Papers

業績

論文発表

2020年4月にbonohulabが立ち上がってからの構成員による主な教育・研究業績のうち、bonohulabが中心となって発表した論文発表をリストしています。 これ以外の業績は、学会・研究会発表をご覧ください。

bonohulabが中心となって発表した査読済み論文

  • 2024 
    • Toga K, Kimoto F, Fujii H, Bono H. Genome-wide Search for Gene Mutations likely Conferring Insecticide Resistance in the Common Bed Bug, Cimex lectularius. DOI: 10.3390/insects15100737
    • Nozu R, Kadota M, Nakamura M, Kuraku S, Bono H. Meta-analysis of gonadal transcriptomes in protogynous fishes provides novel perspective into sex change machinery. DOI: 10.1111/gtc.13166
    • Tamura K, Chiba H, Bono H. Triterpene RDF: Developing a database of plant enzymes and transcription factors involved in triterpene biosynthesis using the Resource Description Framework. DOI: 10.5511/plantbiotechnology.24.0312c
    • Suzuki T, Bono H. A systematic exploration of unexploited genes for oxidative stress in Parkinson’s disease. DOI: 10.1038/s41531-024-00776-1
    • Uno M, Bono H. Transcriptional Signatures of Domestication Revealed through Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data. DOI: 10.3390/ani14131998
    • Toga K, Sakamoto T, Kanda M, Tamura K, Okuhara K, Tabunoki H, Bono H. Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae). DOI: 10.1093/g3journal/jkae127
    • Shintani M, Tamura K, Bono H. Meta-Analysis of Public RNA Sequencing Data of Abscisic Acid-Related Abiotic Stresses in Arabidopsis thaliana. DOI: 10.3389/fpls.2024.1343787
  • 2023
    • Yonezawa S, Bono H. Meta-Analysis of Heat-Stressed Transcriptomes Using the Public Gene Expression Database from Human and Mouse Samples. DOI: 10.3390/ijms241713444
    • Nakamae K, Bono H. DANGER Analysis: Risk-Averse on/off-Target Assessment for CRISPR Editing Without a Reference Genome. DOI: 10.1093/bioadv/vbad114
    • Toga K, Bono H. Meta-Analysis of Public RNA Sequencing Data Revealed Potential Key Genes Associated with Reproductive Division of Labor in Social Hymenoptera and Termites. DOI: 10.3390/ijms24098353
    • Tamura K, Sakamoto M, Tanizawa Y, Mochizuki T, Matsushita S, Kato Y, Ishikawa T, Okuhara K, Nakamura Y, Bono H. A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan. DOI: 10.1093/dnares/dsac044
  • 2022
    • Suzuki T, Bono H. GEM: Genome Editing Meta-database, a dataset of genome editing related metadata systematically extracted from PubMed literatures. DOI:10.1016/j.ggedit.2022.100024
    • Nakamae K, Bono H. Genome editing and bioinformatics. DOI: 10.1016/j.ggedit.2022.100018
    • Yokoi K, Wakamiya T, Bono H. Meta-analysis of the public RNA-Seq data of the Western honeybee Apis mellifera to construct reference transcriptome data. DOI: 10.3390/insects13100931
    • Ono Y, Bono H. Exploratory meta-Analysis of hypoxic transcriptomes using a precise transcript reference sequence set. DOI: 10.26508/lsa.202201518
    • Toga K, Yokoi K, Bono H. Meta-Analysis of Transcriptomes in Insects Showing Density-Dependent Polyphenism. DOI: 10.3390/insects13100864
    • Tamura K, Bono H. Genome Sequence of the Edible Green Alga Ulva prolifera, Originating from the Yoshinogawa River in Japan DOI:10.1128/mra.00430-22
    • Tamura K, Bono H. Meta-analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia. DOI:10.3390/life12071079
    • Bono H, Sakamoto T, Kasukawa T, Tabunoki H. Systematic functional annotation workflow for insects. DOI: 10.3390/insects13070586 
  • 2021
    • Suzuki T, Ono Y, Bono H. Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes. DOI: 10.3390/biomedicines9121830
    • Ono Y, Bono H. Multi-Omic Meta-Analysis of Transcriptomes and the Bibliome Uncovers Novel Hypoxia-Inducible Genes. DOI: 10.3390/biomedicines9050582
    • Sakamoto T, Sasaki S, Yamaguchi N, Nakano M, Sato H, Iwabuchi K, Tabunoki H, Simpson RJ, Bono H. 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). DOI: 10.1186/s13104-021-05600-0
    • Bono H. Meta-Analysis of Oxidative Transcriptomes in Insects. DOI: 10.3390/antiox10030345

bonohulabメンバーが中心となって発表したプレプリント(査読なし)

  • 2024
    • Suzuki T, Bono H. Pipeline to explore information on genome editing using large language models and genome editing meta-database. DOI: 10.1101/2024.10.16.617154
    • Toga K, Kimoto F, Fujii H, Bono H. Genome-wide Search for Gene Mutations likely Conferring Insecticide Resistance in the Common Bed Bug, Cimex lectularius. DOI: 10.1101/2024.08.27.607709
    • Shintani M, Bono H. Meta-analysis of public RNA-sequencing data of drought and salt stresses in different phenotypes of Oryza sativa. DOI: 10.1101/2024.08.06.605779
    • Uno M, Bono H. Transcriptional Signatures of Domestication Revealed by Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data. DOI: 10.1101/2024.05.20.594049
    • Nakamae K, Ide S, Ohnuki N, Nakagawa Y, Okuhara K, Bono H. PtWAVE: A High-Sensitive deconvolution software of sequencing trace for the Detection of Large Indels in Genome Editing. DOI: 10.1101/2024.04.17.589649
    • Suzuki T, Bono H. A systematic exploration of unexploited genes for oxidative stress in Parkinson's disease. DOI:10.1101/2024.03.11.583425
    • Tamura K, Chiba H, Bono H. Triterpene RDF: Developing a database of plant enzymes and transcription factors involved in triterpene biosynthesis using the Resource Description Framework. DOI: 10.1101/2024.01.08.574260
  • 2023
    • Oec N, Hirota T, Nozu R, Bono H. Efforts to analyze pathways in non-model organisms. DOI: 10.37044/osf.io/spf3q
    • Toga K, Sakamoto T, Kanda M, Tamura K, Okuhara K, Tabunoki H, Bono H. Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae). DOI: 10.1101/2023.09.24.559078
    • Nakamae K, Kakuzaki T, Yamamoto K. Machine learning of transcriptome data treated with DNA base editor. DOI: 10.37044/osf.io/zytkj
    • Pico A, Ono H, Nozu R, Oec N, Bono H. BioHackJP 2023 Report R3: Expand the pathway analysis environment to non-model organisms. DOI: 10.37044/osf.io/4uskb
    • Nozu R, Kadota M, Nakamura M, Kuraku S, Bono H. Meta-analysis of gonadal transcriptomes in protogynous fishes provides novel perspective into sex change machinery. DOI: 10.1101/2023.07.09.545663
    • Yonezawa S, Bono H. Meta-analysis of heat-stressed transcriptomes using the public gene expression database from human and mouse samples. DOI: 10.1101/2023.04.30.537112
    • Shintani M, Tamura K, Bono H. Meta-Analysis of Public RNA Sequencing Data of Abscisic Acid-Related Abiotic Stresses in Arabidopsis thaliana. DOI: 10.1101/2023.04.17.537107
    • Nakamae K, Bono H. Danger Analysis: Risk-Averse on/off-Target Assessment for CRISPR Editing Without a Reference Genome. DOI: 10.1101/2023.03.11.531115
  • 2022
    • Toga K, Bono H. Meta-analysis of public RNA sequencing data of queens and workers in social Hymenoptera and termites. DOI: 10.1101/2022.11.20.516280
    • Suzuki T, Bono H. GEM: Genome Editing Meta-database. DOI:10.37044/osf.io/wd3bu
    • Tamura K, Sakamoto M, Tanizawa Y, Mochizuki T, Matsushita S, Kato Y, Ishikawa T, Okuhara K, Nakamura Y, Bono H. A highly contiguous genome assembly of red perilla (Perilla frutescens) domesticated in Japan. DOI:10.1101/2022.09.16.508052
    • Yokoi K, Wakamiya T, Bono H. Meta-analysis of the public RNA-Seq data of the Western honeybee Apis mellifera to construct reference transcriptome data. DOI:10.1101/2022.09.07.506879
    • Tamura K, Bono H. Meta-analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia. DOI:10.1101/2022.06.23.497423
    • Bono H, Sakamoto T, Kasukawa T, Tabunoki H. Systematic functional annotation workflow for insects. DOI:10.1101/2022.05.12.490705
    • Toga K, Yokoi K, Bono H. Meta-analysis of transcriptomes in insects showing density-dependent polyphenism. DOI: 10.1101/2022.05.09.490177
    • Ono Y, Bono H. Exploratory Meta-Analysis of Hypoxic Transcriptomes Using a Precise Transcript Reference Sequence Set. DOI: 10.1101/2022.05.01.489280
  • 2021

bonohulabメンバーが執筆した総説・書籍(査読なし)


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bonohulabLOGOhubchan

広島大学 理学部生物科学科・大学院統合生命科学研究科 ゲノム情報科学研究室 / ゲノム編集イノベーションセンター PtBio共同研究講座 バイオDX研究室

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