letters 368, fnab053 DOI: 10.1093/femsle/fnab053
[109] Peer-reviewed full paper
Terasaki M, Kimura Y, Yamada M, Nishida H* (2021) Genomic information of Kocuria isolates from sake brewing process. AIMS Microbiology 7, 114-123 DOI: 10.3934/microbiol.2021008
[108] Peer-reviewed opinion paper
Nishida H* (2021) Sake brewing and bacteria inhabiting sake breweries. Frontiers in Microbiology 12, 602380 DOI: 10.3389/fmicb.2021.602380
[107] Peer-reviewed review paper
Nishida H* (2020) Factors that affect the enlargement of bacterial protoplasts and spheroplasts. International Journal of Molecular Sciences 21, 7131 DOI: 10.3390/ijms21197131
[106] Peer-reviewed full paper
Tsuchikado R, Kami S, Takahashi S, Nishida H* (2020) Novobiocin inhibits membrane synthesis and vacuole formation of Enterococcus faecalis protoplasts. Microbial Cell 7, 300-308 DOI: 10.15698/mic2020.11.735 [selected as Featured Article]
[105] Peer-reviewed full paper
Terasaki M, Nishida H* (2020) Bacterial DNA diversity among clear and cloudy sakes, and sake-kasu. Open Bioinformatics Journal 13, 74-82 DOI: 10.2174/1875036202013010074
[104] Peer-reviewed full paper
Takahashi S*, Mizuma M, Kami S, Nishida H* (2020) Species-dependent protoplast enlargement involves different types of vacuole generation in bacteria. Scientific Reports 10, 8832 DOI: 10.1038/s41598-020-65759-7
[103] Peer-reviewed review paper
Akaike M, Miyagawa H, Kimura Y, Terasaki M, Kusaba Y, Kitagaki H, Nishida H* (2020) Chemical and bacterial components in sake and sake production process. Current Microbiology 77, 632-637 DOI: 10.1007/s00284-019-01718-4
[102] Peer-reviewed full paper
Kami S, Tsuchikado R, Nishida H* (2019) DNA replication and cell enlargement of Enterococcus faecalis protoplasts. AIMS Microbiology 5, 347-357 DOI: 10.3934/microbiol.2019.4.347
[101] Peer-reviewed full paper
Morita Y, Okumura M, Narumi I, Nishida H* (2019) Sensitivity of Deinococcus grandis rodZ deletion mutant to calcium ions results in enhanced spheroplast size. AIMS Microbiology 5, 176-185 DOI: 10.3934/microbiol.2019.2.176
[100] Peer-reviewed full paper
Nishino K, Tsuchikado R, Nishida H* (2019) Sugar enhances outer membrane fusion in Deinococcus grandis spheroplasts to generate calcium ion-dependent extra-huge cells. FEMS Microbiology Letters 366, fnz087 DOI: 10.1093/femsle/fnz087 [selected as Editor's Choice]
[99] Peer-reviewed full paper
Nishino K, Nishida H* (2019) Calcium ion induces outer membrane fusion of Deinococcus grandis spheroplasts to generate giant spheroplasts with multiple cytoplasms. FEMS Microbiology Letters 366, fny282 DOI: 10.1093/femsle/fny282
[98] Book chapter
Maruyama H, Kent NA, Nishida H, Oshima T (2019) Functions of archaeal nucleoid proteins: archaeal silencers are still missing. Nishida H, Oshima T (eds). DNA Traffic in the Environment, pp. 29-45, Springer
[97] Peer-reviewed full paper
Morita Y, Nishida H* (2018) The common ancestor of Deinococcus species was rod-shaped. Open Bioinformatics Journal 11, 252-258 DOI: 10.2174/1875036201811010252
[96] Peer-reviewed full paper
Nishino K, Morita Y, Takahashi S, Okumura M, Shiratani S, Umemura K, Narumi I, Kondo C, Ochiai R, Oshima T, Nishida H* (2018) Enlargement of Deinococcus grandis spheroplasts requires Mg2+ or Ca2+. Microbiology 164, 1361-1371 DOI: 10.1099/mic.0.000716
[95] Non-peer-reviewed full paper
Morita Y, Narumi I, Nishida H (2018) Transformation efficiency of spheroplasts and normal cells of Deinococcus radiodurans. Bulletin of Toyama Prefectural University 28, 41-43
[94] Peer-reviewed full paper
Terasaki M, Miyagawa S, Yamada M, Nishida H* (2018) Detection of bacterial DNA during the process of sake production using sokujo-moto. Current Microbiology 75, 874-879 DOI: 10.1007/s00284-018-1460-x
[93] Peer-reviewed full paper
Sugiyama J*, Nishida H, Hosoya T, Kakishima M (2018) The enigmatic Mixia osmundae revisited: A systematic review including new distributional data and recent advances in its phylogeny and phylogenomics. Mycologia 110, 179-191
[92] Peer-reviewed full paper
Nishino K, Takahashi S, Nishida H* (2018) Comparison of gene expression levels of appA, ppsR, and EL368 in Erythrobacter litoralis spheroplasts under aerobic and anaerobic conditions, and under blue light, red light, and dark conditions. Journal of General and Applied Microbiology 64, 117-120 DOI: 10.2323/jgam.2017.09.005
[91] Peer-reviewed short paper
Nakazawa M, Nishida H* (2017) Effects of light and oxygen on the enlargement of spheroplasts of the facultative anaerobic anoxygenic photosynthetic bacterium Rhodospirillum rubrum. Jacobs Journal of Biotechnology and Bioengineering 3, 014
[90] Peer-reviewed full paper
Terasaki M, Fukuyama A, Takahashi Y, Yamada M, Nishida H* (2017) Bacterial DNA detected in Japanese rice wines and the fermentation starters. Current Microbiology 74, 1432-1437 DOI: 10.1007/s00284-017-1337-4
[89] Peer-reviewed short paper
Nishino K, Nishida H* (2017) Blue light inhibits the enlargement of Erythrobacter litoralis spheroplasts. Journal of General and Applied Microbiology 63, 203-206 DOI: 10.2323/jgam.2016.10.004
[88] Peer-reviewed full paper
Nakamiya H, Ijima S, Nishida H* (2017) Changes in nucleosome formation at gene promoters in the archiascomycetous yeast Saitoella complicata. AIMS Microbiology 3, 136-142 DOI: 10.3934/microbiol.2017.2.136
[87] Peer-reviewed full paper
Takahashi S, Nishida H* (2017) Comparison of gene expression among normally divided cells, elongated cells, spheroplasts at the beginning of growth, and enlarged spheroplasts at 43 h of growth in Lelliottia amnigena. Gene Reports 7, 87-90 DOI: 10.1016/j.genrep.2017.02.005
[86] Peer-reviewed full paper
Shimizu T, Yin L, Yoshida A, Yokooji Y, Hachisuka S-I, Sato T, Tomita T, Nishida H, Atomi H, Kuzuyama T, Nishiyama M* (2017) Structure and function of an ancestral-type β-decarboxylating dehydrogenase from Thermococcus kodakarensis. Biochemical Journal 474, 105-122 DOI: 10.1042/BCJ20160699
[85] Peer-reviewed short paper
Nakazawa M, Nishida H* (2017) Effects of light and oxygen on the enlargement of Erythrobacter litoralis spheroplasts. Journal of General and Applied Microbiology 63, 58-61 DOI: 10.2323/jgam.2016.08.001
[84] Peer-reviewed full paper
Nishida H*, Oshima T (2017) Archaeal histone distribution is associated with archaeal genome base composition. Journal of General and Applied Microbiology 63, 28-35 DOI: 10.2323/jgam.2016.07.003
[83] Peer-reviewed full paper
Takahashi S, Takayanagi A, Takahashi Y, Oshima T, Nishida H* (2016) Comparison of transcriptomes of enlarged spheroplasts of Erythrobacter litoralis and Lelliottia amnigena. AIMS Microbiology 2, 152-189 DOI: 10.3934/microbiol.2016.2.152
[82] Peer-reviewed full paper
Yamauchi K, Kondo S, Hamamoto M, Suzuki Y, Nishida H* (2016) Genome-wide maps of nucleosomes of the trichostatin A treated and untreated archiascomycetous yeast Saitoella complicata. AIMS Microbiology 2, 69-91 DOI: 10.3934/microbiol.2016.1.69
[81] Non-peer-reviewed full paper
Takahashi S, Nishida H (2016) Growth of Enterobacter amnigenus and Escherichia coli spheroplasts in marine broth containing penicillin. Bulletin of Toyama Prefectural University 26, 27-30
[80] Peer-reviewed full paper
Takayanagi A, Takahashi S, Nishida H* (2016) Requirement of dark culture condition for enlargement of spheroplasts of the aerobic anoxygenic photosynthetic marine bacterium Erythrobacter litoralis. Journal of General and Applied Microbiology 62, 14-17 DOI: 10.2323/jgam.62.14
[79] Peer-reviewed full paper
Takahashi S, Nishida H* (2015) Quantitative analysis of chromosomal and plasmid DNA during the growth of spheroplasts of Escherichia coli. Journal of General and Applied Microbiology 61, 262-265 DOI: 10.2323/jgam.61.262
[78] Peer-reviewed short paper
Yamauchi K, Kondo S*, Hamamoto M, Takahashi Y, Ogura Y, Hayashi T, Nishida H* (2015) Draft genome sequence of the archiascomycetous yeast Saitoella complicata. Genome Announcements 3, e00220-15 DOI: 10.1128/genomeA.00220-15
[77] Peer-reviewed short paper
Nishida H* (2015) Relationship between chromosomal GC content and isoelectric points of histones in fungi. Journal of General and Applied Microbiology 61, 24-26 DOI: 10.2323/jgam.61.24
[76] Peer-reviewed full paper
Takahashi Y, Shintani M, Takase N, Kazo Y, Kawamura F, Hara H, Nishida H, Okada K, Yamane H, Nojiri H* (2015) Modulation of primary cell function of host Pseudomonas bacteria by the conjugative plasmid pCAR1. Environmental Microbiology 17, 134-155 DOI: 10.1111/1462-2920.12515
[75] Peer-reviewed full paper
Nishida H* (2014) Conserved and varied dinucleotide sequences in the genomes of three Aspergillus species. Recent Advances in DNA & Gene Sequences 8, 10-14 DOI: 10.2174/2352092208666141013231001
[74] Peer-reviewed full paper
Nishida H*, Matsumoto T, Kondo S, Hamamoto M, Yoshikawa H (2014) The early diverging ascomycetous budding yeast, Saitoella complicata, has three histone deacetylases belonging to the Clr6, Hos2, and Rpd3 lineages. Journal of General and Applied Microbiology 60, 7-12 DOI: 10.2323/jgam.60.7
[73] Non-peer-reviewed report
Nishida H (2013) Study of Aspergillus nucleosome positioning. Report of the Noda Institute for Scientific Research 57, 38-39
[72] Peer-reviewed full paper
Nishida H*, Katayama T, Suzuki Y, Kondo S, Horiuchi H (2013) Base composition and nucleosome density in exonic and intronic regions in genes of the filamentous ascomycetes Aspergillus nidulans and Aspergillus oryzae. Gene 525, 5-10 DOI: 10.1016/j.gene.2013.04.077
[71] Peer-reviewed full paper
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* (2013) Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nature Chemical Biology 9, 277-283 DOI: 10.1038/nchembio.1200
[70] Peer-reviewed review paper
Nishida H* (2013) Genome DNA sequence variation, evolution, and function in bacteria and archaea. Current Issues in Molecular Biology 15, 19-24 DOI: 10.21775/cimb.015.019
[69] Book chapter
Nishida H (2013) Phylogenetic analyses of phytoplasmas based on whole-genome comparison. Dickinson M, Hodgetts J (eds). Phytoplasma: Methods and Protocols. Methods in Molecular Biology 938, 319-327, Humana Press DOI: 10.1007/978-1-62703-089-2_27
[68] Peer-reviewed opinion paper
Nishida H* (2012) Evolution of genome base composition and genome size in bacteria. Frontiers in Microbiology 3, 420 DOI: 10.3389/fmicb.2012.00420
[67] Peer-reviewed review paper
Nishida H* (2012) Nucleosome positioning. ISRN Molecular Biology 2012, 245706 DOI: 10.5402/2012/245706
[66] Editorial
Nishida H, Kondo S, Nojiri H, Noma K, Oshima K (2012) Evolutionary Mechanisms of Microbial Genomes 2012. International Journal of Evolutionary Biology 2012, 872768 DOI: 10.1155/2012/872768
[65] Peer-reviewed full paper
Ueda K*, Nishida H, Beppu T (2012) Dispensabilities of carbonic anhydrase in Proteobacteria. International Journal of Evolutionary Biology 2012, 324549 DOI: 10.1155/2012/324549
[64] Peer-reviewed full paper
Nishida H*, Kondo S, Matsumoto T, Suzuki Y, Yoshikawa H, Taylor TD, Sugiyama J (2012) Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping. Open Biology 2, 120043 DOI: 10.1098/rsob.120043
[63] Peer-reviewed full paper
Nishida H*, Nishiyama M (2012) Evolution of lysine biosynthesis in the phylum Deinococcus-Thermus. International Journal of Evolutionary Biology 2012, 745931 DOI: 10.1155/2012/745931
[62] Peer-reviewed full paper
Nishida H* (2012) Comparative analyses of base compositions, DNA sizes, and dinucleotide frequency profiles in archaeal and bacterial chromosomes and plasmids. International Journal of Evolutionary Biology 2012, 342482 DOI: 10.1155/2012/342482
[61] Peer-reviewed full paper
Nishida H* (2012) Comparative analyses of homocitrate synthase genes of ascomycetous yeasts. International Journal of Evolutionary Biology 2012, 254941 DOI: 10.1155/2012/254941
[60] Peer-reviewed full paper
Nishida H* (2012) Conservation of nucleosome positions in duplicated and orthologous gene pairs. Scientific World Journal 2012, 298174 DOI: 10.1100/2012/298174
[59] Peer-reviewed full paper
Nishida H*, Abe R, Nagayama T, Yano K (2012) Genome signature difference between Deinococcus radiodurans and Thermus thermophilus. International Journal of Evolutionary Biology 2012, 205274 DOI: 10.1155/2012/205274
[58] Peer-reviewed full paper
Nishida H*, Beppu T, Ueda K (2011) Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae. Genomics 98, 370-375 DOI: 10.1016/j.ygeno.2011.08.001
[57] Peer-reviewed full paper
Shintani M, Tokumaru H, Takahashi Y, Miyakoshi M, Yamane H, Nishida H, Nojiri H* (2011) Alterations of RNA maps of IncP-7 plasmid pCAR1 in various Pseudomonas bacteria. Plasmid 66, 85-92 DOI: 10.1016/j.plasmid.2011.06.001
[56] Peer-reviewed short paper
Nishida H*, Hamamoto M, Sugiyama J (2011) Draft genome sequencing of the enigmatic yeast Saitoella complicata. Journal of General and Applied Microbiology 57, 243-246 DOI: 10.2323/jgam.57.243
[55] Peer-reviewed short paper
Nishida H*, Yun C-S (2011) Extraction of tentative mobile introns in fungal histone genes. Mobile Genetic Elements 1, 78-79 DOI: 10.4161/mge.1.1.15431
[54] Peer-reviewed full paper
Yun C-S, Nishida H* (2011) Distribution of introns in fungal histone genes. PLOS ONE 6, e16548 DOI: 10.1371/journal.pone.0016548
[53] Peer-reviewed full paper
Matsumoto T, Yun C-S, Yoshikawa H, Nishida H* (2011) Comparative studies of genome-wide maps of nucleosomes between deletion mutants of elp3 and hos2 genes of Saccharomyces cerevisiae. PLOS ONE 6, e16372 DOI: 10.1371/journal.pone.0016372
[52] Editorial
Nishida H, Kondo S, Nojiri H, Noma K, Oshima K (2011) Evolutionary Mechanisms of Microbial Genomes. International Journal of Evolutionary Biology 2011,319479 DOI: 10.4061/2011/319479
[51] Peer-reviewed full paper
Oshima K, Ueda K, Beppu T, Nishida H* (2011) Unique evolution of Symbiobacterium thermophilum suggested from gene content and orthologous protein sequence comparisons. International Journal of Evolutionary Biology 2011, 376831 DOI: 10.4061/2011/376831
[50] Peer-reviewed full paper
Nishida H*, Yun C-S (2011) Phylogenetic and guanine-cytosine content analysis of Symbiobacterium thermophilum genes. International Journal of Evolutionary Biology 2011, 634505 DOI: 10.4061/2011/634505
[49] Peer-reviewed short paper
Nishida H*, Nagatsuka Y, Sugiyama J (2011) Draft genome sequencing of the enigmatic basidiomycete Mixia osmundae. Journal of General and Applied Microbiology 57, 63-67 DOI: 10.2323/jgam.57.63
[48] Book chapter
Nishida H, Robert V, Sugiyama J (2011) Mixia C.L. Kramer emend. H. Nishida, K. Ando, Y. Ando, Hirata & Sugiyama. Kurtzman CP, Fell JW, Boekhout T (eds). The Yeasts, a taxonomic study, 5th ed., pp. 1499-1502, Elsevier, Amsterdam
[47] Peer-reviewed commentary
Nishida H* (2010) High adaptability of bacteria for extreme environments. Journal of Cosmology 13, 3625-3627
[46] Peer-reviewed commentary
Nishida H* (2010) Gene transfer, synthetic organisms, and the origins of life. Journal of Cosmology 8, 6
[45] Peer-reviewed full paper
Yun C-S, Suzuki C, Naito K, Takeda T, Takahashi Y, Sai F, Terabayashi T, Miyakoshi M, Shintani M, Nishida H, Yamane H, Nojiri H* (2010) Pmr, a histone-like protein H1 (H-NS) family protein encoded by the IncP-7 plasmid pCAR1, is a key global regulator that alters host function. Journal of Bacteriology 192, 4720-4731 DOI: 10.1128/JB.00591-10
[44] Peer-reviewed full paper
Nishida H*, Motoyama T, Suzuki Y, Yamamoto S, Aburatani H, Osada H (2010) Genome-wide maps of mononucleosomes and dinucleosomes containing hyperacetylated histones of Aspergillus fumigatus. PLOS ONE 5, e9916 DOI: 10.1371/journal.pone.0009916
[43] Peer-reviewed full paper
Shintani M, Takahashi Y, Tokumaru H, Kadota K, Hara H, Miyakoshi M, Naito K, Yamane H, Nishida H, Nojiri H* (2010) Response of the Pseudomonas host chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1. Environmental Microbiology 12, 1413-1426 DOI: 10.1111/j.1462-2920.2009.02110.x
[42] Non-peer-reviewed full paper
Oshima K*, Hoshi A, Ishii Y, Kakizawa S, Kawanishi T, Kojima N, Sugawara K, Ishii Y, Nishida H, Namba S (2009) Evolutionary analysis of mycoplasmas based on whole genomic information. Japanese Journal of Mycoplasmology 36, 74-77
[41] Peer-reviewed full paper
Nishida H* (2009) Calculation of the ratio of the mononucleosome mapping number to the dinucleosome mapping number for each nucleotide position in the Aspergillus fumigatus genome. Open Access Bioinformatics 1, 1-6 DOI: 10.2147/OAB.S7797
[40] Peer-reviewed short paper
Nishida H*, Motoyama T, Yamamoto S, Aburatani H, Osada H (2009) Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus. Bioinformatics 25, 2295-2297 DOI: 10.1093/bioinformatics/btp413
[39] Peer-reviewed full paper
Nishida H* (2009) Evolutionary conservation levels of subunits of histone-modifying protein complexes in fungi. Comparative and Functional Genomics 2009, 379317 DOI: 10.1155/2009/379317
[38] Peer-reviewed full paper
Miyakoshi M, Nishida H, Shintani M, Yamane H, Nojiri H* (2009) High-resolution mapping of plasmid transcriptomes in different host bacteria. BMC Genomics 10, 12 DOI: 10.1186/1471-2164-10-12
[37] Peer-reviewed full paper
Nishida H* (2009) Ureaplasma urease genes have undergone a unique evolutionary process. Open Systems Biology Journal 2, 1-7 DOI: 10.2174/1876392800902010001
[36] Peer-reviewed full paper
Nishida H, Beppu T, Ueda K* (2009) Symbiobacterium lost carbonic anhydrase in the course of evolution. Journal of Molecular Evolution 68, 90-96 DOI: 10.1007/s00239-008-9191-4
[35] Peer-reviewed full paper
Nishida H*, Kondo S, Suzuki T, Tsujimura Y, Komatsu S, Wakayama T, Hayashizaki Y (2008) An epigenetic aberration increased in intergenic regions of cloned mice. Mammalian Genome 19, 667-674 DOI: 10.1007/s00335-008-9146-5
[34] Peer-reviewed full paper
Oshima K, Nishida H* (2008) Detection of the genes evolving under Ureaplasma-specific selection. Journal of Molecular Evolution 66, 529-532 DOI: 10.1007/s00239-008-9106-4
[33] Peer-reviewed full paper
Oshima K, Nishida H* (2007) Phylogenetic relationships among mycoplasmas based on the whole genomic information. Journal of Molecular Evolution 65, 249-258 DOI: 10.1007/s00239-007-9010-3 [selected as Cover Image]
[32] Peer-reviewed full paper
Nishida H*, Ohnishi Y, Beppu T, Horinouchi S (2007) Evolution of γ-butyrolactone synthases and receptors in Streptomyces. Environmental Microbiology 9, 1986-1994 DOI: 10.1111/j.1462-2920.2007.01314.x
[31] Peer-reviewed full paper
Nishida H*, Narumi I (2007) Phylogenetic and disruption analyses of aspartate kinase of Deinococcus radiodurans. Bioscience, Biotechnology, and Biochemistry 71, 1015-1020 DOI: 10.1271/bbb.60671
[30] Peer-reviewed full paper
Nishida H* (2006) Detection and characterization of fungal-specific proteins in Saccharomyces cerevisiae. Bioscience, Biotechnology, and Biochemistry 70, 2646-2652 DOI: 10.1271/bbb.60251
[29] Peer-reviewed full paper
Nishida H*, Suzuki T, Kondo S, Miura H, Fujimura Y, Hayashizaki Y* (2006) Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell. Chromosome Research 14, 203-211 DOI: 10.1007/s10577-006-1036-7
[28] Peer-reviewed full paper
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* (2005) Antisense transcription in the mammalian transcriptome. Science 309, 1564-1566 DOI: 10.1126/science.1112009
[27] Peer-reviewed full paper
Nishida H*, Suzuki T, Ookawa H, Tomaru Y, Hayashizaki Y (2005) Comparative analysis of expression of histone H2a genes in mouse. BMC Genomics 6, 108 DOI: 10.1186/1471-2164-6-108
[26] Peer-reviewed full paper
Nishida H*, Tomaru Y, Oho Y, Hayashizaki Y (2005) Naturally occurring antisense RNA of histone H2a in mouse cultured cell lines. BMC Genetics 6, 23 DOI: 10.1186/1471-2156-6-23
[25] Peer-reviewed full paper
Nishida H*, Suzuki T, Tomaru Y, Hayashizaki Y (2005) A novel replication-independent histone H2a gene in mouse. BMC Genetics 6, 10 DOI: 10.1186/1471-2156-6-10
[24] Peer-reviewed full paper
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 G-H, Lücking R, Lumbsch T, O'Donnell K, Binder M, Diederich P, Ertz D, Gueidan C, Hansen K, Harris RC, Hosaka K, Lim Y-W, Matheny B, Nishida H, Pfister D, Rogers J, Rossman A, Schmitt I, Sipman H, Stone J, Sugiyama J, Yahr R, Vilgalys R (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. American Journal of Botany 91, 1446-1480 DOI: 10.3732/ajb.91.10.1446
[23] Peer-reviewed full paper
An KD, Nishida H*, Miura Y, Yokota A (2003) Molecular evolution of adenylating domain of aminoadipate reductase. BMC Evolutionary Biology 3, 9 DOI: 10.1186/1471-2148-3-9
[22] Peer-reviewed full paper
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* (2003) Cloning and characterization of a jasmonic acid-responsive gene encoding 12-oxophytodienoic acid reductase in suspension-cultured rice cells. Planta 216, 692-698 DOI: 10.1007/s00425-002-0909-z
[21] Peer-reviewed full paper
Nishida H*, Narumi I (2002) Disruption analysis of DR1420 and/or DR1758 in the extremely radioresistant bacterium Deinococcus radiodurans. Microbiology 148, 2911-2914 DOI: 10.1099/00221287-148-9-2911
[20] Peer-reviewed full paper
An KD, Nishida H*, Miura Y, Yokota A (2002) Aminoadipate reductase gene: a new fungal-specific gene for comparative evolutionary analyses. BMC Evolutionary Biology 2, 6 DOI: 10.1186/1471-2148-2-6
[19] Peer-reviewed short paper
Sjamsuridzal W, Nishida H*, Yokota A (2002) Phylogenetic position of Mixia osmundae inferred from 28S rDNA comparison. Journal of General and Applied Microbiology 48, 121-123 DOI: 10.2323/jgam.48.121
[18] Peer-reviewed short paper
Nishida H* (2001) Evolution of amino acid biosynthesis and enzymes with broad substrate specificity. Bioinformatics 17, 1224-1225 DOI: 10.1093/bioinformatics/17.12.1224
[17] Peer-reviewed short paper
Nishida H* (2001) Distribution of genes for lysine biosynthesis through the aminoadipate pathway among prokaryotic genomes. Bioinformatics 17, 189-191 DOI: 10.1093/bioinformatics/17.2.189
[16] Peer-reviewed full paper
Nishida H*, Nishiyama M (2000) What is characteristic of fungal lysine synthesis through the α-aminoadipate pathway? Journal of Molecular Evolution 51, 299-302 DOI: 10.1007/s002390010091
[15] Peer-reviewed full paper
Ohno M, Shiratori H, Park MJ, Saitoh Y, Kumon Y, Yamashita N, Hirata A, Nishida H, Ueda K, Beppu T* (2000) Symbiobacterium thermophilum gen. nov., sp. nov., a symbiotic thermophile that depends on co-culture with a Bacillus strain for growth. International Journal of Systematic and Evolutionary Microbiology 50, 1829-1832 DOI: 10.1099/00207713-50-5-1829
[14] Peer-reviewed short paper
Nishida H*, Ogura A, Yokota A, Yamaguchi I, Sugiyama J (2000) Group I intron located in PR protein homologue gene in Youngia japonica. Bioscience, Biotechnology, and Biochemistry 64, 606-609 DOI: 10.1271/bbb.64.606
[13] Peer-reviewed full paper
Nishida H, Nishiyama M*, Kobashi N, Kosuge T, Hoshino T, Yamane H (1999) A prokaryotic gene cluster involved in synthesis of lysine through the amino adipate pathway: a key to the evolution of amino acid biosynthesis. Genome Research 9, 1175-1183 DOI: 10.1101/gr.9.12.1175
[12] Peer-reviewed full paper
Sjamsuridzal W, Nishida H, Ogawa H, Kakishima M, Sugiyama J* (1999) Phylogenetic positions of rust fungi parasitic on ferns: evidence from 18S rDNA sequence analysis. Mycoscience 40, 21-27 DOI: 10.1007/BF02465669
[11] Peer-reviewed full paper
Nishida H, Tajiri Y, Sugiyama J* (1998) Multiple origins of fungal group I introns located in the same position of nuclear SSU rRNA gene. Journal of Molecular Evolution 46, 442-448 DOI: 10.1007/PL00006324
[10] Peer-reviewed full paper
Sjamsuridzal W, Tajiri Y, Nishida H, Thuan TB, Kawasaki H, Hirata A, Yokota A, Sugiyama J* (1997) Evolutionary relationships of members of the genera Taphrina, Protomyces, Schizosaccharomyces, and related taxa within the archiascomycetes: integrated analysis of genotypic and phenotypic characters. Mycoscience 38, 267-280 DOI: 10.1007/BF02464084
[9] Book chapter
Sugiyama J, Nagahama T, Nishida H (1996) Fungal diversity and phylogeny with emphasis on 18S ribosomal DNA sequence divergence. Colwell RR, Simidu U, Ohwada K (eds). Microbial diversity in time and space, pp.41-51, Plenum Press, New York
[8] Book chapter
Sugiyama J, Nishida H (1995) The higher fungi: their evolutionary relationships and implications for fungal systematics. Arai R, Kato M, Doi Y (eds). Biodiversity and Evolution, pp. 177-195, National Science Museum Foundation, Tokyo, Japan
[7] Peer-reviewed full paper
Nishida H, Sugiyama J* (1995) A common group I intron between a plant parasitic fungus and its host. Molecular Biology and Evolution 12, 883-886 DOI: 10.1093/oxfordjournals.molbev.a040264
[6] Peer-reviewed full paper
Nishida H, Ando K, Ando Y, Hirata A, Sugiyama J* (1995) Mixia osmundae: transfer from the Ascomycota to the Basidiomycota based on evidence from molecules and morphology. Canadian Journal of Botany 73 (suppl. 1), S660-S666 DOI: 10.1139/b95-308
[5] Peer-reviewed full paper
Nishida H, Sugiyama J* (1994) Archiascomycetes: detection of a major new lineage within the Ascomycota. Mycoscience 35, 361-366 DOI: 10.1007/BF02268506
[4] Peer-reviewed short paper
Okuma M, Hwang CW, Masuda Y, Nishida H, Sugiyama J, Ohta A, Takagi M* (1993) Evolutionary position of n-alkane-assimilating yeast Candida maltosa shown by nucleotide sequence of small-subunit ribosomal RNA gene. Bioscience, Biotechnology, and Biochemistry 57, 1793-1794 DOI: 10.1271/bbb.57.1793
[3] Book chapter
Sugiyama J, Nishida H, Suh S-O (1993) The paradigm of fungal diagnoses and descriptions in the era of molecular systematics: Saitoella complicata as an example. Reynolds DR, Taylor JW (eds). The Fungal Holomorph: mitotic, meiotic and pleomorphic speciation in fungal systematics, pp. 261-269, CAB International, Wallingford, UK
[2] Peer-reviewed full paper
Nishida H, Blanz PA, Sugiyama J* (1993) The higher fungus Protomyces inouyei has two group I introns in the 18S rRNA gene. Journal of Molecular Evolution 37, 25-28 DOI: 10.1007/BF00170458
[1] Peer-reviewed full paper
Nishida H, Sugiyama J* (1993) Phylogenetic relationships among Taphrina, Saitoella, and other higher fungi. Molecular Biology and Evolution 10, 431-436 DOI: 10.1093/oxfordjournals.molbev.a040012