HIDEMASA BONO

Last Updated :2021/06/17

Affiliations, Positions
Graduate School of Integrated Sciences for Life, Professor (Special Appointment)
Web Site
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
Bioinformatics teacher in Doctoral Program for World-leading Innovative & Smart Education. As a life scientist, I am specially interested in reverse engineering of signaling network controlling energy metabolisms in an omic scale. I am expert in data-driven approach, especially for the utilization of public databases.

Basic Information

Major Professional Backgrounds

  • 2020/04/01, Hiroshima University, Graduate School of Integrated Sciences for Life, Project 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, 1997/04, 2000/03
  • Kyoto University, 1995/04, 1997/03
  • The University of Tokyo, 1991/04, 1995/03

Academic Degrees

  • Doctor of Science, Kyoto University

Research Fields

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

Research Keywords

  • bioinformatics
  • genome editing
  • transcriptome analysis
  • functional annotation
  • sequence analysis
  • public database
  • open source software
  • hypoxia
  • oxidative stress
  • functional genomics

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. 2021, Graduate Education (Doctoral Program) , 1Term, Research Plans in Life Science
  2. 2021, Graduate Education (Master's Program) , 1Term, Advanced Technologies for Life Science
  3. 2021, Graduate Education (Master's Program) , 1Term, Exercises in Biomedical Science A
  4. 2021, Graduate Education (Master's Program) , 2Term, Exercises in Biomedical Science A
  5. 2021, Graduate Education (Master's Program) , 3Term, Exercises in Biomedical Science B
  6. 2021, Graduate Education (Master's Program) , 4Term, Exercises in Biomedical Science B
  7. 2021, Graduate Education (Master's Program) , Academic Year, Research for Academic Degree Dissertation in Biomedial Science
  8. 2021, Graduate Education (Doctoral Program) , Academic Year, Research for Academic Degree Dissertation in Integrated Life Sciences
  9. 2021, Graduate Education (Master's Program) , 3Term, Bioinformatics

Research Activities

Academic Papers

  1. Polysulfide inhibits hypoxia-elicited hypoxia-inducible factor activation in a mitochondria-dependent manner, Mitochondrion, 10.1016/j.mito.2021.06.007, 20210613
  2. Reference transcriptome data in silkworm Bombyx mori, Insects, 12(6), 519, 20210603
  3. ★, Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes, Biomedicines, 9(5), 582, 20210520
  4. ★, 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
  5. Diversification of mineralocorticoid receptor genes in a subterranean rodent, the naked mole-rat, Journal of Molecular Endocrinology, 66(4), 299-311, 20210401
  6. ★, Multi-omic meta-analysis of transcriptomes and the bibliome uncovers GPR146 as the novel hypoxia-inducible gene, bioRxiv, 2021.03.29.433661, 20210330
  7. 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
  8. ★, Meta-Analysis of Oxidative Transcriptomes in Insects, Antioxidants, 10(3), 345, 20210225
  9. Meta-Analysis of Oxidative Transcriptomes in Insects, bioRxiv, 2021.02.01.427354, 20210202
  10. Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution, BMC Microbiology, 21, 35, 20210126
  11. 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
  12. FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs, Nucleic Acids Research, gkaa1054, 20201119
  13. Characterization of brown adipose tissue thermogenesis in the naked mole-rat (Heterocephalus glaber), a heterothermic mammal, Scientific Reports, 10, 19488, 20201110
  14. Construction of TUATinsecta database that integrated plant and insect database for screening phytophagous insect metabolic products with medicinal potential, Scientific Reports, 10, 17509, 20201015
  15. Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping, Genome Research, 30, 1060-1072, 20200727
  16. TogoEx: the integration of gene expression data, BioHackrXiv, 20200713
  17. Senescent cell death as an aging resistance mechanism in naked mole-rat, bioRxiv, 2020.07.02.155903, 20200703
  18. 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
  19. Characterization of brown adipose tissue thermogenesis in the naked mole-rat (Heterocephalus glaber), a poikilothermic mammal, bioRxiv, 20200429
  20. Detailed classification of mariner-like elements, class II transposable elements, in six Apis species based on Dromar, bioRxiv, 2020.04.15.035063, 20200416
  21. Thyroid Hormone Facilitates in Vitro Decidualization of Human Endometrial Stromal Cells via Thyroid Hormone Receptors, Endocrinology, bqaa049, 20200403
  22. BioHackathon 2015: Semantics of data for life sciences and reproducible research, F1000Research, 20200224
  23. GLIS1, a novel hypoxia-inducible transcription factor, promotes breast cancer cell motility via activation of WNT5A., Carcinogenesis, bgaa010, 20200212
  24. Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum., BMC Genomics, 21(1), 152, 20200211
  25. ★, All of gene expression (AOE): An integrated index for public gene expression databases., PLOS ONE, 15(1), e0227076, 20200124
  26. ★, Meta-Analysis of Hypoxic Transcriptomes from Public Databases., Biomedicines, 8(1), E10, 20200109
  27. Reference transcriptome data in silkworm Bombyx mori, bioRxiv, 20191017
  28. Superoxide dismutase down-regulation and the oxidative stress is required to initiate pupation in Bombyx mori., Scientific Reports, 9(1), 14693, 20191011
  29. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services, F1000Research, 20190923
  30. Apoptosis-mediated vasa down-regulation controls developmental transformation in Japanese Copidosoma floridanum female soldiers., Developmental Biology, 456(2), 226-233, 20190919
  31. Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping, bioRxiv, 20190714
  32. 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
  33. 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
  34. Suppression of mitochondrial oxygen metabolism mediated by the transcription factor HIF-1 alleviates propofol-induced cell toxicity., Scientific Reports, 8(1), 8987, 20180612
  35. Promotion of malignant phenotype after disruption of the three-dimensional structure of cultured spheroids from colorectal cancer., Oncotarget, 9(22), 15968-15983, 20180323
  36. Differentiated embryo chondrocyte plays a crucial role in DNA damage response via transcriptional regulation under hypoxic conditions., PLOS ONE, 13(2), e0192136, 20180221
  37. 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
  38. ★, RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes., Scientific Data, 4, 170105, 20170829
  39. HIF-1-mediated suppression of mitochondria electron transport chain function confers resistance to lidocaine-induced cell death., Scientific Reports, 7(1), 3816, 20170619
  40. ★, 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
  41. 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
  42. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals., Nucleic Acids Research, 45(D1), D737-D743, 20161027
  43. Tumour resistance in induced pluripotent stem cells derived from naked mole-rats., Nature Communications, 7, 11471, 20160510
  44. Can the silkworm (Bombyx mori) be used as a human disease model?, Drug Discoveries & Therapeutics, 10(1), 3-8, 20160207
  45. 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
  46. Gateways to the FANTOM5 promoter level mammalian expression atlas., Genome Biology, 16, 22, 20150105
  47. ★, CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites., Bioinformatics (Oxford, England), 31(7), 1120-1123, 20141120
  48. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains., Journal of Biomedical Semantics, 5(1), 5, 20140205
  49. Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive., 8(10), e77910, 20131022
  50. ★, 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
  51. GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts., Nucleic Acids Research, 40(Web Server issue), W592-W596, 20120528
  52. Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV., Briefings in Bioinformatics, 13(2), 258-268, 20110729
  53. Allie: a database and a search service of abbreviations and long forms., Database, bar013, 20110415
  54. Gene expression profiling in multipotent DFAT cells derived from mature adipocytes., Biochemical and Biophysical Research Communications, 407(3), 562-567, 20110316
  55. Id4, a new candidate gene for senile osteoporosis, acts as a molecular switch promoting osteoblast differentiation., PLOS Genetics, 6(7), e1001019, 20100708
  56. Gendoo: functional profiling of gene and disease features using MeSH vocabulary., Nucleic Acids Research, 37(Web Server issue), W166-W169, 20090604
  57. 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
  58. BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes., In Silico Biology, 8(1), 53-61, 20080101
  59. 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
  60. The transcriptional landscape of the mammalian genome., Science, 309(5740), 1559-1563, 20050901
  61. ★, SayaMatcher: genome scale organization and systematic analysis of nuclear receptor response elements., Gene, 364, 74-78, 20050824
  62. The study of metabolic pathways in tumors based on the transcriptome., Seminars in Cancer Biology, 15(4), 290-299, 20050801
  63. Analysis of gene networks during adipogenesis and osteoblastgenesis focusing on the crosstalk and redundant pathways, 49(17), 2965-2969, 20041215
  64. Identification and functional analysis of consensus androgen response elements in human prostate cancer cells., Biochemical and Biophysical Research Communications, 325(4), 1312-1317, 20041201
  65. Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library., Genomics, 83(6), 1012-1023, 20040601
  66. Integrative annotation of 21,037 human genes validated by full-length cDNA clones., PLOS Biology, 2(6), e162, 20040429
  67. 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
  68. MaXML: mouse annotation XML., In Silico Biology, 4(1), 7-15, 20031226
  69. 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
  70. Gene expression profile of normal lungs predicts genetic predisposition to lung cancer in mice., Carcinogenesis, 24(11), 1819-1826, 20030814
  71. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia., Genome Research, 13(6B), 1273-1289, 20030601
  72. Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling., Genome Research, 13(6B), 1402-1409, 20030601
  73. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays., Genome Research, 13(6B), 1318-1323, 20030601
  74. The mouse secretome: functional classification of the proteins secreted into the extracellular environment., Genome Research, 13(6B), 1350-1359, 20030601
  75. Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage., Genome Research, 13(6B), 1360-1365, 20030601
  76. Analysis of the mouse transcriptome for genes involved in the function of the nervous system., Genome Research, 13(6B), 1395-1401, 20030601
  77. G protein-coupled receptor genes in the FANTOM2 database., Genome Research, 13(6B), 1466-1477, 20030601
  78. ★, Comprehensive analysis of the mouse metabolome based on the transcriptome., Genome Research, 13(6B), 1345-1349, 20030601
  79. Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set., Genome Research, 13(6B), 1496-1500, 20030601
  80. Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure., Physiological Genomics, 12(3), 251-259, 20030206
  81. ★, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs., Nature, 420(6915), 563-573, 20021201
  82. Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data., Genome Research, 12(8), 1286-1293, 20020801
  83. 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
  84. ★, FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones., Nucleic Acids Research, 30(1), 116-118, 20020101
  85. ★, READ: RIKEN Expression Array Database., Nucleic Acids Research, 30(1), 211-213, 20020101
  86. Protein-protein interaction panel using mouse full-length cDNAs., Genome Research, 11(10), 1758-1765, 20011001
  87. ★, Functional annotation of a full-length mouse cDNA collection., Nature, 409(6821), 685-690, 20010201
  88. 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
  89. Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data., Physiological Genomics, 4(3), 183-188, 20010119
  90. KEGG: Kyoto Encyclopedia of Genes and Genomes., Nucleic Acids Research, 27(1), 29-34, 19990101
  91. Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG., Genome informatics. Workshop on Genome Informatics, 10, 94-103, 19990101
  92. Two-component response regulators from Arabidopsis thaliana contain a putative DNA-binding motif., Plant & Cell Physiology, 39(11), 1232-1239, 19981101
  93. ★, Reconstruction of amino acid biosynthesis pathways from the complete genome sequence., Genome Research, 8(3), 203-210, 19980301
  94. Systematic Prediction of Orthologous Units of Genes in the Complete Genomes., Genome informatics. Workshop on Genome Informatics, 9, 32-40, 19980101
  95. Organizing and computing metabolic pathway data in terms of binary relations., Pacific Symposium on Biocomputing, 175-186, 19970101
  96. Next-Generation Sequencing and Bioinformatics, Molecular Targeted Therapy of Lung Cancer, 97-115, 201701
  97. Functional interpretation of omics data by profiling genes and diseases using MeSH-controlled vocabulary., Advances in the Study of Genetic Disorders, 65-80, 2011
  98. 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
  99. Study of mouse metabolic pathways with riken full-length cdna microarrays, Perspectives in Gene Expression, 2003
  100. READ: Practical Analysis System of Mouse Transcriptome with the FANTOM Database, Genome Informatics, 12, 232-233, 2001
  101. Fully-automated spot recognition and quantification from cDNA microarray images, Proc. Int. Conf. Parallel and Distributed Processing Techniques and Applications, 3, 1291-1297, 2001
  102. FANTOM+: The Interface for Functional Annotation of Mouse cDNA, Genome Informatics, 11, 219-221, 2000
  103. Practical Organization and Functional Annotation of RIKEN cDNA Microarray, Genome Informatics, 11, 260-261, 2000
  104. Representing functional annotations of mouse cDNA sequences in XML, Genome Informatics, 11, 376-377, 2000
  105. Cluster analysis of genome-wide expression profiles to predict gene functions with KEGG, Nature Genetics, 23(3), 33-34, 199911
  106. Constructing and annotating GENES database in KEGG, Genome Informatics, 9, 226-227, 1998
  107. Genome Scale Prediction of Two-Component Signal Transducers from the Knowledge of Regulatory Interactions, Genome Informatics, 8, 260-261, 1997
  108. 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. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. '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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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)
  33. DDBJ meets DBCLS: Reorganizing public database core in Japan, Hidemasa Bono, NIG Retreat, 2014/07/04, With Invitation, English, Gotemba, Shizuoka
  34. 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)
  35. 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)
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. 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
  46. RefEx: Reference Expression Dataset for functional transcriptomics, Hiromasa Ono, Hidemasa Bono, ISMB2012, 2012/07/15, Without Invitation, English, Long Beach, CA, USA
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. Visualization of transcriptomes from next generation sequencers by TIBCO Spotfire, Hidemasa Bono, Spotfire User meeting, 2009/11/10, With Invitation, Japanese, Tokyo, Japan
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. Comparative transcriptomes under hypoxic stress, Hidemasa Bono, Cell Biology Summer Meeting (CBSM) 2006, 2006/07/08, With Invitation, English, Hakone, Kanagawa
  74. 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
  75. 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
  76. Exploring transcription regulatory network with SayaMatcher, Hidemasa Bono, Omix Informatics Symposium, 2006/03/21, With Invitation, English, Tokyo, Japan
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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
  86. 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
  87. 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
  88. 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
  89. 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
  90. 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
  91. 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
  92. SayaMatcher, Hidemasa Bono, 2004 Bioinformatics Open Source Conference (BOSC), 2004/07/29, Without Invitation, English, Glasgow, UK
  93. 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
  94. 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
  95. 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
  96. 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
  97. 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
  98. 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
  99. 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
  100. 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
  101. 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
  102. 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
  103. 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
  104. 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
  105. 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
  106. 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
  107. 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
  108. 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
  109. 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
  110. 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
  111. 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
  112. 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
  113. 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
  114. 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
  115. 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
  116. 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
  117. 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
  118. 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
  119. 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
  120. 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
  121. 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
  122. 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
  123. 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
  124. 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
  125. 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
  126. 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
  127. 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
  128. 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
  129. 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
  130. 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
  131. 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
  132. 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
  133. 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
  134. 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
  135. 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
  136. 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
  137. 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
  138. 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
  139. 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
  140. 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
  141. 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
  142. 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
  143. 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
  144. 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
  145. 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
  146. 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
  147. 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
  2. CRISPRdirect, Yuki Naito, Kimihiro Hino, Hidemasa Bono, Kumiko Ui-Tei, 2014/10, Web Service
  3. RefEx (Reference Expression dataset), Hiromasa Ono, Hidemasa Bono, 2011/10, Database
  4. GGRNA, Yuki Naito, Hidemasa Bono, 2011/05, Web Service
  5. DBCLS SRA, Tazro Ohta, Takeru Nakazato, Hidemasa Bono, 2011/04, Database
  6. Togo Picture Gallery, Hiromasa Ono, Hidemasa Bono, and others, 2011/04, The Others
  7. 統合TV, Shin Kawano, Hiromasa Ono, Hidemasa Bono, 2007/07, Educational Materials
  8. SayaMatcher, Hidemasa Bono, 2006/01, 2007/06, Software
  9. MotDB, Hidemasa Bono and others, 2006/02, 2011/03, Educational Materials
  10. READ (Riken Expression Array Database), Hidemasa Bono, Takeya Kasukawa, Yoshihide Hayashizaki, Yasushi Okazaki, 2002/01, 2003/03, Database
  11. FANTOM DB, Hidemasa Bono, Takeya Kasukawa, Masaaki Furuno, Yoshihide Hayashizaki, Yasushi Okazaki, 2002/01, Database

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. BMC Genomics Associate Editor, 2008/12, 2017/09

Organizing Academic Conferences, etc.

  1. The Japanese Association for Cancer and Hypoxia Research, 2015/06, 2015/06