Nishida, Hiromi
Microbio/informatics Scientist; Ph.D. 1995, Biotechnology, University of Tokyo.
Professional experience
Fellow, Japan Society for the Promotion of Science (JSPS) [1994.04-1995.03]; Postdoctoral Fellow, JSPS [1995.04-1996.03] (Research Fellow, John Taylor Lab, University of California, Berkeley [1995.06-1996.03]); Postdoctoral Fellow, RIKEN [1996.04-1997.03]; Research Associate, Institute of Molecular and Cellular Biosciences, University of Tokyo [1997.04-2003.06]; Research Scientist, Genome Science Center, RIKEN [2003.07-2005.10]; Associate Professor, Graduate School of Agricultural and Life Sciences, University of Tokyo [2005.11- ].
Education
Benten Elementary School, Osaka; Ichioka Junior High School, Osaka; Otemae High School, Osaka; University of Tokyo, Tokyo; Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo.
Members
Japan Society for Bioscience, Biotechnology, and Agrochemistry [1989- ]; Society of Genome Microbiology, Japan [2007- ]; Fungal Molecular Biology Society of Japan [2009- ]; Editorial Board, Advances and Applications in Bioinformatics and Chemistry [2008- ]; Editorial Board, Open Access Bioinformatics [2009- ]; Lead Guest Editor, Special Issues on Evolutionary Mechanisms of Microbial Genomes and Evolutionary Mechanisms of Microbial Genomes 2012, International Journal of Evolutionary Biology; Editorial Board, The Scientific World Journal [2011- ].
Keywords
Archiascomycetes; Comparative genomics; DNA base composition; Epigenetics; Evolution; Horizontal gene transfer; Lysine biosynthesis; Mixia osmundae; Nucleosome.
Publications in English (*Corresponding author(s); Peer-reviewed; Co-authors; ResearcherID)
[65] Ueda K*, Nishida H, Beppu T (2012) Dispensabilities of carbonic anhydrase in Proteobacteria. International Journal of Evolutionary Biology vol. 2012, art. ID 324549.
[64] 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 vol. 2, art. ID 120043.
[63] Nishida H*, Nishiyama M (2012) Evolution of lysine biosynthesis in the phylum Deinococcus-Thermus. International Journal of Evolutionary Biology vol. 2012, art. ID 745931.
[62] 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 vol. 2012, art. ID 342482.
[61] Nishida H* (2012) Comparative analyses of homocitrate synthase genes of ascomycetous yeasts. International Journal of Evolutionary Biology vol. 2012, art. ID 254941.
[60] Nishida H* (2012) Conservation of nucleosome positions in duplicated and orthologous gene pairs. The Scientific World Journal vol. 2012, art. ID 298174.
[59] Nishida H*, Abe R, Nagayama T, Yano K (2012) Genome signature difference between Deinococcus radiodurans and Thermus thermophilus. International Journal of Evolutionary Biology vol. 2012, art. ID 205274.
[58] Nishida H*, Beppu T, Ueda K (2011) Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae. Genomics vol. 98, pp. 370-375.
[57] 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 vol. 66, pp. 85-92.
[56] Nishida H*, Hamamoto M, Sugiyama J (2011) Draft genome sequencing of the enigmatic yeast Saitoella complicata. Journal of General and Applied Microbiology vol. 57, pp. 243-246.
[55] Nishida H*, Yun C-S (2011) Extraction of tentative mobile introns in fungal histone genes. Mobile Genetic Elements vol. 1, pp. 78-79.
[54] Yun C-S, Nishida H* (2011) Distribution of introns in fungal histone genes. PLoS ONE vol. 6, art. ID e16548.
[53] 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 vol. 6, art. ID e16372.
[52] Nishida H, Kondo S, Nojiri H, Noma K, Oshima K (2011) Editorial: Evolutionary Mechanisms of Microbial Genomes. International Journal of Evolutionary Biology vol. 2011, art. ID 319479.
[51] 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 vol. 2011, art. ID 376831.
[50] Nishida H*, Yun C-S (2011) Phylogenetic and guanine-cytosine content analysis of Symbiobacterium thermophilum genes. International Journal of Evolutionary Biology vol. 2011, art. ID 634505.
[49] Nishida H*, Nagatsuka Y, Sugiyama J (2011) Draft genome sequencing of the enigmatic basidiomycete Mixia osmundae. Journal of General and Applied Microbiology vol. 57, pp. 63-67.
[48] 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., Elsevier, Amsterdam, pp. 1499-1502.
[47] Nishida H* (2010) High adaptability of bacteria for extreme environments. Journal of Cosmology vol. 13, pp. 3625-3627.
[46] Nishida H* (2010) Gene transfer, synthetic organisms, and the origins of life. Journal of Cosmology vol. 8, art. no. 6.
[45] 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 vol. 192, pp. 4720-4731.
[44] 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 vol. 5, art. ID e9916.
[43] 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 vol. 12, pp. 1413-1426.
[42] 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 vol. 36, pp. 74-77.
[41] 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 vol. 1, pp. 1-6.
[40] Nishida H*, Motoyama T, Yamamoto S, Aburatani H, Osada H (2009) Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus. Bioinformatics vol. 25, pp. 2295-2297.
[39] Nishida H* (2009) Evolutionary conservation levels of subunits of histone-modifying protein complexes in fungi. Comparative and Functional Genomics vol. 2009, art. ID 379317.
[38] Miyakoshi M, Nishida H, Shintani M, Yamane H, Nojiri H* (2009) High-resolution mapping of plasmid transcriptomes in different host bacteria. BMC Genomics vol. 10, art. no. 12.
[37] Nishida H* (2009) Ureaplasma urease genes have undergone a unique evolutionary process. Open Systems Biology Journal vol. 2, pp. 1-7.
[36] Nishida H, Beppu T, Ueda K* (2009) Symbiobacterium lost carbonic anhydrase in the course of evolution. Journal of Molecular Evolution vol. 68, pp. 90-96.
[35] 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 vol. 19, pp. 667-674.
[34] Oshima K, Nishida H* (2008) Detection of the genes evolving under Ureaplasma-specific selection. Journal of Molecular Evolution vol. 66, pp. 529-532.
[33] Oshima K, Nishida H* (2007) Phylogenetic relationships among mycoplasmas based on the whole genomic information. Journal of Molecular Evolution vol. 65, pp. 249-258. [Cover of the September issue]
[32] Nishida H*, Ohnishi Y, Beppu T, Horinouchi S (2007) Evolution of γ-butyrolactone synthases and receptors in Streptomyces. Environmental Microbiology vol. 9, pp. 1986-1994.
[31] Nishida H*, Narumi I (2007) Phylogenetic and disruption analyses of aspartate kinase of Deinococcus radiodurans. Bioscience, Biotechnology, and Biochemistry vol. 71, pp. 1015-1020.
[30] Nishida H* (2006) Detection and characterization of fungal-specific proteins in Saccharomyces cerevisiae. Bioscience, Biotechnology, and Biochemistry vol. 70, pp. 2646-2652.
[29] 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 vol. 14, pp. 203-211.
[28] 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, Mattick J, Hume DA, Lipovich L, Engström PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk A, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C* (2005) Antisense transcription in the mammalian transcriptome. Science vol. 309, pp. 1564-1566.
[27] Nishida H*, Suzuki T, Ookawa H, Tomaru Y, Hayashizaki Y (2005) Comparative analysis of expression of histone H2a genes in mouse. BMC Genomics vol. 6, art. no. 108.
[26] Nishida H*, Tomaru Y, Oho Y, Hayashizaki Y (2005) Naturally occurring antisense RNA of histone H2a in mouse cultured cell lines. BMC Genetics vol. 6, art. no. 23.
[25] Nishida H*, Suzuki T, Tomaru Y, Hayashizaki Y (2005) A novel replication-independent histone H2a gene in mouse. BMC Genetics vol. 6, art. no. 10.
[24] 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 vol. 91, pp. 1446-1480.
[23] An KD, Nishida H*, Miura Y, Yokota A (2003) Molecular evolution of adenylating domain of aminoadipate reductase. BMC Evolutionary Biology vol. 3, art. no. 9.
[22] 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 vol. 216, pp. 692-698.
[21] Nishida H*, Narumi I (2002) Disruption analysis of DR1420 and/or DR1758 in the extremely radioresistant bacterium Deinococcus radiodurans. Microbiology vol. 148, pp. 2911-2914.
[20] An KD, Nishida H*, Miura Y, Yokota A (2002) Aminoadipate reductase gene: a new fungal-specific gene for comparative evolutionary analyses. BMC Evolutionary Biology vol. 2, art. no. 6.
[19] Sjamsuridzal W, Nishida H*, Yokota A (2002) Phylogenetic position of Mixia osmundae inferred from 28S rDNA comparison. Journal of General and Applied Microbiology vol. 48, pp. 121-123.
[18] Nishida H* (2001) Evolution of amino acid biosynthesis and enzymes with broad substrate specificity. Bioinformatics vol. 17, pp. 1224-1225.
[17] Nishida H* (2001) Distribution of genes for lysine biosynthesis through the aminoadipate pathway among prokaryotic genomes. Bioinformatics vol. 17, pp. 189-191.
[16] Nishida H*, Nishiyama M (2000) What is characteristic of fungal lysine synthesis through the α-aminoadipate pathway? Journal of Molecular Evolution vol. 51, pp. 299-302.
[15] 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 vol. 50, pp. 1829-1832.
[14] 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 vol. 64, pp. 606-609.
[13] 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 vol. 9, pp. 1175-1183.
[12] 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 vol. 40, pp. 21-27.
[11] 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 vol. 46, pp. 442-448.
[10] 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 vol. 38, pp. 267-280.
[9] 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, Plenum Press, New York, pp. 41-51.
[8] 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, National Science Museum Foundation, Tokyo, Japan, pp. 177-195.
[7] Nishida H, Sugiyama J* (1995) A common group I intron between a plant parasitic fungus and its host. Molecular Biology and Evolution vol. 12, pp. 883-886.
[6] 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 vol. 73, suppl. 1, pp. S660-S666.
[5] Nishida H, Sugiyama J* (1994) Archiascomycetes: detection of a major new lineage within the Ascomycota. Mycoscience vol. 35, pp. 361-366.
[4] 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 vol. 57, pp. 1793-1794.
[3] Sugiyama J, Nishida H (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, CAB International, Wallingford, UK, pp. 261-269.
[2] 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 vol. 37, pp. 25-28.
[1] Nishida H, Sugiyama J* (1993) Phylogenetic relationships among Taphrina, Saitoella, and other higher fungi. Molecular Biology and Evolution vol. 10, pp. 431-436.
