HIDEMASA BONO

Last Updated :2025/11/11

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Professor
Web Site
https://bonohu.hiroshima-u.ac.jp/index_en.html
https://researchgate.net/profile/Hidemasa_Bono
https://scholar.google.co.jp/citations?user=e6OaeXQAAAAJ&hl=en
https://github.com/bonohu
E-mail
bonohuhiroshima-u.ac.jp
Other Contact Details
3-10-23 Kagamiyama, Higashi-Hiroshima city, Hiroshima 739-0046 Japan, Japan
TEL : (+81)82-424-4013 FAX : (+81)
Self-introduction
I am Bioinformatics teacher in Doctoral Program for World-leading Innovative & Smart Education. We are in charge of development of basic technology for genome editing data analysis and gene function analysis by bioinformatics. We have been working on data-driven approaches, especially data analysis using public databases, and are conducting research on digital breeding through pathway design of metabolic pathways using BioDX.

Basic Information

Major Professional Backgrounds

  • 2025/04/01, Hiroshima University, Department of Biological Science, School of Science, Chair
  • 2025/04/01, Hiroshima University, Genome Editing Innovation Center, Deputy Director
  • 2023/10/01, Hiroshima University, Graduate School of Integrated Sciences for Life, Professor
  • 2022/04/01, Hiroshima University, PtBio Collaborative Research Laboratory, Laboratory of BioDX, Professor, Collaborative Research Laboratory
  • 2020/04/01, 2023/09/30, Hiroshima University, Graduate School of Integrated Sciences for Life, Project Professor
  • 2020/04/01, Research Organization of Information and Systems, Database Center for Life Science, Visiting Professor
  • 2007/07/01, 2020/03/31, Research Organization of Information and Systems, Database Center for Life Science, Project Associate Professor
  • 2007/04/01, 2007/06/30, Saitama Medical University, Research Center for Genomic Medicine, Associate Professor
  • 2005/04/01, 2007/03/31, Saitama Medical University, Research Center for Genomic Medicine, Associate Professor
  • 2003/10/01, 2005/03/31, Saitama Medical University, Research Center for Genomic Medicine, Lecturer
  • 2003/04/01, 2003/09/30, Saitama Medical University, Research Center for Genomic Medicine, Assistant Professor
  • 2000/04/01, 2003/03/31, RIKEN, Genomic Sciences Center, Special Postdoctoral Researcher

Educational Backgrounds

  • Kyoto University, Graduate School of Science, Japan, 1997/04, 2000/03
  • Kyoto University, Graduate School of Science, Japan, 1995/04, 1997/03
  • The University of Tokyo, Japan, 1991/04, 1995/03

Academic Degrees

  • Kyoto University
  • Doctor of Science, Kyoto University

Educational Activity

  • [Bachelor Degree Program] School of Science : Biological Sciences : Biology
  • [Master's Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Mathematical and Life Sciences
  • [Master's Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Biomedical Science
  • [Doctoral Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Mathematical and Life Sciences
  • [Doctoral Program] Graduate School of Integrated Sciences for Life : Division of Integrated Sciences for Life : Program of Biomedical Science

Research Fields

  • Biological Sciences;Genome science;Genome biology
  • Agricultural sciences;Boundary agriculture;Insect science
  • Agricultural sciences;Plant production and environmental agriculture;Science in genetics and breeding
  • Biological Sciences;Genome science;System genome science
  • Biology;Biological Science;Molecular biology
  • Biological Sciences;Oncology;Tumor biology
  • Biological Sciences;Genome science;Medical genome science

Research Keywords

  • meta-analysis
  • BioDX
  • bioinformatics
  • genome editing
  • transcriptome analysis
  • functional annotation
  • public database
  • open source software
  • hypoxia
  • oxidative stress

Affiliated Academic Societies

  • The Japanese Society for Genome Editing, 2021/04
  • The Molecular Biology Society of Japan, 1995/12
  • Japanese Cancer Association, 2008/09

Educational Activity

Course in Charge

  1. 2025, Liberal Arts Education Program1, 1Term, Fundamentals of Biology
  2. 2025, Undergraduate Education, 4Term, Introduction to Biological Sciences B
  3. 2025, Undergraduate Education, 2Term, Advanced Biology
  4. 2025, Undergraduate Education, 2Term, Genome Biology
  5. 2025, Undergraduate Education, Second Semester, Seminar for Molecular Genetics
  6. 2025, Undergraduate Education, First Semester, Special Study for Graduation
  7. 2025, Undergraduate Education, Second Semester, Special Study for Graduation
  8. 2025, Undergraduate Education, Second Semester, Seminar for Genome Informatics
  9. 2025, Undergraduate Education, Second Semester, Practice for Fundamental Biology II
  10. 2025, Undergraduate Education, Second Semester, Practice for Fundamental Biology IV
  11. 2025, Undergraduate Education, First Semester, Practice for Fundamental Biology IV
  12. 2025, Undergraduate Education, Year, Biology Internship
  13. 2025, Graduate Education (Master's Program) , 1Term, Introduction to Life Science
  14. 2025, Graduate Education (Master's Program) , Year, Research for Academic Degree Dissertation in Mathematical and Life Sciences
  15. 2025, Graduate Education (Master's Program) , First Semester, Exercises in Life Science A
  16. 2025, Graduate Education (Master's Program) , Second Semester, Exercises in Life Science B
  17. 2025, Graduate Education (Doctoral Program) , Year, Research for Academic Degree Dissertation in Integrated Life Sciences
  18. 2025, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar A
  19. 2025, Graduate Education (Master's Program) , 3Term, Biomedical Science Seminar B
  20. 2025, Graduate Education (Master's Program) , Year, Research for Academic Degree Dissertation in Biomedial Science
  21. 2025, Graduate Education (Master's Program) , First Semester, Exercises in Biomedical Science A
  22. 2025, Graduate Education (Master's Program) , Second Semester, Exercises in Biomedical Science B
  23. 2025, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar C
  24. 2025, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar D
  25. 2025, Graduate Education (Doctoral Program) , 3Term, Biomedical Science Seminar E
  26. 2025, Graduate Education (Master's Program) , Second Semester, Bioinformatics

Research Activities

Academic Papers

  1. LPS Induces Limited Activation of Hypoxia-Inducible Factor-1alpha (HIF1A) in Macrophages, Journal of Biological Chemistry, 20251111
    Link to Paper Search Results by DOI
  2. Functional Annotation of Novel Heat Stress-responsive Genes in Rice Utilizing Public Transcriptomes and Structurome, bioRxiv, 2025.09.29.679423, 20251001
    Link to Paper Search Results by DOI
  3. ★, Meta-analysis of public RNA-sequencing data of drought and salt stresses in different phenotypes of resistant and susceptible Oryza sativa cultivars, Quantitative Plant Biology, 6, e27, 20250905
    Link to Paper Search Results by DOI
  4. Anti-Obesity Effects of Peucedanum Japonicum Thunb Root Extract With Induction of Hepatic Cyp2b10 Gene Expression in Mice, Journal of Food Science, 90(9), e70524, 20250901
    Link to Paper Search Results by DOI
  5. The metabolic ability of swallowtails results in the production of bioactive substances from plant components, PLoS, 20(7), e0321438, 20250723
    Link to Paper Search Results by DOI
  6. ★, Meta-Analysis of Wild Relatives and Domesticated Species of Rice, Tomato, and Soybean Using Publicly Available Transcriptome Data, Life, 15(7), 1088, 20250711
    Link to Paper Search Results by DOI
  7. Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database, GIGASCIENCE, giaf070, 20250623
    Link to Paper Search Results by DOI
  8. Meta-Analysis of Wild Relatives and Domesticated Species of Rice, Tomato, and Soybean Using Publicly Available Transcriptome Data, bioRxiv, 2025.06.01.656526, 20250603
    Link to Paper Search Results by DOI
  9. Comprehensive expression data for two honey bee species, Apis mellifera and Apis cerana japonica, Scientific Data, 12, 926, 20250602
    Link to Paper Search Results by DOI
  10. Genome assembly and annotation of the naked mole rat Heterocephalus glaber reared in Japan, bioRxiv, 2025.05.20.654782, 20250525
    Link to Paper Search Results by DOI
  11. PtWAVE: a high-sensitive deconvolution software of sequencing trace for the detection of large indels in genome editing, BMC Bioinformatics, 26, 114, 20250429
    Link to Paper Search Results by DOI
  12. ★, Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes, microorganisms, 13(5), 995, 20250426
    Link to Paper Search Results by DOI
  13. ★, Recent Advances in Genome Editing and Bioinformatics: Addressing Challenges in Genome Editing Implementation and Genome Sequencing, International Journal of Molecular Sciences, 26(7), 3442, 20250407
    Link to Paper Search Results by DOI
  14. The metabolic ability of swallowtails results in the production of bioactive substances from plant components, bioRxiv, 2025.03.09.642260, 20250313
    Link to Paper Search Results by DOI
  15. ★, Pipeline to explore information on genome editing using large language models and genome editing meta-database, DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2025, 20250308
    Link to Paper Search Results by DOI
  16. Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database, bioRxiv, 2025.02.17.638570, 20250222
    Link to Paper Search Results by DOI
  17. ★, Risk Prediction of RNA Off-Targets of CRISPR Base Editors in Tissue-Specific Transcriptomes Using Language Models, International Journal of Molecular Sciences, 26(4), 1723, 20250218
    Link to Paper Search Results by DOI
  18. CYP6B Subtype Expression Fluctuates in the Great Mormon, Papilio memnon, with Changes in the Components of the Host Plants, Insects, 16(2), 159, 20250204
    Link to Paper Search Results by DOI
  19. Risk Prediction of RNA Off-Targets of CRISPR Base Editors in Tissue-Specific Transcriptomes Using Language Models, bioRxiv, 2025.01.19.633823, 20250123
    Link to Paper Search Results by DOI
  20. Data-driven workflow for comprehensive gene expression analysis in complex microbiomes, bioRxiv, 2025.01.17.632662, 20250118
    Link to Paper Search Results by DOI
  21. Comprehensive expression data for two honey bee species, Apis mellifera and Apis cerana japonica, bioRxiv, 2024.12.11.627317, 20241213
    Link to Paper Search Results by DOI
  22. Pipeline to explore information on genome editing using large language models and genome editing meta-database, bioRxiv, 2024.10.16.617154, 20241018
    Link to Paper Search Results by DOI
  23. ★, Meta-analysis of gonadal transcriptome provides novel insights into sex change mechanism across protogynous fishes, Genes to Cells, 29(11), 1052-1068, 20240929
    Link to Paper Search Results by DOI
  24. ★, Genome-Wide Search for Gene Mutations Likely Conferring Insecticide Resistance in the Common Bed Bug, Cimex lectularius, Insects, 15, 737, 20240924
    Link to Paper Search Results by DOI
  25. Genome-wide Search for Gene Mutations likely Conferring Insecticide Resistance in the Common Bed Bug, Cimex lectularius, bioRxiv, 20240829
    Link to Paper Search Results by DOI
  26. Triterpene RDF: Developing a database of plant enzymes and transcription factors involved in triterpene biosynthesis using the Resource Description Framework, Plant Biotechnology, 41, 303-308, 20240826
    Link to Paper Search Results by DOI
  27. ★, A systematic exploration of unexploited genes for oxidative stress in Parkinson's disease, npj Parkinson's Disease, 10, 160, 20240817
    Link to Paper Search Results by DOI
  28. Meta-analysis of public RNA-sequencing data of drought and salt stresses in different phenotypes of Oryza sativa, bioRxiv, 2024.08.06.605779, 20240808
    Link to Paper Search Results by DOI
  29. ★, Transcriptional Signatures of Domestication Revealed through Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data, Animals, 14(13), 1998, 20240706
    Link to Paper Search Results by DOI
  30. High expression of serine protease, Brachyurin in the posterior midgut of black soldier fly (Hermetia illucens) during horse dropping processing, BMC Research Notes, 17, 182, 20240629
    Link to Paper Search Results by DOI
  31. Time-course transcriptome data of silk glands in day 0–7 last-instar larvae of Bombyx mori (w1 pnd strain), Scientific Data, 11, 709, 20240628
    Link to Paper Search Results by DOI
  32. Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae), G3 Genes|Genomes|Genetics, jkae127, 20240611
    Link to Paper Search Results by DOI
  33. Transcriptional Signatures of Domestication Revealed by Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data, bioRxiv, 20240522
    Link to Paper Search Results by DOI
  34. The serine protease Brachyuran is highly expressed in the posterior midgut of the black soldier fly, Hermetia illucens, during the processing of horse droppings, Research Square, 20240418
    Link to Paper Search Results by DOI
  35. PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing, bioRxiv, 20240417
    Link to Paper Search Results by DOI
  36. ★, Meta-analysis of public RNA sequencing data of abscisic acid-related abiotic stresses in Arabidopsis thaliana, Frontiers in Plant Science, 15, fpls.2024.1343787, 20240322
    Link to Paper Search Results by DOI
  37. A systematic exploration of unexploited genes for oxidative stress in Parkinson's disease, bioRxiv, 2024.03.11.583425, 20240313
    Link to Paper Search Results by DOI
  38. Time-course transcriptome data of silk glands in day 0-7 last-instar larvae of Bombyx mori (w1 pnd strain), bioRxiv, 2024.03.02.582034, 20240303
    Link to Paper Search Results by DOI
  39. Transcriptome Analysis Reveals Enhancement of Cardiogenesis-Related Signaling Pathways by S-nitroso-N-pivaloyl-D-penicillamine (SNPiP): Implications for Improved Diastolic Function and Cardiac Performance, Journal of Cardiovascular Pharmacology, 83(5), 433-445, 20240229
    Link to Paper Search Results by DOI
  40. Triterpene RDF: Developing a database of plant enzymes and transcription factors involved in triterpene biosynthesis using the Resource Description Framework, bioRxiv, 2024.01.08.574260, 20240109
    Link to Paper Search Results by DOI
  41. An extract from the frass of swallowtail butterfly (Papilio machaon) larvae inhibits HCT116 colon cancer cell proliferation but not other cancer cell types, BMC Genomics, 24(1), 735, 20231204
    Link to Paper Search Results by DOI
  42. Efforts to analyze pathways in non-model organisms, BioHackrXiv, spf3q, 20231025
    Link to Paper Search Results by DOI
  43. Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae), bioRxiv, 2023.09.24.559078, 20230925
    Link to Paper Search Results by DOI
  44. ★, Meta-Analysis of Heat-Stressed Transcriptomes Using the Public Gene Expression Database from Human and Mouse Samples, International Journal of Molecular Sciences, 24(17), 13444, 20230830
    Link to Paper Search Results by DOI
  45. ★, DANGER analysis: Risk-averse on/off-target assessment for CRISPR editing without a reference genome, Bioinformatics Advances, 3(1), vbad114, 20230823
    Link to Paper Search Results by DOI
  46. Genome assembly reconstruction of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae), using homology-based assembly and nanopore long-reads, bioRxiv, 2023.07.26.550500, 20230726
    Link to Paper Search Results by DOI
  47. BioHackJP 2023 Report R3: Expand the pathway analysis environment to non-model organisms, BioHackrXiv, 4uskb, 20230712
    Link to Paper Search Results by DOI
  48. Cellular senescence induction leads to progressive cell death via the INK4a-RB pathway in naked mole-rats, The EMBO Journal, e111133, 20230711
    Link to Paper Search Results by DOI
  49. Meta-analysis of gonadal transcriptomes in protogynous fishes provides novel perspective into sex change machinery, bioRxiv, 2023.07.09.545663, 20230710
    Link to Paper Search Results by DOI
  50. Transcriptome Analysis Reveals Enhancement of Cardiogenesis-Related Signaling Pathways by S-nitroso-N-pivaloyl-D-penicillamine (SNPiP): Implications for Improved Diastolic Function and Cardiac Performance, bioRxiv, 20230620
    Link to Paper Search Results by DOI
  51. Meta-Analysis of Public RNA Sequencing Data Revealed Potential Key Genes Associated with Reproductive Division of Labor in Social Hymenoptera and Termites, International Journal of Molecular Sciences, 24(9), 8353, 20230506
    Link to Paper Search Results by DOI
  52. Meta-analysis of heat-stressed transcriptomes using the public gene expression database from human and mouse samples, bioRxiv, 2023.04.30.537112, 20230501
    Link to Paper Search Results by DOI
  53. Meta-Analysis of Public RNA Sequencing Data of Abscisic Acid-Related Abiotic Stresses in Arabidopsis thaliana, bioRxiv, 2023.04.17.537107, 20230418
    Link to Paper Search Results by DOI
  54. Danger Analysis: Risk-Averse on/off-Target Assessment for CRISPR Editing Without a Reference Genome, bioRxiv, 2023.03.11.531115, 20230312
    Link to Paper Search Results by DOI
  55. ★, GEM: Genome Editing Meta-database, a dataset of genome editing related metadata systematically extracted from PubMed literatures, Gene and Genome Editing, 5, 100024, 20221222
    Link to Paper Search Results by DOI
  56. Reference Genome Sequences of the Oriental Armyworm, Mythimna separata (Lepidoptera: Noctuidae), Insects, 13(12), 1172, 20221217
    Link to Paper Search Results by DOI
  57. Meta-analysis of public RNA sequencing data of queens and workers in social Hymenoptera and termites, bioRxiv, 20221122
    Link to Paper Search Results by DOI
  58. Reference genome sequences of Mythimna separata (Lepidoptera: Noctuidae), bioRxiv, 20221119
    Link to Paper Search Results by DOI
  59. ★, A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan, DNA Research, dsac044, 20221116
    Link to Paper Search Results by DOI
  60. ★, Genome editing and bioinformatics, Gene and Genome Editing, 4, 100018, 20221108
    Link to Paper Search Results by DOI
  61. Meta-analysis of the public RNA-Seq data of the Western honeybee Apis mellifera to construct reference transcriptome data, Insects, 13(10), 931, 20221014
    Link to Paper Search Results by DOI
  62. ★, Exploratory meta-Analysis of hypoxic transcriptomes using a precise transcript reference sequence set, Life Science Alliance, 6(1), e202201518, 20221010
    Link to Paper Search Results by DOI
  63. GEM: Genome Editing Meta-database, BioHackrXiv, 20220926
    Link to Paper Search Results by DOI
  64. Meta-Analysis of Transcriptomes in Insects Showing Density-Dependent Polyphenism, Insects, 13(10), 864, 20220923
    Link to Paper Search Results by DOI
  65. A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan, bioRxiv, 2022.09.16.508052, 20220917
    Link to Paper Search Results by DOI
  66. Meta-analysis of the public RNA-Seq data of the Western honeybee Apis mellifera to construct reference transcriptome data, bioRxiv, 2022.09.07.506879, 20220912
    Link to Paper Search Results by DOI
  67. Genome Sequence of the Edible Green Alga Ulva prolifera, Originating from the Yoshinogawa River in Japan, Microbiology Resource Announcements, 20220829
    Link to Paper Search Results by DOI
  68. Prediction of sex-determination mechanisms in avian primordial germ cells using RNA-seq analysis, Scientific Reports, 12, 13528, 20220817
    Link to Paper Search Results by DOI
  69. Revealing Landscapes of Transposable Elements in Apis Species by Meta-Analysis, Insects, 13(8), 698, 20220803
    Link to Paper Search Results by DOI
  70. Meta-analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia, Life, 12(7), 1079, 20220719
    Link to Paper Search Results by DOI
  71. ★, Systematic functional annotation workflow for insects, Insects, 13(7), 586, 20220627
    Link to Paper Search Results by DOI
  72. Meta-analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia, bioRxiv, 2022.06.23.497423, 20220624
    Link to Paper Search Results by DOI
  73. Systematic functional annotation workflow for insects, bioRxiv, 2022.05.12.490705, 20220513
    Link to Paper Search Results by DOI
  74. Meta-analysis of transcriptomes in insects showing density-dependent polyphenism, bioRxiv, 2022.05.09.490177, 20220510
    Link to Paper Search Results by DOI
  75. Exploratory Meta-Analysis of Hypoxic Transcriptomes Using Precise Transcript Reference Sequence Set, bioRxiv, 2022.05.01.489280, 20220501
    Link to Paper Search Results by DOI
  76. Activation of transcription factor HIF inhibits IL-1beta-induced NO production in primary cultured rat hepatocytes, Nitric Oxide, 20220420
    Link to Paper Search Results by DOI
  77. Resistance to chemical carcinogenesis induction via a dampened inflammatory response in naked mole-rats, Communications Biology, 5, 287, 20220330
    Link to Paper Search Results by DOI
  78. Prediction of sex-determination mechanisms in avian primordial germ cells using RNA-seq analysis, bioRxiv, 2022.02.24.481709, 20220225
    Link to Paper Search Results by DOI
  79. RefEx: Dataset for Reference Gene Expression, Practical Guide to Life Science Databases, 117-133, 20220107
    Link to Paper Search Results by DOI
  80. ★, Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes, Biomedicines, 9(12), 1830, 20211203
    Link to Paper Search Results by DOI
  81. Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes, bioRxiv, 2021.11.01.466837, 20211104
    Link to Paper Search Results by DOI
  82. Resistance to chemical carcinogenesis induction via a dampened inflammatory response in naked mole-rats, bioRxiv, 2021.10.21.465383, 20211023
    Link to Paper Search Results by DOI
  83. Rapid metagenomic workflow using annotated 16S RNA dataset, BioHackrXiv, 20210930
    Link to Paper Search Results by DOI
  84. Neurosecretory protein GL-induced fat accumulation is accompanied by repressing the immune-inflammatory response in the adipose tissue of mice, bioRxiv, 2021.08.27.457926, 20210828
    Link to Paper Search Results by DOI
  85. Inhibiting SARS-CoV-2 infection in vitro by suppressing its receptor, angiotensin-converting enzyme 2, via aryl-hydrocarbon receptor signal, Scientific Reports, 11, 16629, 20210817
    Link to Paper Search Results by DOI
  86. A chromosome-level genome sequence of a model chrysanthemum: evolution and 1 reference for hexaploid cultivated chrysanthemum, bioRxiv, 10.1101/2021.06.28.450068, 20210630
    Link to Paper Search Results by DOI
  87. Polysulfide inhibits hypoxia-elicited hypoxia-inducible factor activation in a mitochondria-dependent manner, Mitochondrion, 59, 255-266, 20210613
    Link to Paper Search Results by DOI
  88. Reference transcriptome data in silkworm Bombyx mori, Insects, 12(6), 519, 20210603
    Link to Paper Search Results by DOIRepository URL
  89. ★, Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes, Biomedicines, 9(5), 582, 20210520
    Link to Paper Search Results by DOI
  90. ★, De novo transcriptome analysis for examination of the nutrition metabolic system related to the evolutionary process through which stick insects gain the ability of flight (Phasmatodea), BMC Research Notes, 14, 182, 20210513
    Link to Paper Search Results by DOI
  91. Diversification of mineralocorticoid receptor genes in a subterranean rodent, the naked mole-rat, Journal of Molecular Endocrinology, 66(4), 299-311, 20210401
    Link to Paper Search Results by DOI
  92. Multi-omic meta-analysis of transcriptomes and the bibliome uncovers GPR146 as the novel hypoxia-inducible gene, bioRxiv, 2021.03.29.433661, 20210330
    Link to Paper Search Results by DOI
  93. Inhibiting SARS-CoV-2 infection in vitro by suppressing its receptor, angiotensin-converting enzyme 2, via aryl-hydrocarbon receptor signal, bioRxiv, 2021.03.04.433658, 20210304
    Link to Paper Search Results by DOI
  94. ★, Meta-Analysis of Oxidative Transcriptomes in Insects, Antioxidants, 10(3), 345, 20210225
    Link to Paper Search Results by DOI
  95. Meta-Analysis of Oxidative Transcriptomes in Insects, bioRxiv, 2021.02.01.427354, 20210202
    Link to Paper Search Results by DOI
  96. Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution, BMC Microbiology, 21, 35, 20210126
    Link to Paper Search Results by DOI
  97. Cigarette Smoke Extract Activates Hypoxia-Inducible Factors in a Reactive Oxygen Species-Dependent Manner in Stroma Cells from Human Endometrium, Antioxidants, 10(1), 48, 20210103
    Link to Paper Search Results by DOI
  98. FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs, Nucleic Acids Research, gkaa1054, 20201119
    Link to Paper Search Results by DOI
  99. Characterization of brown adipose tissue thermogenesis in the naked mole-rat (Heterocephalus glaber), a heterothermic mammal, Scientific Reports, 10, 19488, 20201110
    Link to Paper Search Results by DOI
  100. Construction of TUATinsecta database that integrated plant and insect database for screening phytophagous insect metabolic products with medicinal potential, Scientific Reports, 10, 17509, 20201015
    Link to Paper Search Results by DOI
  101. Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping, Genome Research, 30, 1060-1072, 20200727
    Link to Paper Search Results by DOI
  102. TogoEx: the integration of gene expression data, BioHackrXiv, 20200713
    Link to Paper Search Results by DOI
  103. Senescent cell death as an aging resistance mechanism in naked mole-rat, bioRxiv, 2020.07.02.155903, 20200703
    Link to Paper Search Results by DOI
  104. Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution, bioRxivc, 2020.05.06.078147, 20200508
    Link to Paper Search Results by DOI
  105. Characterization of brown adipose tissue thermogenesis in the naked mole-rat (Heterocephalus glaber), a poikilothermic mammal, bioRxiv, 20200429
    Link to Paper Search Results by DOI
  106. Detailed classification of mariner-like elements, class II transposable elements, in six Apis species based on Dromar, bioRxiv, 2020.04.15.035063, 20200416
    Link to Paper Search Results by DOI
  107. Thyroid Hormone Facilitates in Vitro Decidualization of Human Endometrial Stromal Cells via Thyroid Hormone Receptors, Endocrinology, bqaa049, 20200403
    Link to Paper Search Results by DOI
  108. BioHackathon 2015: Semantics of data for life sciences and reproducible research, F1000Research, 20200224
    Link to Paper Search Results by DOI
  109. GLIS1, a novel hypoxia-inducible transcription factor, promotes breast cancer cell motility via activation of WNT5A., Carcinogenesis, bgaa010, 20200212
    Link to Paper Search Results by DOI
  110. Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum., BMC Genomics, 21(1), 152, 20200211
    Link to Paper Search Results by DOI
  111. ★, All of gene expression (AOE): An integrated index for public gene expression databases., PLOS ONE, 15(1), e0227076, 20200124
    Link to Paper Search Results by DOI
  112. ★, Meta-Analysis of Hypoxic Transcriptomes from Public Databases., Biomedicines, 8(1), E10, 20200109
    Link to Paper Search Results by DOI
  113. Reference transcriptome data in silkworm Bombyx mori, bioRxiv, 20191017
    Link to Paper Search Results by DOI
  114. Superoxide dismutase down-regulation and the oxidative stress is required to initiate pupation in Bombyx mori., Scientific Reports, 9(1), 14693, 20191011
    Link to Paper Search Results by DOI
  115. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services, F1000Research, 20190923
    Link to Paper Search Results by DOI
  116. Apoptosis-mediated vasa down-regulation controls developmental transformation in Japanese Copidosoma floridanum female soldiers., Developmental Biology, 456(2), 226-233, 20190919
    Link to Paper Search Results by DOI
  117. Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping, bioRxiv, 20190714
    Link to Paper Search Results by DOI
  118. Cancerous phenotypes associated with hypoxia-inducible factors are not influenced by the volatile anesthetic isoflurane in renal cell carcinoma., PLOS ONE, 14(4), e0215072, 20190415
    Link to Paper Search Results by DOI
  119. Comparative analysis of seven types of superoxide dismutases for their ability to respond to oxidative stress in Bombyx mori., Scientific Reports, 9(1), 2170, 20190218
    Link to Paper Search Results by DOI
  120. Suppression of mitochondrial oxygen metabolism mediated by the transcription factor HIF-1 alleviates propofol-induced cell toxicity., Scientific Reports, 8(1), 8987, 20180612
    Link to Paper Search Results by DOI
  121. Promotion of malignant phenotype after disruption of the three-dimensional structure of cultured spheroids from colorectal cancer., Oncotarget, 9(22), 15968-15983, 20180323
    Link to Paper Search Results by DOI
  122. Differentiated embryo chondrocyte plays a crucial role in DNA damage response via transcriptional regulation under hypoxic conditions., PLOS ONE, 13(2), e0192136, 20180221
    Link to Paper Search Results by DOI
  123. Construction of a simple evaluation system for the intestinal absorption of an orally administered medicine using Bombyx mori larvae., Drug Discoveries & Therapeutics, 12(1), 7-15, 20180101
    Link to Paper Search Results by DOI
  124. ★, RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes., Scientific Data, 4, 170105, 20170829
    Link to Paper Search Results by DOI
  125. HIF-1-mediated suppression of mitochondria electron transport chain function confers resistance to lidocaine-induced cell death., Scientific Reports, 7(1), 3816, 20170619
    Link to Paper Search Results by DOI
  126. ★, Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive., Gigascience, 6(6), 1-8, 20170601
    Link to Paper Search Results by DOI
  127. Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes., BMC Genomics, 18(1), 83, 20170113
    Link to Paper Search Results by DOI
  128. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals., Nucleic Acids Research, 45(D1), D737-D743, 20161027
    Link to Paper Search Results by DOI
  129. Tumour resistance in induced pluripotent stem cells derived from naked mole-rats., Nature Communications, 7, 11471, 20160510
    Link to Paper Search Results by DOI
  130. Can the silkworm (Bombyx mori) be used as a human disease model?, Drug Discoveries & Therapeutics, 10(1), 3-8, 20160207
    Link to Paper Search Results by DOI
  131. Superoxide dismutases, SOD1 and SOD2, play a distinct role in the fat body during pupation in silkworm Bombyx mori., PLOS ONE, 10(2), e0116007, 20150225
    Link to Paper Search Results by DOI
  132. Gateways to the FANTOM5 promoter level mammalian expression atlas., Genome Biology, 16, 22, 20150105
    Link to Paper Search Results by DOI
  133. ★, CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites., Bioinformatics (Oxford, England), 31(7), 1120-1123, 20141120
    Link to Paper Search Results by DOI
  134. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains., Journal of Biomedical Semantics, 5(1), 5, 20140205
    Link to Paper Search Results by DOI
  135. Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive., 8(10), e77910, 20131022
    Link to Paper Search Results by DOI
  136. ★, Identification of key uric acid synthesis pathway in a unique mutant silkworm Bombyx mori model of Parkinson's disease., PLOS ONE, 8(7), e69130, 20130724
    Link to Paper Search Results by DOI
  137. GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts., Nucleic Acids Research, 40(Web Server issue), W592-W596, 20120528
    Link to Paper Search Results by DOI
  138. Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV., Briefings in Bioinformatics, 13(2), 258-268, 20110729
    Link to Paper Search Results by DOI
  139. Allie: a database and a search service of abbreviations and long forms., Database, bar013, 20110415
    Link to Paper Search Results by DOI
  140. Gene expression profiling in multipotent DFAT cells derived from mature adipocytes., Biochemical and Biophysical Research Communications, 407(3), 562-567, 20110316
    Link to Paper Search Results by DOI
  141. Id4, a new candidate gene for senile osteoporosis, acts as a molecular switch promoting osteoblast differentiation., PLOS Genetics, 6(7), e1001019, 20100708
    Link to Paper Search Results by DOI
  142. Gendoo: functional profiling of gene and disease features using MeSH vocabulary., Nucleic Acids Research, 37(Web Server issue), W166-W169, 20090604
    Link to Paper Search Results by DOI
  143. Identification of novel PPARgamma target genes by integrated analysis of ChIP-on-chip and microarray expression data during adipocyte differentiation., Biochemical and Biophysical Research Communications, 372(2), 362-366, 20080519
    Link to Paper Search Results by DOI
  144. BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes., In Silico Biology, 8(1), 53-61, 20080101
  145. Identification of novel steroid target genes through the combination of bioinformatics and functional analysis of hormone response elements., Biochemical and Biophysical Research Communications, 339(1), 99-106, 20051108
    Link to Paper Search Results by DOI
  146. The transcriptional landscape of the mammalian genome., Science, 309(5740), 1559-1563, 20050901
    Link to Paper Search Results by DOI
  147. ★, SayaMatcher: genome scale organization and systematic analysis of nuclear receptor response elements., Gene, 364, 74-78, 20050824
    Link to Paper Search Results by DOI
  148. The study of metabolic pathways in tumors based on the transcriptome., Seminars in Cancer Biology, 15(4), 290-299, 20050801
    Link to Paper Search Results by DOI
  149. Analysis of gene networks during adipogenesis and osteoblastgenesis focusing on the crosstalk and redundant pathways, 49(17), 2965-2969, 20041215
  150. Identification and functional analysis of consensus androgen response elements in human prostate cancer cells., Biochemical and Biophysical Research Communications, 325(4), 1312-1317, 20041201
    Link to Paper Search Results by DOI
  151. Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library., Genomics, 83(6), 1012-1023, 20040601
    Link to Paper Search Results by DOI
  152. Integrative annotation of 21,037 human genes validated by full-length cDNA clones., PLOS Biology, 2(6), e162, 20040429
    Link to Paper Search Results by DOI
  153. Gene discovery in genetically labeled single dopaminergic neurons of the retina., Proceedings of the National Academy of Sciences of the United States of America, 101(14), 5069-5074, 20040326
    Link to Paper Search Results by DOI
  154. MaXML: mouse annotation XML., In Silico Biology, 4(1), 7-15, 20031226
  155. Molecular basis of constitutive production of basement membrane components. Gene expression profiles of Engelbreth-Holm-Swarm tumor and F9 embryonal carcinoma cells., The Journal of Biological Chemistry, 278(50), 50691-50701, 20030910
    Link to Paper Search Results by DOI
  156. Gene expression profile of normal lungs predicts genetic predisposition to lung cancer in mice., Carcinogenesis, 24(11), 1819-1826, 20030814
    Link to Paper Search Results by DOI
  157. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia., Genome Research, 13(6B), 1273-1289, 20030601
    Link to Paper Search Results by DOI
  158. Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling., Genome Research, 13(6B), 1402-1409, 20030601
    Link to Paper Search Results by DOI
  159. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays., Genome Research, 13(6B), 1318-1323, 20030601
    Link to Paper Search Results by DOI
  160. The mouse secretome: functional classification of the proteins secreted into the extracellular environment., Genome Research, 13(6B), 1350-1359, 20030601
    Link to Paper Search Results by DOI
  161. Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage., Genome Research, 13(6B), 1360-1365, 20030601
    Link to Paper Search Results by DOI
  162. Analysis of the mouse transcriptome for genes involved in the function of the nervous system., Genome Research, 13(6B), 1395-1401, 20030601
    Link to Paper Search Results by DOI
  163. G protein-coupled receptor genes in the FANTOM2 database., Genome Research, 13(6B), 1466-1477, 20030601
    Link to Paper Search Results by DOI
  164. ★, Comprehensive analysis of the mouse metabolome based on the transcriptome., Genome Research, 13(6B), 1345-1349, 20030601
    Link to Paper Search Results by DOI
  165. Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set., Genome Research, 13(6B), 1496-1500, 20030601
    Link to Paper Search Results by DOI
  166. Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure., Physiological Genomics, 12(3), 251-259, 20030206
    Link to Paper Search Results by DOI
  167. ★, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs., Nature, 420(6915), 563-573, 20021201
    Link to Paper Search Results by DOI
  168. Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data., Genome Research, 12(8), 1286-1293, 20020801
    Link to Paper Search Results by DOI
  169. Functional transcriptomes: comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts., Current Opinion in Structural Biology, 12(3), 355-361, 20020601
    Link to Paper Search Results by DOI
  170. ★, FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones., Nucleic Acids Research, 30(1), 116-118, 20020101
    Link to Paper Search Results by DOI
  171. ★, READ: RIKEN Expression Array Database., Nucleic Acids Research, 30(1), 211-213, 20020101
    Link to Paper Search Results by DOI
  172. Protein-protein interaction panel using mouse full-length cDNAs., Genome Research, 11(10), 1758-1765, 20011001
    Link to Paper Search Results by DOI
  173. ★, Functional annotation of a full-length mouse cDNA collection., Nature, 409(6821), 685-690, 20010201
    Link to Paper Search Results by DOI
  174. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays., Proceedings of the National Academy of Sciences of the United States of America, 98(5), 2199-2204, 20010201
    Link to Paper Search Results by DOI
  175. Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data., Physiological Genomics, 4(3), 183-188, 20010119
    Link to Paper Search Results by DOI
  176. KEGG: Kyoto Encyclopedia of Genes and Genomes., Nucleic Acids Research, 27(1), 29-34, 19990101
    Link to Paper Search Results by DOI
  177. Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG., Genome informatics. Workshop on Genome Informatics, 10, 94-103, 19990101
  178. Two-component response regulators from Arabidopsis thaliana contain a putative DNA-binding motif., Plant & Cell Physiology, 39(11), 1232-1239, 19981101
    Link to Paper Search Results by DOI
  179. ★, Reconstruction of amino acid biosynthesis pathways from the complete genome sequence., Genome Research, 8(3), 203-210, 19980301
    Link to Paper Search Results by DOI
  180. Systematic Prediction of Orthologous Units of Genes in the Complete Genomes., Genome informatics. Workshop on Genome Informatics, 9, 32-40, 19980101
  181. Organizing and computing metabolic pathway data in terms of binary relations., Pacific Symposium on Biocomputing, 175-186, 19970101
  182. Next-Generation Sequencing and Bioinformatics, Molecular Targeted Therapy of Lung Cancer, 97-115, 201701
    Link to Paper Search Results by DOI
  183. Cluster analysis of genome-wide expression profiles to predict gene functions with KEGG, Nature Genetics, 23(3), 33-34, 199911
  184. Functional interpretation of omics data by profiling genes and diseases using MeSH-controlled vocabulary., Advances in the Study of Genetic Disorders, 65-80, 2011
  185. Expression profiling of parietal endoderm cells and development of systems for large scale production of laminins, Animal Cell Technology: Basic & Applied Aspects, 7-11, 2003
  186. Study of mouse metabolic pathways with riken full-length cdna microarrays, Perspectives in Gene Expression, 2003
  187. READ: Practical Analysis System of Mouse Transcriptome with the FANTOM Database, Genome Informatics, 12, 232-233, 2001
  188. Fully-automated spot recognition and quantification from cDNA microarray images, Proc. Int. Conf. Parallel and Distributed Processing Techniques and Applications, 3, 1291-1297, 2001
  189. FANTOM+: The Interface for Functional Annotation of Mouse cDNA, Genome Informatics, 11, 219-221, 2000
  190. Practical Organization and Functional Annotation of RIKEN cDNA Microarray, Genome Informatics, 11, 260-261, 2000
  191. Representing functional annotations of mouse cDNA sequences in XML, Genome Informatics, 11, 376-377, 2000
  192. Constructing and annotating GENES database in KEGG, Genome Informatics, 9, 226-227, 1998
  193. Genome Scale Prediction of Two-Component Signal Transducers from the Knowledge of Regulatory Interactions, Genome Informatics, 8, 260-261, 1997
  194. Genome scale prediction of enzyme genes utilizing the knowledge of metabolic interactions, Genome Informatics, 7, 252-253, 1996

Invited Lecture, Oral Presentation, Poster Presentation

  1. Systematic analysis of novel heat stress-related long non-coding RNAs through FANTOM6 datasets and meta-analysis of public transcriptome data, Sora Yonezawa, Takeya Kasukawa; Hidemasa Bono, The 48th Annual Meeting of the Molecular Biology Society of Japan, 2025/12/03, Without Invitation, Japanese, The Molecular Biology Society of Japan, Pacifico Yokohama
  2. Comparative Genomic Analysis of the Hattan Lineage of Hiroshima Sake Rice, Ryo Nozu, Miyuki Kanda; Zennosuke Katsuba; Ayane Fujita; Shuji Matsushita; Hidemasa Bono, The 48th Annual Meeting of the Molecular Biology Society of Japan, 2025/12/03, Without Invitation, Japanese, The Molecular Biology Society of Japan, Pacifico Yokohama
  3. Genome sequencing of the naked mole rat Heterocephalus glaber reared in Japan, Kouhei Toga, Kaori Oka; Hidemasa Bono; Kyoko Miura, The 48th Annual Meeting of the Molecular Biology Society of Japan, 2025/12/03, With Invitation, English, The Molecular Biology Society of Japan, Pacifico Yokohama
  4. Developing Efficient Metadata Extraction and Curation Methods for Gene Expression Databases Using Large Language Models, Mitsuo Shintani, Daniel Andrade; Hidemasa Bono, The 48th Annual Meeting of the Molecular Biology Society of Japan, 2025/12/03, Without Invitation, Japanese, The Molecular Biology Society of Japan, Pacifico Yokohama
  5. Analysis of Age-Related Changes in the Damaraland Mole-Rat, a Long-Lived Rodent, Kurumi Ota, Yusuke Sakai; Koki Sekiguchi; Yusuke Suzuki; Nagaki Ohnuki; Miyuki Kanda; Keisuke Okuhara; Hidemasa Bono; Kaori Oka; Kyouko Miura, The 48th Annual Meeting of the Molecular Biology Society of Japan, 2025/12/03, Without Invitation, Japanese, The Molecular Biology Society of Japan, Pacifico Yokohama
  6. Meta-analysis of Temperature Stress Responses in Human and Mouse Using Public Transcriptome Datasets, Kotaro Uchida, Hidemasa Bono, The 48th Annual Meeting of the Molecular Biology Society of Japan, 2025/12/03, Without Invitation, Japanese, The Molecular Biology Society of Japan, Pacifico Yokohama
  7. Comprehensive Analysis of Hypoxia-Responsive Genes from Public Gene Expression Data by Meta-Analysis Using Machine Learning, Motoki Uno, Daniel Andrade; Hidemasa Bono, The 48th Annual Meeting of the Molecular Biology Society of Japan, 2025/12/03, Without Invitation, Japanese, The Molecular Biology Society of Japan, Pacifico Yokohama
  8. A genome assembly and gene functional annotation of Hiroshima-derived Pacific oyster (Magallana gigas), Misako Imai, Miyuki Kanda; Moriya Mino; Kazuhiko Koike; Keisuke Okuhara; Hidemasa Bono, The 48th Annual Meeting of the Molecular Biology Society of Japan, 2025/12/03, Without Invitation, Japanese, The Molecular Biology Society of Japan, Pacifico Yokohama
  9. RNAOffScan: Prediction software for CBE-Induced RNA Off-Target Risks using DNA Language Model, Kazuki Nakamae, Takayuki Suzuki; Sora Yonezawa; Kentaro Yamamoto; Taro Kakuzaki; Hiromasa Ono; Yuki Naito; Hidemasa Bono, The 48th Annual Meeting of the Molecular Biology Society of Japan, 2025/12/03, Without Invitation, Japanese, The Molecular Biology Society of Japan, Pacifico Yokohama
  10. A DNA language model-based approach for estimating CBE-induced RNA off-target risks, Kazuki Nakamae, Takayuki Suzuki; Sora Yonezawa; Kentaro Yamamoto; Taro Kakuzaki; Hiromasa Ono; Yuki Naito; Hidemasa Bono, The 54th Naito Conference on Forefront of Biology with Genome Editing, 2025/10/07, Without Invitation, English, THE NAITO FOUNDATION., Sapporo, Japan
  11. The mouthwash containing cetylpyridinium chloride suppresses gingivitis and dysbiosis during orthodontic treatment – a double-blind randomized controlled study -, Kado I, SHIBA F.; KUNIMATSU R.; YOSHIMI Y.; KOIZUMI Y.; OGASAWARA T.; ABE F.; OGASHIRA S.; OKAZAKI K.; TSAI S.; BONO H.; TANIMOTO K., The 84th Annual Meeting of the Japanese Orthodontic Society, 2025/09/29, Without Invitation, Japanese, The Japanese Orthodontic Society, Sapporo
  12. Development of Genome Editing Data Analysis Platform by Utilizing Public Databases, Hidemasa Bono, The 84th Annual Meeting of the Japanese Cancer Association, 2025/09/25, With Invitation, English, The Japanese Cancer Association, Kanazawa
  13. Construction of "Triterpene RDF": An RDF-based Database of Plant Enzymes and Transcription Factors Involved in Triterpene Biosynthesis, Keita Tamura, Hirokazu Chiba; Hidemasa Bono, The Annual Meeting of the Japanese Society for Plant Biotechnology, 2025/09/05, Without Invitation, Japanese, The Japanese Society for Plant Biotechnology, Kobe
  14. Development of a functional annotation workflow for fungal RNA-seq data, Nagisa Morihara, Hidemasa Bono, The 69th Annual Meeting of The Mycological Society of Japan, 2025/05/18, Without Invitation, English, The Mycological Society of Japan, Chiba
  15. Functional Annotation Workflow for Genome Editing of Novel Model Organisms, Hidemasa Bono, Biology of Genomes, 2025/05/06, Without Invitation, English, Cold Spring Harbor Laboratory, New York, USA
  16. New pathway analysis environment using WikiPathways mechanism, Ryo Nozu, Naoya Oec Shota Matsumoto Alexander R Pico Hidemasa Bono, Biology of Genomes, 2025/05/06, Without Invitation, English, Cold Spring Harbor Laboratory, New York, USA
  17. A Pathway Analysis Environment for Non-Model Organisms: Development and Application of Qpx, Ryo Nozu, Naoya Oec; Shota Matsumoto; Hidemasa Bono, Plant and Animal Genome Conference / PAG 32, 2025/01/10, Without Invitation, English, San Diego, CA, USA
  18. Exploration of Novel Heat Stress-Responsive Genes Using Public Database Resources and Structural Similarity Search, Sora Yonezawa, Hidemasa Bono, Plant and Animal Genome Conference / PAG 32, 2025/01/10, Without Invitation, English, San Diego, CA, USA
  19. Meta-Analysis of Public RNA-Seq Data reveals Novel Drought and Salt Stress-Responsive Genes in Oryza sativa and Corresponding Genes in Arabidopsis thaliana, Mitsuo Shintani, Hidemasa Bono, Plant and Animal Genome Conference / PAG 32, 2025/01/10, Without Invitation, English, San Diego, CA, USA
  20. Highly contiguous and well-annotated genome assemblies of Japanese insect strains using HiFi read sequencing, BRAKER, and Fanflow4insects: Case studies from the parasitic wasp Copidosoma floridanum and the common bed bug Cimex lectularius, Kouhei Toga, Hidemasa Bono, The 4th International Collaborative Workshop on Functional Genomics, Molecular Biology, and Biochemistry of Insect Cuticular Extracellular Matrix, 2024/12/26, With Invitation, English, The Center of Innovation for Bio-Digital Transformation (Bio-DX), Fuchu, Tokyo
  21. Opening remarks, Hidemasa Bono, The 4th International Collaborative Workshop on Functional Genomics, Molecular Biology, and Biochemistry of Insect Cuticular Extracellular Matrix, 2024/12/26, With Invitation, English, The Center of Innovation for Bio-Digital Transformation (Bio-DX), Fuchu, Tokyo
  22. A Quarter Century of Functional Annotation, Hidemasa Bono, RIKEN IMS Seminar, 2024/12/13, With Invitation, Japanese, RIKEN IMS, Yokohama
  23. Novel Bioinformatics Tools for Enhanced Safety and Activity Estimation of Genome Editing in Plant Science, Kazuki Nakamae, Saya Ide; Nagaki Ohnuki; Yoshiko Nakagawa; Keisuke Okuhara; Hidemasa Bono1,3, IPSR International Forum 2024 on Plant Stress Sciences by/for Junior Scientists, 2024/12/06, With Invitation, English, Okayama University, Institute of Plant Science and Resources, Kurashiki
  24. Exploring the phenotype-specific drought and salt stress responsive genes in Oryza sativa through meta-analysis of public transcriptome data, Mitsuo Shintani, Hidemasa Bono, IPSR International Forum 2024 on Plant Stress Sciences by/for Junior Scientists, 2024/12/06, With Invitation, English, Okayama University, Institute of Plant Science and Resources, Kurashiki
  25. Exploration of Target Genes for Parkinson's disease​ using Transcriptomics and Unknomics, Takayuki Suzuki, Hidemasa Bono, Biological Data Science, 2024/11/13, Without Invitation, English, Cold Spring Harbor Laboratory, New York, USA
  26. Application of Genome Editing to Plant Breeding, Hidemasa Bono, 146th meeting of Japanese Society of Breeding, 2024/09/23, With Invitation, Japanese, Japanese Society of Breeding, Higashi-Hiroshima, Japan
  27. Integrating public databases to identify heat stress-related genes for breeding in rice. Meta-analysis of transcriptome data and structural similarity search., Sora Yonezawa, Hidemasa Bono, 146th meeting of Japanese Society of Breeding, 2024/09/19, Without Invitation, Japanese, Japanese Society of Breeding, Higashi-Hiroshima, Japan
  28. Meta-analysis of public RNA-sequencing data of drought and salt stresses in different phenotypes of Oryza sativa, Mitsuo Shintani, Hidemasa Bono, 146th meeting of Japanese Society of Breeding, 2024/09/19, Without Invitation, Japanese, Japanese Society of Breeding, Higashi-Hiroshima, Japan
  29. Opening remarks and general introduction, Hidemasa Bono, XXVII International Congress of Entomology, 2024/08/25, With Invitation, English, Kyoto, Japan
  30. Genome analysis of the pupal parasitoid of the stable fly, Spalangia cameroni (Hymenoptera: Spalangiidae), Hiromitsu Araki, Kouhei Toga; Makito Shindo; Kazunori Matsuo; Hidemasa Bono, XXVII International Congress of Entomology (ICE2024), 2024/08/25, With Invitation, English, Kyoto, Japan
  31. Meta-analysis of publicly available RNA sequencing data of queens and workers in social hymenopterans and termites, Kouhei Toga, Hidemasa Bono, XXVII International Congress of Entomology (ICE2024), 2024/08/25, With Invitation, English, Kyoto, Japan
  32. Functional annotation for insect transcriptomes, Takeya Kasukawa, Hiroko Tabunoki; Hidemasa Bono, XXVII International Congress of Entomology (ICE2024), 2024/08/25, With Invitation, English, Kyoto, Japan
  33. PtWAVE: A Deconvolution Software of Sequencing Trace for the Detection of Large Indels, Saya Ide, Kazuki Nakamae; Nagaki Ohnuki; Yoshiko Nakagawa; Hidemasa Bono, The 9th Annual Meeting of the Japanese Society for Genome Editing, 2024/06/17, Without Invitation, Japanese, The Japanese Society for Genome Editing, Osaka, Japan
  34. Data driven metatranscriptome analysis of complex microbiome for genome editing, Ryo Mameda, Hidemasa Bono, The 9th Annual Meeting of the Japanese Society for Genome Editing, 2024/06/17, Without Invitation, Japanese, The Japanese Society for Genome Editing, Osaka, Japan
  35. Meta-analysis of transcriptomes for Selecting Genome Editing Target Genes in Livestock Breeding, Motoki Uno, Hidemasa Bono, The 9th Annual Meeting of the Japanese Society for Genome Editing, 2024/06/17, Without Invitation, Japanese, The Japanese Society for Genome Editing, Osaka, Japan
  36. Meta-analysis of public RNA-Seq for selection of genome editing targets for stress tolerance in rice, Mitsuo Shintani, Hidemasa Bono, The 9th Annual Meeting of the Japanese Society for Genome Editing, 2024/06/17, Without Invitation, Japanese, The Japanese Society for Genome Editing, Osaka, Japan
  37. Meta-analysis of heat stressed transcriptomes in rice for novel genome editing target genes, Sora Yonezawa, Hidemasa Bono, The 9th Annual Meeting of the Japanese Society for Genome Editing, 2024/06/17, Without Invitation, Japanese, The Japanese Society for Genome Editing, Osaka, Japan
  38. Selection of starvation-related genome editing target genes by meta-analysis of public databases, Jin Mitsunari, Hidemasa Bono, The 9th Annual Meeting of the Japanese Society for Genome Editing, 2024/06/17, Without Invitation, Japanese, The Japanese Society for Genome Editing, Osaka, Japan
  39. Uncovering New Insights into Sex Change Mechanisms: A Meta-analysis of Gonadal Transcriptomes in Protogynous Fish Species, Ryo Nozu, Mitsutaka Kadota, Masaru Nakamura, Shigehiro Kuraku, Hidemasa Bono, International Plant & Animal Genome / PAG 31, 2024/01/12, Without Invitation, English, San Diego, CA, USA
  40. Meta-analysis of heat stressed transcriptomes using public gene expression database for human, mouse, and rice, Sora Yonezawa, Hidemasa Bono, The 46th Annual Meeting of the Molecular Biology Society of Japan, 2023/12/06, Without Invitation, Japanese, The Molecular Biology Society of Japan, Kobe Port Island, Japan
  41. Meta-Analysis of Public RNA Sequencing Data of Abscisic Acid-Related Abiotic Stresses inArabidopsis thaliana, Mitsuo Shintani, Keita Tamura, Hidemasa Bono, The 46th Annual Meeting of the Molecular Biology Society of Japan, 2023/12/06, Without Invitation, Japanese, The Molecular Biology Society of Japan, Kobe Port Island, Japan
  42. Development of the candidate gene search method for oxidative stress in Parkinson's disease, Takayuki Suzuki, Hidemasa Bono, The 46th Annual Meeting of the Molecular Biology Society of Japan, 2023/12/06, Without Invitation, Japanese, The Molecular Biology Society of Japan, Kobe Port Island, Japan
  43. Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae), Kouhei Toga, Takuma Sakamoto, Miyuki Kanda, Keita Tamura, Keisuke Okuhara, Hiroko Tabunoki, Hidemasa Bono, The 46th Annual Meeting of the Molecular Biology Society of Japan, 2023/12/06, Without Invitation, Japanese, The Molecular Biology Society of Japan, Kobe Port Island, Japan
  44. Meta-analysis of gonadal transcriptome in protogynous fishes, Ryo Nozu, Mitsutaka Kadota, Masaru Nakamura, Shigehiro Kuraku, Hidemasa Bono, The 46th Annual Meeting of the Molecular Biology Society of Japan, 2023/12/06, Without Invitation, Japanese, The Molecular Biology Society of Japan, Kobe Port Island, Japan
  45. Bio-DX, multi-omic meta-analysis of transcriptomes and bibliome identifies novel hypoxia-inducible genes, Yoko Ono, Hidemasa Bono, The 46th Annual Meeting of the Molecular Biology Society of Japan, 2023/12/06, With Invitation, Japanese, The Molecular Biology Society of Japan, Kobe Port Island, Japan
  46. Identification of key factors for heat tolerance: genome sequencing and gene expression analysis of "hot-spring frog" Buergeria japonica, Takeshi Igawa, Kento Shiraga, Priambodo Bagus, Yuka Asaeda, Hidemasa Bono, Hajime Ogino, The 46th Annual Meeting of the Molecular Biology Society of Japan, 2023/12/06, With Invitation, Japanese, The Molecular Biology Society of Japan, Kobe Port Island, Japan
  47. Identification of feminization-related potential factors and processes in chicken primordial germ cells, Kennosuke Ichikawa, Yoshiaki Nakamura, Hidemasa Bono, Ryo Ezaki, Mei Matsuzaki, Mike McGrew, Hiroyuki Horiuchi, 11th Avian Model Systems Meeting, 2023/09/11, Without Invitation, English, The University of Portsmouth, UK
  48. A highly contiguous genome assembly of red perilla (Perilla frutescens) using PacBio HiFi sequencing data, Keita Tamura, Mika Sakamoto, Yasuhiro Tanizawa, Takako Mochizuki, Shuji Matsushita, Yoshihiro Kato, Takeshi Ishikawa, Keisuke Okuhara, Yasukazu Nakamura, Hidemasa Bono, The 40th Annual Meeting of the Japanese Society for Plant Biotechnology (Chiba), 2023/09/10, Without Invitation, Japanese, The Japanese Society for Plant Biotechnology, Chiba, Japan
  49. DANGER Analysis: A Novel Off-target Analysis Software to Assess Phenotypic Impact, Kazuki Nakamae, Hidemasa Bono, 8th Annual Meeting of The Japanese Society for Genome Editing, 2023/06/06, Without Invitation, Japanese, The Japanese Society for Genome Editing, Tokyo
  50. Genome Editing Meta-database for data analysis, Takayuki Suzuki, Hidemasa Bono, 8th Annual Meeting of The Japanese Society for Genome Editing, 2023/06/06, Without Invitation, Japanese, The Japanese Society for Genome Editing, Tokyo
  51. Meta-analysis of heat stressed transcriptomes using public gene expression database, Sora Yonezawa, Hidemasa Bono, 8th Annual Meeting of The Japanese Society for Genome Editing, 2023/06/06, Without Invitation, Japanese, The Japanese Society for Genome Editing, Tokyo
  52. Meta-Analysis of Public RNA Sequencing Data of Multiple Abiotic Stresses in Arabidopsis thaliana Provides New Insights into both ABA-Dependent and ABA-Independent Stress Responsive Genes, Mitsuo Shintani, Keita Tamura; Hidemasa Bono, The 33rd International Conference on Arabidopsis Research, 2023/06/05, Without Invitation, English, Chiba, Japan
  53. Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia, Keita Tamura, Hidemasa Bono, The 33rd International Conference on Arabidopsis Research, 2023/06/05, Without Invitation, English, Chiba, Japan
  54. De novo genome sequencing with PacBio HiFi reads, Hidemasa Bono, PacBio HIFI SEQUENCING EXPERIENCE TOUR, 2023/05/18, With Invitation, Japanese, PacBio, Toyonaka, Osaka
  55. A Highly Contiguous Genome Assembly of Red Perilla (Perilla frutescens) Using PacBio HiFi Sequencing Data, Keita Tamura, Mika Sakamoto Yasuhiro Tanizawa Takako Mochizuki Shuji Matsushita Yoshihiro Kato Takeshi Ishikawa Keisuke Okuhara Yasukazu Nakamura Hidemasa Bono, Plant & Animal Genome Conference (PAG30), 2023/01/13, Without Invitation, English, San Diego, CA, USA
  56. Genome Editing Meta-Database By Computationally Automated Knowledge Extraction from Literatures, Takayuki Suzuki, Hidemasa Bono, Plant & Animal Genome Conference (PAG30), 2023/01/13, Without Invitation, English, San Diego, CA, USA
  57. Meta-Analysis of Public Apis Genomes and Transcriptomes, Hidemasa Bono, Kakeru Yokoi, Plant & Animal Genome Conference (PAG30), 2023/01/13, Without Invitation, English, San Diego, CA, USA
    Related URL
  58. Meta-analysis of RNA-sequencing data in insects that show density-dependent phenotypic plasticity, Kouhei Toga, Kakeru Yokoi, Hidemasa Bono, The 45th Annual Meeting of the Molecular Biology Society of Japan, 2022/12/02, With Invitation, Japanese, Makuhari, Chiba, Japan
  59. Nanopore sequencing and assembly of edible green alga Ulva prolifera originated from Yoshinogawa river in Japan, Keita Tamura, Hidemasa Bono, The 45th Annual Meeting of the Molecular Biology Society of Japan, 2022/11/30, Without Invitation, Japanese, Makuhari, Chiba, Japan
  60. Genome Editing Metadatabase ~Knowledge Extraction from Literature~, Takayuki Suzuki, Hidemasa Bono, The 45th Annual Meeting of the Molecular Biology Society of Japan, 2022/11/30, Without Invitation, Japanese, Makuhari, Chiba, Japan
  61. Systematic Functional Annotation Workflow for Insects, Hidemasa Bono, Takuma Sakamoto, Takeya Kasukawa, Hiroko Tabunoki, The 45th Annual Meeting of the Molecular Biology Society of Japan, 2022/11/30, Without Invitation, Japanese, Makuhari, Chiba, Japan
  62. Genome sequencing of edible green alga Ulva prolifera originated from Yoshinogawa river in Japan using Oxford Nanopore Technologies' MinION sequencer, Keita Tamura, Hidemasa Bono, The 39th Annual Meeting of the Japanese Society for Plant Biotechnology, 2022/09/11, Without Invitation, Japanese, Japanese Society for Plant Biotechnology, Sakai
  63. Database of genome editing target genes, Takayuki Suzuki, Hidemasa Bono, 7th Annual Meeting of the Japanese Society for Genome Editing, 2022/06/07, Without Invitation, Japanese, The Japanese Society for Genome Editing, Online
  64. Current status and issues in the use of preprints and SNS in life science research, Hidemasa Bono, The 2nd SPARC Japan Seminar 2020, 2020/12/18, With Invitation, Japanese, National Institute of Informatics, Online
  65. Development of genome editing data analysis environment for cancer research, Hidemasa Bono, The 79th Annual Meeting of the Japanese Cancer Association, 2020/10/01, Without Invitation, English, Hiroshima
  66. RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes, Hiromasa Ono, Shuya Ikeda, Hidemasa Bono, International Plant & Animal Genome XXVIII (PAG), 2020/01/11, Without Invitation, English, San Diego, CA, USA
  67. Indices for NGS data and gene expression data registered in public databases, Hidemasa Bono, Tazro Ohta, Takeru Nakazato, International Plant & Animal Genome XXVIII (PAG), 2020/01/11, Without Invitation, English, San Diego, CA, USA, published
    Attached File's URL
  68. Introduction to DRY-intensive cancer research that makes full use of public databases, Hidemasa Bono, The 78th Annual Meeting of the Japanese Cancer Association, 2019/09/28, With Invitation, Japanese, Kyoto, Japan
  69. An integrated index of public gene expression databases and its application for meta-analysis of hypoxic transcriptomes, Hidemasa Bono, The Biology of Genomes, 2019/05/07, Without Invitation, English, Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory, New York, USA
  70. RefEx: a reference gene expression dataset as a web tool for the functional analysis of genes, Hiromasa Ono, Hidemasa Bono, International Plant & Animal Genome XXVII (PAG), 2019/01/12, Without Invitation, English, San Diego, CA, USA
  71. Systematic functional gene annotation pipeline for application to broad insect species, Hidemasa Bono, Hiroko Tabunoki, 2018 ESA, ESC and ESBC Joint Annual Meeting (Entomology 2018), 2018/11/11, Without Invitation, English, Vancouver, BC, Canada
  72. Utility of Preprints in Life Science, Hidemasa Bono, The 2nd SPARC Japan Seminar 2018 (Open Access Summit 2018) "Quality Control in the Age of Open Science", 2018/10/25, With Invitation, Japanese, SPARC JAPAN, Tokyo, Japan, other, 発表動画
    Related URL, Attached File's URL
  73. CRISPRdirect & GGGenome: Web-Based Software for CRISPR-Cas9 Guide RNA Design with Fast and Sensitive OffTarget Searches, Yuki Naito, Hidemasa Bono, International Plant & Animal Genome XXVI (PAG), 2018/01/13, Without Invitation, English, San Diego, CA, USA
  74. RefEx, a Reference Gene Expression Dataset As a Web Tool for the Functional Analysis of Genes, Hiromasa Ono, Hidemasa Bono, International Plant & Animal Genome XXVI (PAG), 2018/01/13, Without Invitation, English, San Diego, CA, USA
  75. Integrated Search of Public NGS Data for Non-Canonical Model Organisms, Takeru Nakazato, Tazro Ohta, Hidemasa Bono, International Plant & Animal Genome XXVI (PAG), 2018/01/13, Without Invitation, English, San Diego, CA, USA
  76. RefEx: a reference gene expression dataset as a web tool for the functional analysis of genes, Hidemasa Bono, Hiromasa Ono, Genome Informatics, 2017/11/01, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  77. Opening Greeting / Outline, Hidemasa Bono, The 2nd SPARC Japan Seminar 2017 (Open Access Summit 2017) "Preprint and Open Access", 2017/10/30, With Invitation, Japanese, SPARC Japan, National Institute for Informatics, other, 発表動画
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  78. Facilitating the use of Public High-Throughput Sequencing Data for Plant Omics Research, Hidemasa Bono, Tazro Ohta, Hiromasa Ono, Yuki Naito, Takeru Nakazato, Plant & Animal Genome (PAG) Asia, 2017/05/29, Without Invitation, English, Seoul, South Korea
  79. Differentially Expressed in Chondrocyte plays a crucial role in DNA damage response via transcriptional regulations, Keiji Tanimoto, Chiyo Oda, Hideaki Nakamura, Hidemasa Bono, Hiromasa Ono, Hidetaka Eguchi, The 1st International Symposium of the network-type Joint Usage/Research Center for Radiation Disaster Medical Science, 2017/02/21, Without Invitation, English, Hiroshima, Japan
  80. RefEx, a Reference Gene Expression Dataset As a Web Tool for the Functional Analysis of Genes, Hiromasa Ono, Hidemasa Bono, International Plant & Animal Genome XXV (PAG), 2017/01/14, Without Invitation, English, San Diego, CA, USA
  81. DBCLS SRA: Integrated Search of Public NGS Database, the Sequence Read Archive (SRA), and Its Relevant Databases, Takeru Nakazato, Tazro Ohta, Hidemasa Bono, International Plant & Animal Genome XXV (PAG), 2017/01/14, Without Invitation, English, San Diego, CA, USA
  82. Can the silkworm (Bombyx mori) be used as a human disease model?, Hiroko Tabunoki, Katsuhiko Ito, Hidemasa Bono, Takeshi Yokoyama, XXV International Congress of Entomology (ICE2016), 2016/09/25, Without Invitation, English, Orlando, FL, USA
  83. Bombyx mori superoxide dismutase 1 and 2 play a role as metamorphosis initiator, Yosui Nojima, Katsuhiko Ito, Hidemasa Bono, Takeshi Yokoyama, Hiroko Tabunoki, XXV International Congress of Entomology (ICE2016), 2016/09/25, Without Invitation, English, Orlando, FL, USA
  84. GGGenome & CRISPRdirect: web tools for designing CRISPR/Cas9 guide RNA, Yuki Naito, Hidemasa Bono, Genome Informatics 2016, 2016/09/19, Without Invitation, English, Hinxton, UK
  85. 'What is the best journal for my paper?' Open access journals and life science, Hidemasa Bono, The 1st SPARC Japan Seminar 2016 "Roads to Open Access for Japan", 2016/09/09, With Invitation, Japanese, SPARC Japan, National Institute of Informatics, Tokyo, Japan, published
    Related URL, Attached File's URL
  86. GGGenome & CRISPRdirect update: efficient off-target search tools for designing CRISPR/Cas guide RNA, Yuki Naito, Hidemasa Bono, RNA 2016, 2016/06/28, Without Invitation, English, Kyoto, Japan
  87. DBCLS SRA: Functional characterization of public NGS data, Takeru Nakazato, Tazro Ohta, Hidemasa Bono, International Plant & Animal Genome XXIV (PAG), 2016/01/09, Without Invitation, English, San Diego, CA, USA
  88. Functional Organization of Public Gene Expression Data, Hidemasa Bono, Hiromasa Ono, International Plant & Animal Genome XXIV (PAG), 2016/01/09, Without Invitation, English, San Diego, CA, USA
  89. CRISPRdirect: web-based tool for designing CRISPR/Cas guide RNA with reduced off-target sites, Yuki Naito, Kimihiro Hino, Kumiko Ui-Tei, Hidemasa Bono, CRISPR 2015, 2015/03/23, Without Invitation, English
  90. Facilitating the Use of Next-Gen Sequence Data for Data-Driven Biology, Hidemasa Bono, Tazro Ohta, Hiromasa Ono, Yuki Naito, Takeru Nakazato, International Plant & Animal Genome XXIII (PAG), 2015/01/10, Without Invitation, English
  91. Promoting the use of next-gen sequence data to maintain the research environment for data-driven biology, Hidemasa Bono, Tazro Ohta, Hiromasa Ono, Yuki Naito, Takeru Nakazato, Biological Data Science, 2014/11/05, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  92. RefEx: Reference Expression Dataset for cell and tissue transcriptome, Hiromasa Ono, Hidemasa Bono, Genome Informatics 2014, 2014/09/21, Without Invitation, English, Chrchill College, Cambridge, UK
  93. GGRNA and GGGenome: ultrafast search engines for nucleotide sequence database, Yuki Naito, Hidemasa Bono, Genome Informatics 2014, 2014/09/21, Without Invitation, English, Chrchill College, Cambridge, UK
  94. DBCLS SRA: Functional mining and characterization of public NGS data, Takeru Nakazato, Tazro Ohta, Hidemasa Bono, 13th European Conference on Computational Biology (ECCB'14), 2014/09/07, Without Invitation, English, Strasbourg, France
  95. Identification of key uric acid synthesis pathway in a unique mutant silkworm Bombyx mori, Hiroko Tabunoki, Katsuhiko Ito, Takeshi Yokoyama, Hidemasa Bono, Hajime Fugo, Seventh International Symposium on Molecular Insect Science, 2014/07/13, Without Invitation, English, Amsterdam (Netherlands)
  96. DDBJ meets DBCLS: Reorganizing public database core in Japan, Hidemasa Bono, NIG Retreat, 2014/07/04, With Invitation, English, Gotemba, Shizuoka
  97. Epigenetic Modification in Macrophages Critically Regulates HIF-1alpha Mediated Stress Responses, Hiroaki Semba, Norihiko Takeda, Takayuki Isagawa, Masaki Morioka, Hidemasa Bono, Hajime Abe, Katsura Soma, Katsuhiro Koyama, Ichiro Manabe, Issei Komuro and Ryozo Nagai, Keystone Symposia Conference Chromatin Mechanisms and Cell Physiology, 2014/03/23, Without Invitation, English, Oberstdorf (Germany)
  98. HIF-1alpha mediated glycolytic reprogramming regulates LPS induced macrophage activation, Hiroaki Semba, Norihiko Takeda, Takayuki Isagawa, Masaki Morioka, Hidemasa Bono, Hajime Abe, Katsura Soma, Katsuhiro Koyama, Ichiro Manabe, Issei Komuro and Ryozo Nagai, Keystone Symposia Conference Metabolism and Angiogenesis, 2014/03/16, Without Invitation, English, Whistler (Canada)
  99. Epigenetic Modification in Macrophages Critically Regulates HIF-1alpha Mediated Stress Responses, Hiroaki Semba, Norihiko Takeda, Takayuki Isagawa, Masaki Morioka, Hidemasa Bono, Hajime Abe, Katsura Soma, Katsuhiro Koyama, Ichiro Manabe, Issei Komuro, Ryozo Nagai, Keystone Symposia Conference Sensing and Signaling of Hypoxia: Interfaces with Biology and Medicine, 2014/01/07, Without Invitation, English, Colorado, USA
  100. TECHNOLOGY DEVELOPMENT OF DATABASE INTEGRATION TO MAKE FULL USE OF BIG DATA IN LIFESCIENCE, Hidemasa Bono, Tazro Ohta, Hiromasa Ono, Yuki Naito, Takeru Nakazato, Functional Genomics and Systems Biology, 2013/11/21, Without Invitation, English, Hinxton, UK
  101. GGRNA: a Google-like, ultrafast search engine for genes and transcripts, Yuki Naito, Hidemasa Bono, Genome Informatics, 2013/10/30, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  102. RefEx—Reference expression dataset for tissue transcriptome, Hiromasa Ono, Hidemasa Bono, Genome Informatics, 2013/10/30, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  103. Technology Development of Database Integration in Life Science, Hidemasa Bono, The 3rd SPARC Japan Seminar 2013 "Redefining the Impact of Research Outputs in the Age of Open Access: Current State of Reuse and Altmetrics", 2013/10/25, With Invitation, Japanese, SPARC Japan, Tokyo, Japan, published
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  104. Technology development of database integration to make sense of big data in lifescience, Hidemasa Bono, Tazro Ohta, Hiromasa Ono, Yuki Naito, Takeru Nakazato, QMB 2013, 2013/08/25, Without Invitation, English, Rydges Hotel Queenstown, New Zealand
    Related URL
  105. Updating the Survey of Read Archives - integrating GEO and BioProject with SRA, Takeru Nakazato, Tazro Ohta, Hidemasa Bono, Genome Informatics, 2012/09/06, Without Invitation, English, Robinson College, Cambridge, UK
  106. Sequence quality and metadata of all public NGSeq data in Sequence Read Archive, Tazro Ohta, Takeru Nakazato, Hidemasa Bono, Genome Informatics, 2012/09/06, Without Invitation, English, Robinson College, Cambridge, UK
  107. GGRNA: a Google-like, ultrafast search engine for genes and transcripts, Yuki Naito, Hidemasa Bono, Genome Informatics, 2012/09/06, Without Invitation, English, Robinson College, Cambridge, UK
  108. Technology development of database integration to make re-use of public biological data, Hidemasa Bono, ISMB2012, 2012/07/15, Without Invitation, English, Long Beach, CA, USA
  109. RefEx: Reference Expression Dataset for functional transcriptomics, Hiromasa Ono, Hidemasa Bono, ISMB2012, 2012/07/15, Without Invitation, English, Long Beach, CA, USA
  110. Technology development for database integration to make use of huge amount of public biological data, Hidemasa Bono, Akinori Yonezawa, Genome Informatics, 2011/11/02, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  111. SRAs: The Survey of Read Archives, Takeru Nakazato, Tazro Ohta, Akinori Yonezawa, Hidemasa Bono, Genome Informatics, 2011/11/02, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  112. RefEx: Reference Expression Dataset for comparative transcriptomics, Hiromasa Ono, Akinori Yonezawa, Hidemasa Bono, Genome Informatics, 2011/11/02, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  113. Bridging the gap between data from clinical medicine, genome epidemiology and pharmacological genomics -deployment of TIBCO Spotfire, Hidemasa Bono, Spotfire User meeting, 2011/10/07, With Invitation, Japanese, Tokyo, Japan
  114. Practical approach to make biological sense of huge amount of public data for transcripts, Hidemasa Bono, Hiromasa Ono, Tazro Ohta, Yuki Naito, Takeru Nakazato, Akinori Yonezawa, QMB 2011& QMB Bioinformatics, 2011/08/29, Without Invitation, English, Rydges Hotel Queenstown, NewZealand
  115. Visualization and sharing of DNA sequence data from next generation sequencing(NGS) technology by TIBCO Spotfire Web Player, Hidemasa Bono, Tenth workshop on Spotfire Users' meeting, 2011/07/01, With Invitation, Japanese, Osaka
  116. RefEx: Reference Expression Dataset for Functional Curation of Transcriptomes, Hiromasa Ono, Kosaku Okubo, Toshihisa Takagi, and Hidemasa Bono, Biocuration2010, 2010/10/11, Without Invitation, English, Tokyo, Japan
  117. RefEx: Reference expression dataset for practical use of gene expression data, Hidemasa Bono, Hiromasa Ono, Kousaku Okubo, Toshihisa Takagi, Genome Informatics, 2010/09/15, Without Invitation, English
  118. Functional indexing and curation of next-generation sequencing data, Takeru Nakazato, Hidemasa Bono, Toshihisa Takagi, Genome Informatics, 2010/09/15, Without Invitation, English, Hinxton, UK
  119. DDBJ Omics Archive with web-based read annotation pipeline: Data repository and high-throughput analysis for quantitative information from next-generation sequencers, Yuichi Kodama, Eli Kaminuma, Takako Mochizuki, Hidemasa Bono, Hideaki Sugawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura, MGED13: High Throughput Sequencing, 2010/07/13, Without Invitation, English, Boston, MA, USA
  120. DDBJ Read Archive and DDBJ Read Annotation Pipeline:An Archive Database and an Analyti- cal Tool for Next-Generation Sequence Data, Eli Kaminuma, Yuichi Kodama, Satoshi Saruhashi, Takeshi Konno, Takako Mochizuki, Hidemasa Bono, Hideaki Sugawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura, The 20th International Conference on Genome Informatics (GIW2009), 2009/12/14, Without Invitation, English, Yokohama, Japan
  121. Visualization of transcriptomes from next generation sequencers by TIBCO Spotfire, Hidemasa Bono, Spotfire User meeting, 2009/11/10, With Invitation, Japanese, Tokyo, Japan
  122. Functional organization of transcript sequences as gene expression data, Hidemasa Bono, Kousaku Okubo, Toshihisa Takagi, GENOME INFORMATICS, 2009/10/27, Without Invitation, English, Cold Spring Harbor, New York, USA
  123. Systematic organization of gene expression data in Japan, Hidemasa Bono, Eli Kaminuma, Yuichi Kodama, Yasukazu Nakamura, Kousaku Okubo, Toshihisa Takagi, 12th International MGED Meeting, focusing on translational genomics and high throughput sequencing, 2009/10/05, Without Invitation, English, Phoenix, Arizona, USA
  124. Different contribution of retroelements to intergenic transcription units, Saneyuki Higashino, Hidemasa Bono, Kunio Kikuchi, Yasunori Aizawa, 2nd International Conference and Workshop Genomic Impact of Eukaryotic Transposable Elements, 2009/02/06, Without Invitation, English, The Asilomar Conference Center, Pacific Grove, CA, USA
  125. Functional profiling of OMIM data using MeSH vocabulary, Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, Toshihisa Takagi, The 2008 Annual Conference of the Japanese Society for Bioinformatics (JSBi2008, 2008/12/15, Without Invitation, English, Osaka, Japan
  126. Life Science Database Portal Site: lifesciencedb.jp, Shin Kawano, Hidemasa Bono, Shoko Kawamoto, Kousaku Okubo, Toshihisa Takagi, 19th International Conference on Genome Informatics (GIW2008), 2008/12/01, Without Invitation, English, Gold Coast, Australia
  127. Functional organization of transcript sequences as gene expression data, Hidemasa Bono, Shoko Kawamoto, Kousaku Okubo, Toshihisa Takagi, 19th International Conference on Genome Informatics (GIW2008), 2008/12/01, Without Invitation, English, Gold Coast, Australia
  128. PRACTICAL ORGANIZATION OF SEQUENCE DATA AS GENE EXPRESSION DATA, Hidemasa Bono, Shoko Kawamoto, Kousaku Okubo, Toshihisa Takagi, Genome Informatics, 2008/09/10, Without Invitation, English, Hinxton, UK
  129. Japan started data-sharing center for publicly-funded biomedical science, Kousaku Okubo, Shoko Kawamoto, Hidemasa Bono, Toshihisa Takagi, Genome Informatics, 2008/09/10, Without Invitation, English, Hinxton, UK
  130. FUNCTIONAL ANALYSIS OF GROUPS OF GENES WITH MESH HIERARCHY, Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, Toshihisa Takagi, SYSTEMS BIOLOGY:GLOBAL REGULATION OF GENE EXPRESSION, 2008/03/27, Without Invitation, English, Cold Spring Harbor, New York, USA
  131. TogoTV - a broadcast station of tutorial movies about bioinformatics resources, Shin Kawano, Hiromoasa Ono, Hidemasa Bono, Shoko Kawamoto, Toshihisa Takagi, JSBi2007, 2007/12/17, Without Invitation, English, Tokyo, Japan
    Related URL
  132. YUZ: an environment for integration AND ANALYSIS of gene regulatory networks, Hidemasa Bono, Shin Kawano, Shoko Kawamoto, Toshihisa Takagi, GENOME INFORMATICS, 2007/11/01, Without Invitation, English, Cold Spring Harbor, New York, USA
  133. An approach to decifer gene regulatory networks from the federation of databases in life science, Hidemasa Bono, Shin Kawano, Shoko Kawamoto, Toshihisa Takagi, FUNCTIONAL GENOMICS & SYSTEMS BIOLOGY, 2007/10/10, Without Invitation, English, Hinxton, UK
  134. Expression data integration: application of SayaMatcher to practical microarray analysis, Hidemasa Bono, Receptor tyrosine kinase (RTK) training cource (Workshop on The Seventh International Conference on Systems Biology), 2006/10/12, With Invitation, English, Tokyo, Japan
  135. MINING GENE REGULATORY NETWORKS WITH SAYAMATCHER, Hidemasa Bono, Joint Cold Spring Harbor Laboratory/ Wellcome Trust Meeting on Genome Informatics, 2006/09/13, Without Invitation, English, Hinxton, Cambridge, UK
  136. Comparative transcriptomes under hypoxic stress, Hidemasa Bono, Cell Biology Summer Meeting (CBSM) 2006, 2006/07/08, With Invitation, English, Hakone, Kanagawa
  137. SayaMatcher: genome scale organization and systematic analysis of transcription factor binding sites, Hidemasa Bono, 20th IUBMB International Congress of Biochemistry and Molecular Biology, 2006/06/18, Without Invitation, English, Kyoto, Japan
  138. Comparative transcriptome analyses of metabolic pathway activity under hypoxic stress, Hidemasa Bono, Yutaka Nakachi, Ken Yagi, Itoshi Nikaido, Yasushi Okazaki, The 50th Anniversary of Oxygenases - Advances and Reflections - ( The 14th Takeda Science Foundation Symposium on Bioscience), 2006/04/10, Without Invitation, English, Kyoto, Japan
  139. Exploring transcription regulatory network with SayaMatcher, Hidemasa Bono, Omix Informatics Symposium, 2006/03/21, With Invitation, English, Tokyo, Japan
  140. Cross-species transcriptome comparisons under hypoxic stress, Hidemasa Bono, Ken Yagi, Yutaka Nakachi, Lorenza D'alessandro, Alessandra Gentile, Enzo Medico, Yoshihide Hayashizaki, Yasushi Okazaki, 28th Annual Meeting of the Molecular Biology Society of Japan, 2005/12/07, Without Invitation, Japanese, Fukuoka, Japan
  141. ChIP on chip assay for PPARgamma-regulated genes in macrophage, Yutaka Nakachi, Itoshi Nikaido, Ken Yagi, Mio Tonouchi, Hidemasa Bono, Yasushi Okazaki, 28th Annual Meeting of the Molecular Biology Society of Japan, 2005/12/07, Without Invitation, Japanese, Fukuoka, Japan
  142. Genome-wide linkage analysis of liver transcriptome and serum lipid content, Itoshi Nikaido, Minowa M., Yagi K., Sakuraba Y., Bono H., Gondo Y., Noda T., Shiroishi T., Hayashizaki Y., Okazaki Y., 28th Annual Meeting of the Molecular Biology Society of Japan, 2005/12/07, Without Invitation, Japanese, Fukuoka, Japan
  143. Gene expression linkage analysis to predict gene regulatory networks of fat metabolism, Itoshi Nikaido, Minowa O., Yagi K., Bono H., Noda T., Shiroishi T., Hayashizaki Y., Okazaki Y., 4th Annual meeting of the complex trait consortium, 2005/06/26, Without Invitation, English, Groningen, the Netherlands
  144. The study of transcriptional regulation by genome-wide analysis of nuclear receptor response elements, Hidemasa Bono, HGM2005 (HUGO's 10th Human Genome Meeting), 2005/04/18, Without Invitation, English, Kyoto, Japan
  145. Development of genome-scale oligonucleotide microarray system for the detection of binding sites of transcription factors, Yutaka Nakachi, Nikaido I., Yagi K., Tonouchi M., Bono H., Okazaki Y, HGM2005 (HUGO's 10th Human Genome Meeting), 2005/04/18, Without Invitation, English, Kyoto, Japan
  146. SayaMatcher: genome scale organization and systematic analysis of nuclear receptor response elements, Hidemasa Bono, Systems Biology: Global Regulation of Gene Expression, 2005/03/17, Without Invitation, English, Cold Spring Harbor, NY, USA
  147. Gene expression linkage analysis to predict gene regulatory networks of fat metabolism, Itoshi Nikaido, Ken Yagi, Hidemasa Bono, Yasushi Okazaki, Systems Biology: Global Regulation of Gene Expression, 2005/03/17, Without Invitation, English, Cold Spring Harbor, NY, USA
  148. SayaMatcher: in silico system for genome scale analysis of nuclear receptor responsive elements, Hidemasa Bono, 27th Annual Meeting of the Molecular Biology Society of Japan, 2004/12/08, Without Invitation, Japanese, Kobe, Japan
  149. Genetic architecture of gene regulatory network for lipid metabolism in mouse, Itoshi Nikaido, Ken Yagi, Hidemasa Bono, Yasushi Okazaki, 27th Annual Meeting of the Molecular Biology Society of Japan, 2004/12/08, Without Invitation, Japanese, Kobe, Japan
  150. Development of genome-scale oligonucleotide microarray for chromatin immunoprecipitation of transcription factors, Yutaka Nakachi, Itoshi Nikaido, Ken Yagi, Mio Tonouchi, Hidemasa Bono, Yasushi Okazaki, 27th Annual Meeting of the Molecular Biology Society of Japan, 2004/12/08, Without Invitation, Japanese, Kobe, Japan
  151. Systematic gene network analysis from genome scale prediction of transcription factor binding sites and microarray data, Hidemasa Bono, 2nd Spotfire Users Meeting, 2004/11/11, With Invitation, Japanese, Tokyo, Japan
  152. Genome scale organization and systematic in silico analysis of nuclear receptor responsive elements, Hidemasa Bono, 2nd symposium on Research Center for Genomic Medicine, Saitama Medical School, 2004/11/02, Without Invitation, Japanese, Saitama
  153. Systematic analysis of nuclear receptor responsive elements in a genome scale, Hidemasa Bono, 14th International Workshop Beyond the Identification of Transcribed Sequences: Functional, Expression and Evolutionary Analysis (BITS), 2004/10/29, Without Invitation, English, Kazusa, Chiba, Japan
  154. Genome scale organization and systematic analysis of nuclear receptor responsive elements, Hidemasa Bono, 12th International conference on Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference on Computational Biology (ECCB), 2004/07/31, Without Invitation, English, Glasgow, UK
  155. SayaMatcher, Hidemasa Bono, 2004 Bioinformatics Open Source Conference (BOSC), 2004/07/29, Without Invitation, English, Glasgow, UK
  156. Cross referencing framework for comparative functional genomics, Hidemasa Bono, Yasushi Okazaki, 26th Annual Meeting of the Molecular Biology Society of Japan, 2003/12/10, Without Invitation, Japanese, Kobe, Japan
  157. Cross referencing resource for functional genomics, Hidemasa Bono, Yasushi Okazaki, Comparative and Functional Genomics Workshop, 2003/11/02, Without Invitation, English, Hinxton Hall Conference Centre, The Wellcome Trust Genome Campus, Cambridgeshire, UK
  158. Practical application of GO annotation in the FANTOM project, Hidemasa Bono, International Workshop on Ontology and Genome, 2003/05/20, With Invitation, English, Tokyo, Japan
  159. Genome meets Transcriptome: Functional annotation of 60,770 mouse full-length cDNAs facilitates systematic gene expression profiling of the mouse transcriptome, Hidemasa Bono, Spotfire seminar, 2003/05/06, With Invitation, Japanese, Tokyo, Japan
  160. Comprehensive analysis of the mouse metabolome based on the transcriptome, Hidemasa Bono, Itoshi Nikaido, Takeya Kasukawa, Yoshihide Hayashizaki, Yasushi Okazaki, Systems Biology: Genomic Approaches to Transcriptional Regulation, 2003/03/06, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  161. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays, Yasushi Okazaki, Bono, H., Yagi, K., Kasukawa, T., Nikaido, I., Tominaga, N., Miki, R., Mizuno, Y., Tomaru, Y., Goto, H., Nitanda, H., Shimizu, D., Makino, H., Morita, T., Fujiyama, J., Sakai, T., Shimoji, T., RIKEN GER Group Members, and Hayashizaki, Y., Systems Biology: Genomic Approaches to Transcriptional Regulation, 2003/03/06, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  162. Metabolome analysis of mouse transcriptome, Hidemasa Bono, Kasukawa, T., Furuno, M., Nikaido, I., Hayashizaki, Y., and Okazaki, Y., 3rd International Conference on Systems Biology, 2002/12/13, Without Invitation, English
  163. Expression profiling of parietal endoderm cells and development of systems for large scale production of laminins, Hayashi, Y., Futaki, S., Yagi, K., Bono, H., Hayashizaki, Y., Okazaki, Y., and Sekiguchi, K., The Fifteenth Annual and International Meeting of Japanese Association for Animal Cell Technology (JAACT2002 FUCHU), 2002/11/11, Without Invitation, Japanese, Tokyo
  164. Research Environment Associated with READ (RIKEN Expression Array Database), Hidemasa Bono, 5th Microarray Gene Expression Data Society Meeting, 2002/09/24, Without Invitation, English, Tokyo, Japan
  165. Practical application of GO to RIKEN mouse cDNA clones, Hidemasa Bono, Kasukawa, T., Furuno, M., Nikaido, I., Hayashizaki, Y., Okazaki, Y., and FANTOM Consortium, Gene Ontology Users Meeting, 2002/09/09, Without Invitation, English
  166. Funtome to Transcriptome: Minging Gene Expression Patterns with FANTOM2, Hidemasa Bono, Kasukawa, T., Furuno, M., Nikaido, I., Hayashizaki, Y., Okazaki, Y., and FANTOM Consortium, 2nd Joint Cold Spring Harbor Laboratory / Wellcome Trust Conference on Genome Informatics, 2002/09/04, Without Invitation, English
  167. Progress to construct the mouse full-length cDNA encyclopedia, Piero Carninci, Shibata, K., Itoh, M., Arakawa, T., Ishii, Y., Yasunishi, A., Sasaki, D., Konno, H., Sato, K., Shiraki, T., Hirozane, T., Nakamura, M., Aizawa, K., Bono, H., Kondo, S., Yoshiki, A., Okazaki, Y., Kawai, J., and Hayashizaki, Y., Genome Sequencing & Biology, 2002/05/07, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  168. RIKEN mouse encyclopedia: full-length cDNA collection with well curated functional annotation (FANTOM2), Yasushi Okazaki, Hayashizaki, Y., RIKEN Phase1 group, Phase2 group, microarray group, PPI group, and FANTOM consortium, Genome Sequencing & Biology, 2002/05/07, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  169. FANTOM EPISODE II - Metabolome Analysis of the Clones, Hidemasa Bono, Nikaido, I., Hayashizaki, Y., and Okazaki, Y., FANTOM2 Cherry Blossum Meeting, 2002/04/29, Without Invitation, English, Yokohama, Japan
  170. Transcriptome analysis of RIKEN mouse cDNA library and microarray with FANTOM2 MATRICS, Hidemasa Bono, Yagi, K., Nikaido, I., Kasukawa, T., Carninci, P., Hayashizaki, Y., and Okazaki, Y., FANTOM2 Cherry Blossum Meeting, 2002/04/29, Without Invitation, English, Yokohama, Japan
  171. MaXML: Functional Annotation of Mouse cDNA clones in XML, Hidemasa Bono, Takeya Kasukawa, Workshop on Natural Language Processing and ontology building in biology, 2002/02/18, With Invitation, Japanese, Tokyo, Japan
  172. READ: RIKEN Expression Array Database, Hidemasa Bono, Kasukawa, T., Hayashizaki, Y. and Okazaki, Y., The Fourth International Meeting on Microarray Data Standards, Annotations, Ontologies, and Databases(MGED4), 2002/02/13, Without Invitation, English, Boston, MA, USA
  173. READ: Practical analysis system of mouse transcriptome with the FANTOM database, Hidemasa Bono, Kasukawa, T., Nikaido, I., Furuno, M., Hayashizaki, Y. and Okazaki, Y., The Twelfth International Conference on Genome Informatics (GIW2001), 2001/12/17, Without Invitation, English, Tokyo, Japan
  174. Metabolic reconstruction of mouse transcriptome using the RIKEN set of 18,816 mouse cDNA arrays, Hidemasa Bono, Matsuda, H., Kasukawa, T., Nikaido, I., Hayashizaki, Y. and Okazaki, Y., 2nd International Conference on Systems Biology (ICSB2001), 2001/11/04, Without Invitation, English, California Institute of Technology, Pasadena, USA
  175. cDNA clone-based practical analysis system of transcritome in the RIKEN mouse cDNA project: FANTOM and more, Hidemasa Bono, Kasukawa, T., Nikaido, I., Okazaki, Y., and Hayashizaki, Y., Joint Cold Spring Harbor Laboratory / Wellcome Trust Conference on Genome Informatics, 2001/08/08, Without Invitation, English
  176. Practical transcriptome analysis system in the RIKEN mouse cDNA project, Hidemasa Bono, Kasukawa, T., Nikaido, I., Okazaki, Y., and Hayashizaki, Y., ISMB2001: 9th International Conference on Intelligent Systems for Molecular Biology, 2001/07/21, Without Invitation, English, Copenhagen, Denmark
  177. Analysis of gene expression profiles between interaction protein pairs in M.musculus, Saito, R., Suzuki, H., Kagawa, I., Miki, R., Bono, H., Okazaki, Y., and Hayashizaki, Y., ISMB2001: 9th International Conference on Intelligent Systems for Molecular Biology, 2001/07/21, Without Invitation, English, Copenhagen, Denmark
  178. Open access to the FANTOM (Functional ANnoTation Of Mouse), Hidemasa Bono, Kasukawa, T., Nikaido, I., Matsuda, H., Okazaki, Y., and Hayashizaki, Y., BOSC2001: Bioinformatics Open Source Conference, 2001/07/19, Without Invitation, English, Copenhagen, Denmark
  179. MaXML: Functional Annotation of Mouse cDNA Sequences in XML, Takeya Kasukawa, Matsuda, H., Bono, H., Okazaki, Y., Kohtsuki, S., Hayashizaki, Y., and Hashimoto, A., NETTAB - Network Tools and Applications in Biology CORBA and XML, 2001/05/17, Without Invitation, English, Genova, Italy
  180. Mining cDNA microarray expression profiles of RIKEN full-length mouse clones with functional annotation, Hidemasa Bono, Miki, R., Kasukawa, T., Okazaki, Y., and Hayashizaki, Y., Genome Sequencing & Biology, 2001/05/09, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  181. Comprehensive selection of full-length cDNAs for the completion of the mouse cDNA encyclopedia, Piero Carninci, Shibata, K., Itoh, M., Konno, H., Shibata, Y., Sato, K., Hayatsu, N., Shiraki, T., Hirozane, T., Aizawa, K., Bono, H., Kondo, S., Kawai, J., Yoshiki, A., Kusakabe, M., Okazaki, Y., and Hayashizaki, Y., Genome Sequencing & Biology, 2001/05/09, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  182. Genome-wide search for genes contributing to the diabetes genetic background using differential expression profile of NOD congenic mice, Rika Miki, Bono, H., Carninci, P., Kiyosawa, H., Yamanaka, I., Lyons, P., Todd, J., Hayashizaki, Y. and Okazaki, Y., Genome Sequencing & Biology, 2001/05/09, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  183. Practical organization of RIKEN cDNA microarray data with FANTOM annotation, Hidemasa Bono, Miki, R., Kasukawa, T., Kohtsuki, S., Okazaki, Y., and Hayashizaki, Y., The Third International Meeting on Microarray Data Standards, Annotations, Ontologies, and Databases(MGED3), 2001/03/29, Without Invitation, English, Stanford, CA, USA
  184. Delineating biological cascades in vivo by microarray expression profiling using the 19K set of RIKEN full-length cDNAs, Rika Miki, Bono, H., *Okazaki, Y., and Hayashizaki, Y, The Third International Meeting on Microarray Data Standards, Annotations, Ontologies, and Databases(MGED3), 2001/03/29, Without Invitation, English, Stanford, CA, USA
  185. Practical Organization and Functional Annotation of RIKEN cDNA Microarray, Hidemasa Bono, Kasukawa, T., Miki, R., Kadota, K., Okazaki, Y., and Hayashizaki, Y., The Eleventh Workshop on Genome Informatics(GIW2000), 2000/12/18, Without Invitation, English, Tokyo, Japan
  186. FANTOM+: The interface for functional annotation of mouse cDNA, Hidemasa Bono, Kasukawa, T., Okido, T., Sakai, K., Furuno, M., Kohtsuki, S., Yoshida, K., Okazaki, Y., and Hayashizaki, Y., The Eleventh Workshop on Genome Informatics(GIW2000), 2000/12/18, Without Invitation, English, Tokyo, Japan
  187. Representing Functional Annotation of Mouse cDNA Sequences in XML, Takeya Kasukawa, Bono, H., Matsuda, H., Okazaki, Y., Kohtsuki, S. and Hayashizaki, Y., The Eleventh Workshop on Genome Informatics(GIW2000), 2000/12/18, Without Invitation, English, Tokyo, Japan
  188. READ: RIKEN Expression Array Database, Hidemasa Bono, Miki, R., Kadota, K., Okazaki, Y., and Hayashizaki, Y., The 14th International Mouse Genome Conference, 2000/11/06, Without Invitation, English, Narita, Chiba, Japan
  189. FANTOM+: web interface for the functional annotation of mouse, Takeya Kasukawa, Bono, H., Sakai, K., Furuno, M., Okido, T., Kohtsuki, S., Yoshida, K., Okazaki, Y., and Hayashizaki, Y., The 14th International Mouse Genome Conference, 2000/11/06, Without Invitation, English, Narita, Chiba, Japan
  190. Fluctuation and Identification of Housekeeping Genes on Large-Scale RIKEN Mouse cDNA Microarray, Koji Kadota, Okazaki, Y., Bono, H., Miki, R., Shimizu, K., and Hayashizaki, Y., The 14th International Mouse Genome Conference, 2000/11/06, Without Invitation, English, Narita, Chiba, Japan
  191. Large Coverage of the Mouse Genome with Cap-Selected Full-Length cDNAs, Piero Carninci, Shibata, K., Itoh, M., Konno, H., Shibata, Y., Sato, K., Hayatsu, N., Shiraki, T., Hirozane, T., Aizawa, K., Bono, H., Kadota, K., Kondo, S., Kawai, J., Yoshiki, A., Kusakabe, M., Muramatsu, M., Okazaki, Y. and Hayashizaki, Y., The 14th International Mouse Genome Conference, 2000/11/06, Without Invitation, English, Narita, Chiba, Japan
  192. Protein-Protein Interaction Panel Using RIKEN Mouse Full-Length cDNAs, Harukazu Suzuki, Fukunishi, Y., Kagawa, I., Bono, H., Saito, R., Oda, H., Endo, T., Kondo, S., Okazaki, Y. and Hayashizaki, Y., The 14th International Mouse Genome Conference, 2000/11/06, Without Invitation, English, Narita, Chiba, Japan
  193. Exploring Metabolic Pathways in 49 Tissues using RIKEN Full-Length Mouse 19K cDNA Microarray, Rika Miki, Bono, H., Mizuno, Y., Kadota, K., Tomaru, Y., Carninci, P., Shibata, K., Itoh, M., Kawai, J., Konno, H., Tokusumi, Y., Ishii, Y., Muramatsu, M., DeRisi, J., Iyer, V., Eisen, M., Brown, P.O., Okazaki, Y. and Hayashizaki, Y., The 14th International Mouse Genome Conference, 2000/11/06, Without Invitation, English, Narita, Chiba, Japan
  194. Efficient data processing method for large-scale cDNA microarray analysis, Koji Kadota, Okazaki, Y., Bono, H., Miki, R., Hayashizaki, Y., and Shimizu, K., 8th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2000/08/19, Without Invitation, English, San Diego, CA, USA
  195. Global gene expression profileing using RIKEN full-length mouse 17K cDNA microarray, Yasushi Okazaki, Miki, R., Mizuno, Y., Tomaru, Y., Kadota, K., Carninci, P., Shibata, K., Itoh, M., Kawai, J., Konno, H., Fukunishi, Y., Endo, T., Bono, H., Muramatsu, M., Yoshiki, J., Kusakabe, M., DeRisi, J., Iyer, V., Eisen, M., Brown, P.O., and Hayashizaki, Y., Genome Sequencing & Biology, 2000/05/10, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  196. Genome-scale gene expression analysis and pathway reconstruction in KEGG, Mitsuteru Nakao, Bono, H., Kawashima, S., Kamiya T., Sato, K., Goto, S., and Kanehisa, M., The Tenth Workshop on Genome Informatics (GIW'99), 1999/12/14, Without Invitation, English, Tokyo, Japan
  197. Cluster Analysis of Genome-wide Expression Profiles to Predict Gene Functions with KEGG, Hidemasa Bono, Mitsuteru Nakao, Minoru Kanehisa, The Microarray Meeting, 1999/09/22, Without Invitation, English, Mountain Shadows Marriott Resort Scottsdale, Arizona, USA
  198. Gene Function Prediction from Sequence and Expression Information with KEGG, Hidemasa Bono, Susumu Goto, Minoru Kanehisa, Genome Sequencing & Biology, 1999/05/19, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  199. Analysis of gene expression profiles using KEGG pathway maps and genome maps, Mitsuteru Nakao, Hidemasa Bono, Minoru Kanehisa, The 4th International Symposium on Biology: Computational Biology: Analysis of Complex Biological Processes, 1999/02/10, Without Invitation, English, Hamamatsu, Japan
  200. Systematic Prediction of Orthologous Units of Genes in the Complete Genomes, Hidemasa Bono, Goto, S., Fujibuchi, W., Ogata, H. and Kanehisa, M., The Ninth Workshop on Genome Informatics (GIW'98), 1998/12/10, Without Invitation, English, Tokyo, Japan
  201. Constructing and Annotating GENES Database in KEGG, Susumu Goto, Shirahashi, K., Okamoto, K., Ishida, H., Asanuma, S., Bono, H, Ogata, H., Fujibuchi, W., and Kanehisa, M., The Ninth Workshop on Genome Informatics (GIW'98), 1998/12/10, Without Invitation, English, Tokyo, Japan
  202. Database of two-component signal transduction system in KEGG, Hidemasa Bono, Minoru Kanehisa, 10th International Genome Sequencing and Analysis Conference, 1998/09/17, Without Invitation, English, Fontainebleau Hilton Resort, Miami Beach, Florida, USA
  203. Reconstruction of Microbial Metabolic Pathways in KEGG, Susumu Goto, Ogata, H., Bono, H., Fujibuchi, W., Sato, K., Kanehisa, M., 1998 Annual Meeting of the Society for Industrial Microbiology, 1998/08/09, Without Invitation, English, Adam's Mark Hotel, Denver, Colorado, USA
  204. Genome scale prediction of two-component signal transducers from the knowledge of regulatory interactions, Hidemasa Bono, Goto, S., Ogata, H., and Kanehisa, M., The Eighth Workshop on Genome Informatics (GIW'97), 1997/12/12, Without Invitation, English, Tokyo, Japan
  205. Gene Function Identification System based on the Metabolic Pathway Database, Hidemasa Bono, Ogata, H., Goto, S., Fujibuchi, W. and Kanehisa, M., Genome Mapping & Sequencing, 1997/05/14, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  206. Correlation between the chromosomal location of enzyme genes and the organization of metabolic pathways, Hiroyuki Ogata, Bono, H., Goto, S., Fujibuchi, W. and Kanehisa, M., Genome Mapping & Sequencing, 1997/05/14, Without Invitation, English, Cold Spring Harbor Laboratory, NY, USA
  207. Organizing and computing metabolic pathway data in terms of binary relations, Susumu Goto, Bono, H., Ogata, H., Fujubuchi, W., Nishioka, T., Sato, K., and Kanehisa, M., Pacific Symposium on Biocomputing '97, 1997/01/06, Without Invitation, English, Hawaii, USA
  208. Genome scale prediction of enzyme genes utilizing the knowledge of metabolic interactions, Hidemasa Bono, Ogata, H., Goto, S., and Kanehisa, M., The Seventh Workshop in Genome Informatics, 1996/12/02, Without Invitation, English, Tokyo, Japan
  209. Analysis of Binary Relations and Hierarchies of Enzymes in the Metabolic Pathways, Hiroyuki Ogata, Bono, H., Fujibuchi, W., Goto, S., and Kanehisa, M., The Seventh Workshop in Genome Informatics, 1996/12/02, Without Invitation, English, Tokyo, Japan
  210. Systematic prediction of enzyme genes by the metabolic pathway database, Hidemasa Bono, Goto, S., Ogata, H., and Kanehisa, M., Recent Advance in Genome Biology of Micro-organisms, 1996/10/27, Without Invitation, English, Makuhari, Chiba, Japan

Works, etc.

  1. AOE (All of gene expression), Hidemasa Bono, 2014/10, Database
    Related URL
  2. CRISPRdirect, Yuki Naito, Kimihiro Hino, Hidemasa Bono, Kumiko Ui-Tei, 2014/10, Web Service
    Related URL
  3. RefEx (Reference Expression dataset), Hiromasa Ono, Hidemasa Bono, 2011/10, Database
    Related URL
  4. GGRNA, Yuki Naito, Hidemasa Bono, 2011/05, Web Service
    Related URL
  5. DBCLS SRA, Tazro Ohta, Takeru Nakazato, Hidemasa Bono, 2011/04, Database
    Related URL
  6. Togo Picture Gallery, Hiromasa Ono, Hidemasa Bono, and others, 2011/04, The Others
    Related URL
  7. 統合TV, Shin Kawano, Hiromasa Ono, Hidemasa Bono, 2007/07, Educational Materials
    Related URL
  8. SayaMatcher, Hidemasa Bono, 2006/01, 2007/06, Software
    Related URL
  9. MotDB, Hidemasa Bono and others, 2006/02, 2011/03, Educational Materials
    Related URL
  10. READ (Riken Expression Array Database), Hidemasa Bono, Takeya Kasukawa, Yoshihide Hayashizaki, Yasushi Okazaki, 2002/01, 2003/03, Database
    Related URL
  11. FANTOM DB, Hidemasa Bono, Takeya Kasukawa, Masaaki Furuno, Yoshihide Hayashizaki, Yasushi Okazaki, 2002/01, Database
    Related URL

External Funds

Acceptance Results of Competitive Funds

  1. COI-NEXT, 2021, 2022
  2. ROIS-DS-JOINT, Development of the public data integration workflow for genome editing data analyses, 2020, 2021

Social Activities

History as Committee Members

  1. Members of the Public Relations Committee, 2024/08, 2026/06, The Japanese Society for Genome Editing
  2. Visiting Professor, 2020/04, 2025/03, Research Organization of Information and Systems
  3. Scientific Advisor, 2020/04, 2023/09, PtBio Inc.
  4. Member of the Information Steering Committee, 2022/06, National BioResource Project (NBRP)
  5. Insects Guest Editor, 2022/02, 2023/01
  6. IJMS Guest Editor, 2024/06, 2025/07
  7. IJMS Guest Editor, 2023/03, 2024/01
  8. BMC Genomics Associate Editor, 2008/12, 2017/09

Organizing Academic Conferences, etc.

  1. Insect Bio Digital Transformation (Insect BioDX) symposium in XXVII International Congress of Entomology, Organizer, 2024/08, 2024/08
  2. Insects genome and transcriptome data analysis symposium in XXVII International Congress of Entomology, Organizer, 2024/08, 2024/08
  3. The Japanese Association for Cancer and Hypoxia Research, 2015/06, 2015/06