All Stories

  1. The Common Ancestor of Species was Rod-Shaped

    Article • The Open Bioinformatics Journal, October 2018, Bentham Science Publishers

    Dr Hiromi Nishida

  2. Corrigendum

    Article • Mycologia, July 2018, Taylor & Francis

    Dr Hiromi Nishida

  3. Draft Genome Sequence of the Archiascomycetous Yeast Saitoella complicata

    Article • Genome Announcements, May 2015, ASM Journals

    Dr Hiromi Nishida

  4. Relationship between chromosomal GC content and isoelectric points of histones in fungi

    Article • The Journal of General and Applied Microbiology, January 2015, Microbiology Research Foundation

    Dr Hiromi Nishida

  5. Conserved and Varied Dinucleotide Sequences in the Genomes of Three Aspergillus Species

    Article • Recent Advances in DNA & Gene Sequences (Formerly Recent Patents on DNA & Gene Sequences), October 2014, Bentham Science Publishers

    Dr Hiromi Nishida

  6. Modulation of primary cell function of hostPseudomonasbacteria by the conjugative plasmid pCAR1

    Article • Environmental Microbiology, June 2014, Wiley

    Dr Hideaki Nojiri, Dr Hiromi Nishida, Dr Masaki Shintani

  7. The early diverging ascomycetous budding yeast Saitoella complicata has three histone deacetylases belonging to the Clr6, Hos2, and Rpd3 lineages

    Article • The Journal of General and Applied Microbiology, January 2014, Microbiology Research Foundation

    Dr Hiromi Nishida

  8. Base composition and nucleosome density in exonic and intronic regions in genes of the filamentous ascomycetes Aspergillus nidulans and Aspergillus oryzae

    Article • Gene, August 2013, Elsevier

    Dr Hiromi Nishida

  9. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus

    Article • Nature Chemical Biology, February 2013, Springer Science + Business Media

    Professor Sonja-Verena Albers, Dr Hiromi Nishida

  10. Phylogenetic Analyses of Phytoplasmas Based on Whole-Genome Comparison

    Article • August 2012, Springer Science + Business Media

    Dr Hiromi Nishida

  11. Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping

    Article • Open Biology, April 2012, Royal Society Publishing

    Dr Hiromi Nishida

  12. Nucleosome Positioning

    Article • ISRN Molecular Biology, January 2012, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  13. Evolution of genome base composition and genome size in bacteria

    Article • Frontiers in Microbiology, January 2012, Frontiers

    Dr Hiromi Nishida

  14. Comparative Analyses of Homocitrate Synthase Genes of Ascomycetous Yeasts

    Article • International Journal of Evolutionary Biology, January 2012, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  15. Comparative Analyses of Base Compositions, DNA Sizes, and Dinucleotide Frequency Profiles in Archaeal and Bacterial Chromosomes and Plasmids

    Article • International Journal of Evolutionary Biology, January 2012, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  16. Genome Signature Difference between Deinococcus radiodurans and Thermus thermophilus

    Article • International Journal of Evolutionary Biology, January 2012, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  17. Evolutionary Mechanisms of Microbial Genomes 2012

    Article • International Journal of Evolutionary Biology, January 2012, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  18. Evolution of Lysine Biosynthesis in the Phylum Deinococcus-Thermus

    Article • International Journal of Evolutionary Biology, January 2012, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  19. Conservation of Nucleosome Positions in Duplicated and Orthologous Gene Pairs

    Article • The Scientific World JOURNAL, January 2012, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  20. Dispensabilities of Carbonic Anhydrase in Proteobacteria

    Article • International Journal of Evolutionary Biology, January 2012, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  21. Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae

    Article • Genomics, November 2011, Elsevier

    Dr Hiromi Nishida

  22. Alterations of RNA maps of IncP-7 plasmid pCAR1 in various Pseudomonas bacteria

    Article • Plasmid, July 2011, Elsevier

    Dr Hiromi Nishida, Dr Masaki Shintani

  23. Extraction of tentative mobile introns in fungal histone genes

    Article • Mobile Genetic Elements, May 2011, Taylor & Francis

    Dr Hiromi Nishida

  24. Comparative Studies of Genome-Wide Maps of Nucleosomes between Deletion Mutants of elp3 and hos2 Genes of Saccharomyces cerevisiae

    Article • PLoS ONE, January 2011, PLOS

    Dr Hiromi Nishida

  25. Distribution of Introns in Fungal Histone Genes

    Article • PLoS ONE, January 2011, PLOS

    Dr Hiromi Nishida

  26. Mixia C.L. Kramer emend. H. Nishida, K. Ando, Y. Ando, Hirata & Sugiyama (1995)

    Article • January 2011, Elsevier

    Dr Hiromi Nishida

  27. Phylogenetic and Guanine-Cytosine Content Analysis of Symbiobacterium thermophilum Genes

    Article • International Journal of Evolutionary Biology, January 2011, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  28. Evolutionary Mechanisms of Microbial Genomes

    Article • International Journal of Evolutionary Biology, January 2011, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  29. Draft genome sequencing of the enigmatic yeast Saitoella complicata

    Article • The Journal of General and Applied Microbiology, January 2011, Microbiology Research Foundation

    Dr Hiromi Nishida

  30. Draft genome sequencing of the enigmatic basidiomycete Mixia osmundae

    Article • The Journal of General and Applied Microbiology, January 2011, Microbiology Research Foundation

    Dr Hiromi Nishida

  31. Unique Evolution of Symbiobacterium thermophilum Suggested from Gene Content and Orthologous Protein Sequence Comparisons

    Article • International Journal of Evolutionary Biology, January 2011, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  32. Genome-Wide Maps of Mononucleosomes and Dinucleosomes Containing Hyperacetylated Histones of Aspergillus fumigatus

    Article • PLoS ONE, March 2010, PLOS

    Dr Hiromi Nishida

  33. Response of thePseudomonashost chromosomal transcriptome to carriage of the IncP-7 plasmid pCAR1

    Article • Environmental Microbiology, December 2009, Wiley

    Dr Hiromi Nishida, Dr Masaki Shintani

  34. Calculation of the ratio of the mononucleosome mapping number to the dinucleosome mapping number for each nucleotide position in the Aspergillus fumigatus genome

    Article • Open Access Bioinformatics, November 2009, Taylor & Francis

    Dr Hiromi Nishida

  35. Ureaplasma Urease Genes have Undergone a Unique Evolutionary Process

    Article • The Open Systems Biology Journal, January 2009, Bentham Science Publishers

    Dr Hiromi Nishida

  36. Symbiobacterium Lost Carbonic Anhydrase in the Course of Evolution

    Article • Journal of Molecular Evolution, January 2009, Springer Science + Business Media

    Dr Hiromi Nishida

  37. High-resolution mapping of plasmid transcriptomes in different host bacteria

    Article • BMC Genomics, January 2009, Springer Science + Business Media

    Dr Hiromi Nishida, Dr Masaki Shintani

  38. Evolutionary Conservation Levels of Subunits of Histone-Modifying Protein Complexes in Fungi

    Article • Comparative and Functional Genomics, January 2009, Hindawi Publishing Corporation

    Dr Hiromi Nishida

  39. An epigenetic aberration increased in intergenic regions of cloned mice

    Article • Mammalian Genome, October 2008, Springer Science + Business Media

    Dr Hiromi Nishida

  40. Detection of the Genes Evolving Under Ureaplasma-Specific Selection

    Article • Journal of Molecular Evolution, April 2008, Springer Science + Business Media

    Dr Hiromi Nishida

  41. Phylogenetic Relationships Among Mycoplasmas Based on the Whole Genomic Information

    Article • Journal of Molecular Evolution, August 2007, Springer Science + Business Media

    Dr Hiromi Nishida

  42. Evolution of ?-butyrolactone synthases and receptors in Streptomyces

    Article • Environmental Microbiology, August 2007, Wiley

    Dr Hiromi Nishida

  43. Phylogenetic and Disruption Analyses of Aspartate Kinase ofDeinococcus radiodurans

    Article • Bioscience Biotechnology and Biochemistry, April 2007, Taylor & Francis

    Dr Hiromi Nishida

  44. Detection and Characterization of Fungal-Specific Proteins inSaccharomyces cerevisiae

    Article • Bioscience Biotechnology and Biochemistry, November 2006, Taylor & Francis

    Dr Hiromi Nishida

  45. Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell

    Article • Chromosome Research, March 2006, Springer Science + Business Media

    Dr Hiromi Nishida

  46. Antisense Transcription in the Mammalian Transcriptome

    Article • Science, September 2005, American Association for the Advancement of Science

    Dr Hiromi Nishida, Piero Carninci

  47. Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

    Article • American Journal of Botany, October 2004, Botanical Society of America

    Dr Hiromi Nishida

  48. Disruption analysis of DR1420 and/or DR1758 in the extremely radioresistant bacterium Deinococcus radiodurans

    Article • Microbiology, September 2002, Society for General Microbiology

    Dr Hiromi Nishida

  49. Phylogenetic position of Mixia osmundae inferred from 28S rDNA comparison.

    Article • The Journal of General and Applied Microbiology, January 2002, Microbiology Research Foundation

    Dr Hiromi Nishida

  50. Evolution of amino acid biosynthesis and enzymes with broad substrate specificity

    Article • Bioinformatics, December 2001, Oxford University Press (OUP)

    Dr Hiromi Nishida

  51. Distribution of genes for lysine biosynthesis through the aminoadipate pathway among prokaryotic genomes

    Article • Bioinformatics, February 2001, Oxford University Press (OUP)

    Dr Hiromi Nishida

  52. Group I Intron Located in PR Protein Homologue Gene inYoungia japonica

    Article • Bioscience Biotechnology and Biochemistry, January 2000, Taylor & Francis

    Dr Hiromi Nishida

  53. A Prokaryotic Gene Cluster Involved in Synthesis of Lysine through the Amino Adipate Pathway: A Key to the Evolution of Amino Acid Biosynthesis

    Article • Genome Research, December 1999, Cold Spring Harbor Laboratory Press

    Dr Hiromi Nishida

  54. Phylogenetic positions of rust fungi parasitic on ferns: Evidence from 18S rDNA sequence analysis

    Article • Mycoscience, February 1999, Elsevier

    Dr Hiromi Nishida

  55. Multiple origins of fungal group I introns located in the same position of nuclear SSU rRNA gene

    Article • Journal of Molecular Evolution, April 1998, Springer Science + Business Media

    Dr Hiromi Nishida

  56. Evolutionary relationships of members of the genera Taphrina, Protomyces, Schizosaccharomyces, and related taxa within the archiascomycetes: Integrated analysis of genotypic and phenotypic characters

    Article • Mycoscience, October 1997, Elsevier

    Dr Hiromi Nishida

  57. Mixia osmundae : transfer from the Ascomycota to the Basidiomycota based on evidence from molecules and morphology

    Article • Canadian Journal of Botany, December 1995, Canadian Science Publishing

    Dr Hiromi Nishida

  58. Archiascomycetes: detection of a major new lineage within the Ascomycota

    Article • Mycoscience, December 1994, Elsevier

    Dr Hiromi Nishida

  59. Phylogeny and Molecular Evolution among Higher Fungi.

    Article • Nippon Nōgeikagaku Kaishi, January 1994, Japan Society for Bioscience, Biotechnology, and Agrochemistry

    Dr Hiromi Nishida

  60. The higher fungus Protomyces inouyei has two group I introns in the 18S rRNA Gene

    Article • Journal of Molecular Evolution, July 1993, Springer Science + Business Media

    Dr Hiromi Nishida

  61. Evolutionary Position ofn-Alkane-assimilating YeastCandida maltosaShown by Nucleotide Sequence of Small-subunit Ribosomal RNA Gene

    Article • Bioscience Biotechnology and Biochemistry, January 1993, Taylor & Francis

    Dr Hiromi Nishida

  62. Fungal Diversity and Phylogeny with Emphasis on 18S Ribosomal DNA Sequence Divergence

    Article • Springer Science + Business Media

    Dr Hiromi Nishida