{
 "journals": [
  {
   "n": 1,
   "citation": "Satomura K., Ogura A. “Molecular Divergence Between Two Geographically Overlapping Cryptic Crickets: Loxoblemmus campestris and L. sylvestris”, 2026, Ecology and Evolution",
   "year": 2026,
   "doi": "https://doi.org/10.1002/ece3.74457",
   "url": null,
   "topics": [
    "insects"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The study examines molecular divergence between Loxoblemmus campestris and L. sylvestris, two cricket species whose geographic ranges overlap despite being difficult to distinguish morphologically. The results clarify the genetic boundary between these cryptic species, extending the group's ongoing work on cricket diversity and evolution in Japan.",
    "ja": "形態的によく似て区別が難しいにもかかわらず分布域が重なる2種のコオロギ、Loxoblemmus campestrisとL. sylvestrisの間の分子的な分化を調べた。両種の遺伝的な境界を明らかにし、同グループが進めてきた日本産コオロギの多様性と進化に関する研究を発展させるものとなった。"
   }
  },
  {
   "n": 2,
   "citation": "Le BTN., Nguyen PT., Tran HS., Dang LT., Tran TTH., Ogura A., Yura K., Kim OTP. “Transcriptomic and Metagenomic Analyses of Snout Otter Clams (Lutraria rhynchaena) Infected with Swollen-Siphon Disease”, 2026, Journal of Shellfish Research, 45(2):241-254",
   "year": 2026,
   "doi": "https://doi.org/10.2983/035.045.0202",
   "url": null,
   "topics": [
    "symbiosis-virus"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Combining host transcriptomics with environmental metagenomics, the team profiled snout otter clams (Lutraria rhynchaena) affected by swollen-siphon disease. The data point to a host viral-immunity response alongside shifts in the surrounding microbial community, extending the group's earlier metagenomic work on this Vietnamese aquaculture disease.",
    "ja": "宿主のトランスクリプトーム解析と環境メタゲノム解析を組み合わせ、水管腫脹病に罹患したミルクイ（Lutraria rhynchaena）を解析した。宿主側のウイルス免疫応答と、周辺微生物群集の変化が示唆され、同グループがベトナムのこの養殖病害について進めてきたメタゲノム研究を発展させるものとなった。"
   }
  },
  {
   "n": 3,
   "citation": "Kamba S., Kuroki M., Takemura I., Tabata H., Minei R., Shimamoto M., Ogura A., Hasegawa M., Ishikawa M. “Enrichment of Lysobacter in a long-term organically managed agricultural field with low soilborne disease incidence”, 2026, Journal of Bioscience and Bioengineering",
   "year": 2026,
   "doi": "https://doi.org/10.1016/j.jbiosc.2026.07.002",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "biofunction",
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "In a field under long-term organic management, where soilborne disease is rare, the study found the biocontrol-associated bacterial genus Lysobacter to be enriched in the soil. The result links sustained organic practice to a disease-suppressive soil microbiome.",
    "ja": "長期にわたり有機管理され、土壌病害の発生が少ない農地の土壌において、生物防除に関わる細菌属Lysobacterが増加していることを見いだした。長期的な有機農法が、病害を抑制する土壌微生物叢の形成につながる可能性を示す。"
   }
  },
  {
   "n": 4,
   "citation": "Matano Y., Kubota H., Sakagami K., Nagai N., Ogura A. “Antioxidant and Renal Protective Effects of House Cricket (Acheta domesticus) Powder in a Streptozotocin-Induced Diabetic Nephropathy Model”, 2026, Applied Food Research, 6(1):101598",
   "year": 2025,
   "doi": "https://doi.org/10.1016/j.afres.2025.101598",
   "url": null,
   "topics": [
    "insects"
   ],
   "themes": [
    "biofunction"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using a streptozotocin-induced diabetic mouse model, the study tested house cricket (Acheta domesticus) powder as a functional food. The powder showed organ-specific antioxidant activity, notably in liver and kidney, and eased the renal dysfunction of diabetic nephropathy.",
    "ja": "ストレプトゾトシンで糖尿病を誘発したマウスを用い、食用コオロギ（イエコオロギ）粉末を機能性食品として評価した。粉末は肝臓や腎臓で臓器特異的な抗酸化作用を示し、糖尿病性腎症に伴う腎機能の低下を緩和した。"
   }
  },
  {
   "n": 5,
   "citation": "Kawakami Y., Shishioh N., Ogura A. “Development of the FP121 series: Hybrid proteins mimicking marine adhesive proteins with cell adhesion and proliferation activity”, 2025, Materials & Design, 255:114153",
   "year": 2025,
   "doi": "https://doi.org/10.1016/j.matdes.2025.114153",
   "url": null,
   "topics": [
    "bioadhesive"
   ],
   "themes": [
    "biofunction"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "The team engineered a new series of recombinant proteins, FP121, that fuse the sticky FP1 domain of mussel adhesive proteins with an EGF-containing FP2 domain. The hybrids adhered to cells without chemical modification and boosted cell proliferation and migration even in serum-free culture.",
    "ja": "ムール貝の接着タンパク質の粘着ドメインFP1と、EGFを含むFP2ドメインを融合させた組換えタンパク質FP121シリーズを新たに開発した。化学修飾なしで細胞に接着し、血清を含まない培養でも細胞の増殖と遊走を促進した。"
   }
  },
  {
   "n": 6,
   "citation": "Sustainable Cephalopod Aquaculture and Welfare Group, including Ogura A. “A balanced approach to the potential of octopus aquaculture”, 2025, Marine Policy, 179:106682",
   "year": 2025,
   "doi": "https://doi.org/10.1016/j.marpol.2025.106682",
   "url": null,
   "topics": [
    "cephalopod-eye"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "In this position paper, cephalopod specialists from dozens of institutions worldwide argue for a balanced view of octopus farming. Rather than blanket bans, they call for development under rigorous scientific and welfare oversight so the still-experimental field can contribute to sustainable food systems.",
    "ja": "世界各国の頭足類研究者による提言論文。タコ養殖を一律に禁止するのではなく、動物福祉と科学的な管理のもとで慎重に発展させるべきだと主張する。まだ実験段階のこの分野が持続可能な食料生産に貢献しうる可能性を指摘している。"
   }
  },
  {
   "n": 7,
   "citation": "Takekata H., Satomura K., Ogura A., Takemura A. “Chilling induces prompt and synchronised hatching after obligatory diapause in the subtropical cricket Cardiodactylus guttulus”, 2025, Physiological Entomology, 50",
   "year": 2025,
   "doi": "https://doi.org/10.1111/phen.12482",
   "url": null,
   "topics": [
    "insects"
   ],
   "themes": [
    "biofunction"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The subtropical cricket Cardiodactylus guttulus overwinters as diapausing eggs. Experiments showed that chilling at about 16°C for roughly one month is enough to break this obligatory egg diapause and trigger prompt, synchronised hatching, revealing the temperature cue that times its life cycle.",
    "ja": "亜熱帯性のコオロギCardiodactylus guttulusは卵で休眠して越冬する。約16℃で1か月ほど冷却すると義務的な卵休眠が打破され、速やかにそろって孵化することを示し、生活環を季節に同調させる温度の手がかりを明らかにした。"
   }
  },
  {
   "n": 8,
   "citation": "Nagai S., Minei R., Takemura I., Tabata H., Töpel M., Pinder M., Kourtchenko O., Lee-Kuo K., Van Nguyen N., Sildever S., Ogura A., Gojobori T. “The draft genome sequences of the cosmopolitan centric diatom, the genus Skeletonema”, 2025, Scientific Data, 12(1):1358",
   "year": 2024,
   "doi": "https://doi.org/10.1038/s41597-025-05432-8",
   "url": null,
   "topics": [
    "algae",
    "genome-tools"
   ],
   "themes": [
    "biofunction",
    "infobiology"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "The study reports draft genome assemblies and annotations for 11 strains across 9 species of Skeletonema, a globally common coastal diatom. The 40–69 Mbp genomes, with 15,000–21,000 predicted genes, provide a resource for studying the group's speciation, phylogeography and ecological success.",
    "ja": "沿岸域に広く分布する珪藻Skeletonema属について、9種11株のドラフトゲノム配列と注釈を報告した。約40〜69 Mbpのゲノムに1万5千〜2万余りの遺伝子を予測し、この属の種分化や系統地理、繁栄の解明に役立つ基盤資源を提供した。"
   }
  },
  {
   "n": 9,
   "citation": "Murata K., Kataoka K., Sanno R., Satomura K., Ogura A., Asahi T., Yura K., Suzuki T. “Complete mitochondrial genome sequences of two ground crickets, Dianemobius fascipes nigrofasciatus and Polionemobius taprobanensis (Orthoptera: Grylloidea: Trigonidiidae)”, 2023, Mitochondrial DNA Part B: Resources, 8(12):1311-1315",
   "year": 2023,
   "doi": "https://doi.org/10.1080/23802359.2023.2285400",
   "url": null,
   "topics": [
    "insects",
    "genome-tools"
   ],
   "themes": [
    "biofunction",
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The researchers sequenced the complete mitochondrial genomes of two Japanese ground crickets, Dianemobius fascipes nigrofasciatus and Polionemobius taprobanensis. Gene content and arrangement matched other Trigonidiidae, and amino-acid comparisons supported treating each as a distinct species, aiding cricket phylogenetics.",
    "ja": "日本産のコオロギ2種、シバスズとフタホシコオロギ類縁のPolionemobius taprobanensisの完全なミトコンドリアゲノムを解読した。遺伝子構成はコオロギ科と一致し、アミノ酸配列の比較から各々を独立した種とみなせることを支持し、系統・分類研究に貢献する。"
   }
  },
  {
   "n": 10,
   "citation": "Motomura K., Matsuzaka T., Shichino S., Ogawa T., Pan H., Nakajima T., Asano Y., Okayama T., Takeuchi T., Ohno H., Han SI., Miyamoto T., Takeuchi Y., Sekiya M., Sone H., Yahagi N., Nakagawa Y., Oda T., Ueha S., Ikeo K., Ogura A., Matsushima K., Shimano H. “Single-Cell Transcriptome Profiling of Pancreatic Islets From Early Diabetic Mice Identifies Anxa10 for Ca2+ Allostasis Toward β-Cell Failure”, 2024, Diabetes, 73(1):75-92",
   "year": 2023,
   "doi": "https://doi.org/10.2337/db23-0212",
   "url": null,
   "topics": [
    "single-cell"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "Using single-cell RNA sequencing of pancreatic islets from prediabetic and diabetic db/db mice, the study mapped β- and α-cell subpopulations and identified a new prediabetic marker, Anxa10. Anxa10 suppressed glucose-stimulated Ca2+ signalling and insulin secretion, pointing toward β-cell failure.",
    "ja": "糖尿病前期と発症後のdb/dbマウスの膵島を1細胞RNAシークエンスで解析し、β細胞・α細胞の亜集団を明らかにするとともに、新たな糖尿病前期マーカーAnxa10を同定した。Anxa10は細胞内カルシウム応答とインスリン分泌を抑え、β細胞の機能不全につながることを示した。"
   }
  },
  {
   "n": 11,
   "citation": "Díaz-MacAdoo D., Nagai S., Mata MT., Minei R., Ogura A., Riquelme C. “Comparative analysis of carotenoid synthesis and transcriptome of a microalga Chlorophyta MCH-35, potential lutein producer, in response to different quality light”, 2023, Algal Research, 74:103206",
   "year": 2023,
   "doi": "https://doi.org/10.1016/j.algal.2023.103206",
   "url": null,
   "topics": [
    "algae"
   ],
   "themes": [
    "biofunction"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "This study examined how light of different wavelengths affects the lutein-producing green microalga strain MCH-35, combining measurements of carotenoid synthesis with transcriptome analysis. It links specific light qualities to shifts in pigment production and the underlying gene-expression changes.",
    "ja": "ルテインを産生する緑藻の株MCH-35を対象に、波長の異なる光がカロテノイド合成に与える影響を、色素量の測定とトランスクリプトーム解析を組み合わせて調べた。特定の光質が色素産生と、それを支える遺伝子発現の変化にどう結びつくかを示している。"
   }
  },
  {
   "n": 12,
   "citation": "Nakagawa S., Sakaguchi S., Ogura A., Mineta K., Endo T., Suzuki Y., Gojobori T. “Current trends in RNA virus detection through metatranscriptome sequencing data”, 2023, FEBS Open Bio, 13(6):992-1000",
   "year": 2023,
   "doi": "https://doi.org/10.1002/2211-5463.13626",
   "url": null,
   "topics": [
    "symbiosis-virus"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "This review surveys how metatranscriptome sequencing of animal and environmental samples has uncovered many previously unknown RNA viruses, including work related to SARS-CoV-2. It introduces current bioinformatics tools and databases for RNA virus discovery and discusses links to endogenous viral elements in host genomes.",
    "ja": "動物や環境試料のメタトランスクリプトーム解析によって、未知のRNAウイルスが数多く見つかってきた流れを、SARS-CoV-2関連の研究も含めて概観した総説。RNAウイルス探索のための解析ツールやデータベースを紹介し、宿主ゲノム中の内在性ウイルス配列との関係も論じている。"
   }
  },
  {
   "n": 13,
   "citation": "Minei R., Aoki H., Ogura A., Kunisada T. “Compensatory gene expression potentially rescues impaired brain development in Kit mutant mice”, 2023, Scientific Reports, 13(1):4166",
   "year": 2023,
   "doi": "https://doi.org/10.1038/s41598-023-30032-0",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Mutations in the mouse Kit gene damage many tissues, yet the brain—where Kit is most expressed—shows few defects. Transcriptome analysis of mutant embryos found that ribosomal-protein and oxidative-phosphorylation genes were coordinately downregulated, suggesting a compensatory system that protects brain development.",
    "ja": "マウスのKit遺伝子の変異は多くの組織を傷害するが、最も強く発現する脳では異常が少ない。変異胚のトランスクリプトーム解析から、リボソームタンパク質と酸化的リン酸化の遺伝子が一斉に低下しており、脳の発生を守る代償的な仕組みが働いている可能性を示した。"
   }
  },
  {
   "n": 14,
   "citation": "Mori T., Machida K., Kudou Y., Kimishima M., Sassa K., Goto-Inoue N., Minei R., Ogura A., Kobayashi Y., Kamiya K., Nakaya D., Yamamoto N., Kashiwagi A., Kashiwagi K. “Novel predator-induced phenotypic plasticity by hemoglobin and physiological changes in the brain of Xenopus tropicalis”, 2023, Frontiers in Physiology, 14:1178869",
   "year": 2023,
   "doi": "https://doi.org/10.3389/fphys.2023.1178869",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Xenopus tropicalis tadpoles show little outward change when facing a novel predator. Combining RNA-seq and metabolomics of the brain, the study found a shift toward glycolytic ATP production, raised antioxidant defences, and increased hemoglobin, indicating that the tadpoles adapt by tuning brain physiology rather than body shape.",
    "ja": "ネッタイツメガエルのオタマジャクシは、初めて出会う捕食者に対して外見をほとんど変えない。脳のRNA-seqと代謝解析から、解糖系によるATP産生への傾き、抗酸化能の上昇、ヘモグロビンの増加が見られ、体形ではなく脳の生理機能を調整して適応することが示された。"
   }
  },
  {
   "n": 15,
   "citation": "Matano Y., Sakagami K., Nojiri Y., Nomura K., Masuda A., Moriike Y., Yamamoto A., Nagai N.*, Ogura A. “Toxicity of House Cricket (Acheta domesticus) in Mice ” 2022, Clinical & Medical Biochemistry, Vol. 08 Iss. 04 No: 1000128",
   "year": 2022,
   "doi": null,
   "url": "https://www.walshmedicalmedia.com/open-access/toxicity-of-house-cricket-emacheta-domesticusem-in-mice-113380.html",
   "topics": [
    "insects"
   ],
   "themes": [
    "biofunction"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "To assess the safety of edible house crickets, mice were given cricket powder orally at up to 3,000 mg/kg for 14 or 90 days, with no differences in body weight, blood chemistry or organ weights versus controls. In vitro and in vivo genotoxicity tests were also negative, indicating no toxicity at these doses.",
    "ja": "食用イエコオロギの安全性を調べるため、マウスに最大3,000 mg/kgの粉末を14日または90日間経口投与したが、体重・血液生化学・臓器重量に対照群との差はなかった。培養細胞と動物での遺伝毒性試験も陰性で、この用量では毒性がないことを示した。"
   }
  },
  {
   "n": 16,
   "citation": "Khedkar G., Kambayashi C., Tabata H., Takemura I., Minei R., Ogura A., Kurabayashi A. “The draft genome sequence of the Brahminy blindsnake Indotyphlops braminus”, 2022, Scientific Data, 9(1):410",
   "year": 2022,
   "doi": "https://doi.org/10.1038/s41597-022-01530-z",
   "url": null,
   "topics": [
    "genome-tools"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "This study reports the first draft genome of the Brahminy blindsnake, the only known snake that reproduces solely by parthenogenesis. The 1.86-Gbp assembly, with over 23,000 genes, provides a resource for studying snake evolution and how parthenogenetic vertebrates arise.",
    "ja": "ヘビ類で唯一、単為生殖のみで繁殖するブラーミニメクラヘビの最初のドラフトゲノムを解読した研究。約1.86Gbp、2万3千超の遺伝子を含むこのゲノムは、ヘビの進化や単為生殖する脊椎動物の成り立ちを解明する基盤となる。"
   }
  },
  {
   "n": 17,
   "citation": "Nakajima Y., Ogura A. “Genomics and effective trait candidates of edible insects”, 2022, Food Bioscience, 48:101793",
   "year": 2022,
   "doi": "https://doi.org/10.1016/j.fbio.2022.101793",
   "url": null,
   "topics": [
    "insects"
   ],
   "themes": [
    "biofunction"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "A review of how genome-wide DNA sequencing can support insect farming for food and feed. It surveys the genomics of edible insects and discusses candidate traits, such as growth and nutritional quality, that could guide breeding of this sustainable, resource-efficient protein source.",
    "ja": "食用・飼料用の昆虫養殖をゲノム解読で後押しする可能性を論じた総説。食用昆虫のゲノム情報を整理し、成長や栄養価など育種に役立つ形質候補を検討することで、資源効率が高く持続可能なタンパク源としての昆虫利用を展望する。"
   }
  },
  {
   "n": 18,
   "citation": "Sato T., Goto-Inoue N., Kimishima M., Toyoharu J., Minei R., Ogura A., Nagoya H., Mori T. “A novel ND1 mitochondrial DNA mutation is maternally inherited in growth hormone transgenesis in amago salmon (Oncorhynchus masou ishikawae)”, 2022, Scientific Reports, 12(1):6720",
   "year": 2022,
   "doi": "https://doi.org/10.1038/s41598-022-10521-4",
   "url": null,
   "topics": [
    "genome-tools"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "In growth-hormone-transgenic amago salmon that showed hypoglycemia, the authors found deletion mutations concentrated in the mitochondrial ND1 gene, inherited maternally across generations. The results suggest GH transgenesis can induce heritable mitochondrial mutations that alter cellular energy production.",
    "ja": "低血糖を示した成長ホルモン遺伝子導入アマゴを解析し、母系で世代を超えて受け継がれる欠失変異がミトコンドリアND1遺伝子に集中することを見いだした。成長ホルモン導入が、細胞のエネルギー産生を変える遺伝性のミトコンドリア変異を誘発しうることを示唆する。"
   }
  },
  {
   "n": 19,
   "citation": "Yin X., Kamba S., Yamamoto K., Ogura A., Wandera EA., Shah MM., Seto H., Kondo T., Ichinose Y., Hasegawa M. “Analysis of Environmental and Pathogenic Bacteria Attached to Aerosol Particles Size-Separated with a Metal Mesh Device”, 2022, International Journal of Environmental Research and Public Health, 19(9)",
   "year": 2022,
   "doi": "https://doi.org/10.3390/ijerph19095773",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using palm-sized collectors fitted with metal mesh devices of differing pore sizes, the team size-separated airborne particles at a Kenyan farm and identified attached bacteria by next-generation sequencing. Microbial composition varied with particle size, and lung-disease-causing mycobacteria were detected.",
    "ja": "孔径の異なる金属メッシュデバイスを備えた手のひらサイズの採取器で、ケニアの農場の空気中粒子をサイズ別に分離し、付着細菌を次世代シークエンサーで同定した。細菌組成は粒子サイズによって異なり、肺疾患を起こす非結核性抗酸菌も検出された。"
   }
  },
  {
   "n": 20,
   "citation": "Asano Y., Ogawa T., Shichino S., Ueha S., Matsushima K., Ogura A. “Time-Series Analysis of Gene Correlation Networks based on Single-Cell Transcriptome Data”, 2021, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2134-2141",
   "year": 2021,
   "doi": "https://doi.org/10.1109/BIBM52615.2021.9669412",
   "url": null,
   "topics": [
    "single-cell"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The authors present a computational method to build gene correlation networks from single-cell transcriptome data and to visualize and rank how those networks change over time. They demonstrate it on time-series single-cell data from mice with silica-induced pulmonary fibrosis.",
    "ja": "一細胞トランスクリプトームデータから遺伝子相関ネットワークを構築し、その時系列変化を可視化・ランク付けする計算手法を提案した研究。シリカ粒子で肺線維症を誘導したマウスの経時的な一細胞データに適用し、手法の有効性を示した。"
   }
  },
  {
   "n": 21,
   "citation": "Jiang L., Kon T., Chen C., Ichikawa R., Zheng Q., Pei L., Takemura I., Nsobi LH., Tabata H., Pan H., Omori Y., Ogura A. “Whole-genome sequencing of endangered Zhoushan cattle suggests its origin and the association of MC1R with black coat colour”, 2021, Scientific Reports, 11(1):17359",
   "year": 2021,
   "doi": "https://doi.org/10.1038/s41598-021-96896-2",
   "url": null,
   "topics": [
    "genome-tools"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "Whole-genome sequencing of the endangered, isolated Zhoushan cattle showed they are genetically close to Bos indicus cattle of southeastern China. Comparison with black-coated Angus cattle pointed to an MC1R mutation (p.F195L) as a likely cause of the breed's distinctive dark black coat.",
    "ja": "絶滅危惧の隔離集団である舟山牛を全ゲノム解読し、中国南東部のコブウシに遺伝的に近いことを示した。黒毛のアンガス牛との比較から、この品種特有の濃い黒毛にはMC1R遺伝子の変異(p.F195L)が関与する可能性を指摘した。"
   }
  },
  {
   "n": 22,
   "citation": "Kon T., Pei L., Ichikawa R., Chen C., Wang P., Takemura I., Ye Y., Yan X., Guo B., Li W., Lauden HN., Tabata H., Pan H., Omori Y., Ogura A., Jiang L. “Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation”, 2021, Scientific Reports, 11(1):11235",
   "year": 2021,
   "doi": "https://doi.org/10.1038/s41598-021-90645-1",
   "url": null,
   "topics": [
    "genome-tools"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Resequencing 198 large yellow croaker, an economically vital fish in East Asia, revealed population structure reflecting wild versus farmed and regional environments, with declining effective population sizes. Genomic regions under selection highlighted genes linked to adaptation to different living environments.",
    "ja": "東アジアで重要な養殖魚キグチ(フウセイ)198個体を再解読し、天然・養殖や地域の環境を反映した集団構造と有効集団サイズの減少を明らかにした。選択を受けたゲノム領域から、異なる生息環境への適応に関わる遺伝子群を浮かび上がらせた。"
   }
  },
  {
   "n": 23,
   "citation": "Kamba S., Ogura A., Miura Y., Hasegawa M. “Enrichment of Uncommon Bacteria in Soil by Fractionation Using a Metal Mesh Device”, 2021, Analytical Sciences, 37:1295-1300",
   "year": 2021,
   "doi": "https://doi.org/10.2116/analsci.21P042",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using metal mesh devices of four pore sizes to fractionate bacteria from two soils, the authors showed by metagenomics that the fractions became enriched for all eight tested compound-degrading species. The device can concentrate low-abundance bacteria from environmental samples.",
    "ja": "4種の孔径の金属メッシュデバイスで2種類の土壌の細菌を分画し、メタゲノム解析により、試験した8種の有機物分解菌すべてが特定の画分に濃縮されることを示した。環境試料中の低頻度の細菌を濃縮できる手法である。"
   }
  },
  {
   "n": 24,
   "citation": "Jiang L., Pei L., Wang P., Liu L., Li G., Liu B., Lu Z., Tabata H., Pan H., Ogura A. “Molecular Characterization and Evolution Analysis of Two Forms of TLR5 and TLR13 Genes Base on Larimichthys crocea Genome Data”, 2020, International Journal of Genomics, 2020:4895037",
   "year": 2020,
   "doi": "https://doi.org/10.1155/2020/4895037",
   "url": null,
   "topics": [
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Drawing on the large yellow croaker genome, the study characterized the immune receptor genes TLR5 (membrane and soluble forms) and TLR13, describing their sequences, tissue expression, subcellular localization, and evolutionary relationships. The findings deepen understanding of innate immunity in teleost fish.",
    "ja": "キグチのゲノム情報をもとに、免疫受容体遺伝子TLR5(膜型・可溶型)とTLR13を解析し、配列・組織発現・細胞内局在・進化的関係を明らかにした。硬骨魚類の自然免疫におけるTLRの役割の理解を深める成果である。"
   }
  },
  {
   "n": 25,
   "citation": "Kim OTP., Kagaya Y., Tran HS., Minei R., Tran TTH., Duong HTT., Le BTN., Dang LT., Kinoshita K., Ogura A., Yura K. “A novel circular ssDNA virus of the phylum Cressdnaviricota discovered in metagenomic data from otter clams (Lutraria rhynchaena)”, 2020, Archives of Virology, 165(12):2921-2926",
   "year": 2020,
   "doi": "https://doi.org/10.1007/s00705-020-04819-9",
   "url": null,
   "topics": [
    "symbiosis-virus"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "From metagenomic sequences of diseased otter clam siphon tissue, the authors identified a novel circular single-stranded DNA virus. Genomic and phylogenetic analyses placed it within the phylum Cressdnaviricota, only distantly related to known members.",
    "ja": "シフォンが腫れる病気のミルクイ(オッタークラム)の組織のメタゲノム配列から、新規の環状一本鎖DNAウイルスを発見した。ゲノムの特徴と系統解析により、既知種とは遠縁ながらCressdnaviricota門に属するウイルスと判定した。"
   }
  },
  {
   "n": 26,
   "citation": "Bonadè M., Ogura A., Corre E., Bassaglia Y., Bonnaud-Ponticelli L. “Diversity of Light Sensing Molecules and Their Expression During the Embryogenesis of the Cuttlefish (Sepia officinalis)”, 2020, Frontiers in Physiology, 11:521989",
   "year": 2020,
   "doi": "https://doi.org/10.3389/fphys.2020.521989",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Tracing the evolution of light-sensing genes in molluscs, the study identified six opsins, two cryptochromes, and a visual arrestin in the cuttlefish and tracked their expression during embryogenesis. Several were active in the eyes, and some also in skin and nervous tissue, revealing broader light-detection machinery than previously known.",
    "ja": "軟体動物の光受容遺伝子の進化を追い、コウイカで6種のオプシン、2種のクリプトクロム、視覚アレスチンを同定し、胚発生中の発現を調べた。多くは眼で、一部は皮膚や神経組織でも働いており、これまで知られていたより多様な光受容の仕組みが存在することを示した。"
   }
  },
  {
   "n": 27,
   "citation": "Yoshida MA., Imoto J., Kawai Y., Funahashi S., Minei R., Akizuki Y., Ogura A., Nakabayashi K., Yura K., Ikeo K. “Genomic and Transcriptomic Analyses of Bioluminescence Genes in the Enope Squid Watasenia scintillans”, 2020, Marine Biotechnology, 22(6):760-771",
   "year": 2020,
   "doi": "https://doi.org/10.1007/s10126-020-10001-8",
   "url": null,
   "topics": [
    "cephalopod-eye"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "By analyzing genome and transcriptome data of the sparkling enope (firefly) squid, the authors obtained a draft genome and characterized its bioluminescence genes. They found RNA editing diversifies the luciferase transcripts and identified two distinct luciferase types, possibly linked to the squid's varied light colors.",
    "ja": "発光するホタルイカのゲノムとトランスクリプトームを解析し、ドラフトゲノムを得て発光関連遺伝子を特徴づけた。RNA編集がルシフェラーゼの転写産物を多様化させることを見いだし、発光の色の多様さに関わりうる2種類のルシフェラーゼを同定した。"
   }
  },
  {
   "n": 28,
   "citation": "Kataoka K., Minei R., Ide K., Ogura A., Takeyama H., Takeda M., Suzuki T., Yura K., Asahi T. “The Draft Genome Dataset of the Asian Cricket Teleogryllus occipitalis for Molecular Research Toward Entomophagy”, 2020, Frontiers in Genetics, 11:470",
   "year": 2020,
   "doi": "https://doi.org/10.3389/fgene.2020.00470",
   "url": null,
   "topics": [
    "insects"
   ],
   "themes": [
    "biofunction"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "A resource paper presenting a draft genome for the Asian cricket Teleogryllus occipitalis, built by hybrid assembly of long and short reads together with the complete mitochondrial genome, to support molecular research on crickets as an edible-insect (entomophagy) food source.",
    "ja": "アジア産コオロギ（Teleogryllus occipitalis）のドラフトゲノムを、ロングリードとショートリードのハイブリッドアセンブリで構築し、ミトコンドリアゲノムも併せて報告したデータ論文。食用昆虫としての分子研究の基盤を提供する。"
   }
  },
  {
   "n": 29,
   "citation": "Kagaya Y., Minei R., Duong HTT., Le BTN., Dang LT., Tran TTH., Nguyen HT., Kinoshita K., Yura K., Ogura A., Kim OTP. “Metagenome Sequences from the Environment of Diseased Otter Clams, Lutraria rhynchaena, from a Farm in Vietnam”, 2020, Microbiology Resource Announcements, 9(2)",
   "year": 2020,
   "doi": "https://doi.org/10.1128/mra.01068-19",
   "url": null,
   "topics": [
    "symbiosis-virus"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The authors report metagenome sequences of microorganisms extracted from the siphon tissue of otter clams (Lutraria rhynchaena) affected by swollen-siphon disease on a Vietnamese farm. The bacterial and viral data likely include the disease-causing agent.",
    "ja": "ベトナムの養殖場で「水管腫脹病」に罹患したミルクイ（Lutraria rhynchaena）の水管組織から抽出した微生物のメタゲノム配列を報告。細菌・ウイルス由来配列には病原体が含まれると考えられる。"
   }
  },
  {
   "n": 30,
   "citation": "*Asano Y., Ogura A., Shichino S., Ueha S., Matsushima K. “Analysis of Time Sequence Data of Single-cell Transcriptome using Gene Correlation Networks”, 2019, JCIM, Vol.39th, ROMBUNNO.4-F-1-03",
   "year": 2019,
   "doi": null,
   "url": null,
   "topics": [
    "single-cell"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "A methodological study on analyzing time-series single-cell transcriptome data by constructing gene correlation networks, aiming to capture how gene co-expression relationships change over time during biological processes.",
    "ja": "単一細胞トランスクリプトームの時系列データを、遺伝子相関ネットワークを構築して解析する手法研究。生命現象の過程で遺伝子の共発現関係が時間とともにどう変化するかを捉えることを目指す。"
   }
  },
  {
   "n": 31,
   "citation": "Ogura A., Akizuki Y., Imoda H., Mineta K., Gojobori T., Nagai S. “Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom”, 2018, BMC Genomics, 19(1):765",
   "year": 2018,
   "doi": "https://doi.org/10.1186/s12864-018-5144-5",
   "url": null,
   "topics": [
    "algae",
    "evolution"
   ],
   "themes": [
    "biofunction",
    "evolution"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "The team sequenced the genome and transcriptome of the diatom Skeletonema costatum, a dominant cause of harmful algal blooms (red tides) in Japan. They found that bloom-forming diatoms have gained extra copies of genes for oxidative-stress and cytokinin responses, enabling intense expression during blooms.",
    "ja": "日本の有害赤潮の主因となる珪藻Skeletonema costatumのゲノムと発現を解読。赤潮を起こす珪藻では酸化ストレス応答やサイトカイニン応答に関わる遺伝子が重複して増え、増殖時に強く発現できるようになっていることを示した。"
   }
  },
  {
   "n": 32,
   "citation": "Minei R., Hoshina R., Ogura A. “De novo assembly of middle-sized genome using MinION and Illumina sequencers”, 2018, BMC Genomics, 19(1):700",
   "year": 2018,
   "doi": "https://doi.org/10.1186/s12864-018-5067-1",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "A methods study establishing a low-cost, high-quality de novo assembly pipeline for middle-sized genomes by combining Oxford Nanopore MinION long reads with Illumina short reads, demonstrated on the symbiotic alga Chlorella variabilis for comparative genomics of plastid acquisition.",
    "ja": "Oxford Nanopore MinIONのロングリードとIlluminaのショートリードを組み合わせ、中規模ゲノムを低コストかつ高品質にデノボアセンブリするパイプラインを確立。共生藻Chlorella variabilisで実証し、葉緑体獲得の比較ゲノム研究に道を開いた。"
   }
  },
  {
   "n": 33,
   "citation": "Komiyama T., Ogura A., Kajiwara T., Okada Y., Kobayashi H. “Analysis of Candidate Idarubicin Drug Resistance Genes in MOLT-3 Cells Using Exome Nuclear DNA”, 2018, Genes, 9(8)",
   "year": 2018,
   "doi": "https://doi.org/10.3390/genes9080390",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using exome analysis of nuclear DNA from the leukemia cell line MOLT-3 and its idarubicin-resistant derivative, the study identified candidate resistance mutations in polymerase- and lipid-associated genes, and found the resistant cells took up the drug more slowly.",
    "ja": "白血病細胞株MOLT-3とそのイダルビシン耐性株の核DNAエクソーム解析から、ポリメラーゼや脂質関連遺伝子に耐性候補変異を同定。耐性株では薬剤の取り込みが遅いことも見いだした。"
   }
  },
  {
   "n": 34,
   "citation": "Tabata H., Koinui A., Ogura A., Nishihara D., Yamamoto H. “A novel nuclear localization signal spans the linker of the two DNA-binding subdomains in the conserved paired domain of Pax6”, 2018, Genes & Genetic Systems, 93(2):75-81",
   "year": 2018,
   "doi": "https://doi.org/10.1266/ggs.17-00057",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Through in ovo electroporation in the developing chick midbrain, the authors mapped the nuclear localization signal (NLS) within the paired domain of the developmental master gene Pax6, showing it is an unusually long 36-residue signal spanning the linker between the PAI and RED DNA-binding subdomains.",
    "ja": "発生の司令塔遺伝子Pax6のペアードドメインにある核移行シグナル（NLS）を、ニワトリ中脳への in ovo エレクトロポレーションで解析。NLSは異例に長い36残基で、PAIとREDサブドメインをつなぐリンカー部分にまたがることを示した。"
   }
  },
  {
   "n": 35,
   "citation": "Yonezawa K., Nakata K., Minei R., Ogura A. “DASE2: differential alternative splicing variants estimation method without reference genome, and comparison with mapping strategy”, 2017, International Journal of Data Mining and Bioinformatics, 18:56-73",
   "year": 2017,
   "doi": "https://doi.org/10.1504/IJDMB.2017.086101",
   "url": null,
   "topics": [
    "genome-tools"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Presents DASE2, a method to estimate differential alternative splicing variants directly from de novo transcriptome assemblies without a reference genome. Compared against a mapping-based strategy, it detects splicing at a comparable level, making it useful for non-model organisms.",
    "ja": "参照ゲノムを使わず、デノボアセンブリしたトランスクリプトームから差次的な選択的スプライシング変異体を推定する手法DASE2を提案。マッピング法と同等の検出性能を示し、非モデル生物のスクリーニングに有用とした。"
   }
  },
  {
   "n": 36,
   "citation": "Komiyama T., Ogura A., Hirokawa T., Zhijing M., Kamiguchi H., Asai S., Miyachi H., Kobayashi H. “Analysis to Estimate Genetic Variations in the Idarubicin-Resistant Derivative MOLT-3”, 2016, International Journal of Molecular Sciences, 18(1)",
   "year": 2017,
   "doi": "https://doi.org/10.3390/ijms18010012",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Comparing the leukemia cell line MOLT-3 with its idarubicin-resistant derivative via complete mitochondrial and nuclear DNA analysis, the study identified distinguishing genetic variations, including a mitochondrial ND3 mutation and a stop-codon mutation in the GALNT2 gene that may contribute to drug resistance.",
    "ja": "白血病細胞株MOLT-3とそのイダルビシン耐性株を、ミトコンドリアと核DNAの全解析で比較。ミトコンドリアND3変異や、薬剤耐性に関与しうるGALNT2遺伝子の終止コドン変異など、両者を分ける遺伝的変異を同定した。"
   }
  },
  {
   "n": 37,
   "citation": "Masakiyo, Y., Ogura, A., Ichihara, K., Yura, K., *Shimada, S. “Candidate key genes for low-salinity adaptation identified by RNA-seq comparison between closely related Ulvarian species in marine and brackish waters.”, 2017, Algal Resources, 9(2), 61-76",
   "year": 2017,
   "doi": null,
   "url": "https://www.jstage.jst.go.jp/article/jsap/9/2/9_61/_article",
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using RNA-seq to compare closely related Ulva green-algae species living in marine versus brackish water, the study identified candidate genes underlying adaptation to low salinity, shedding light on how these algae tolerate reduced-salt environments.",
    "ja": "海水域と汽水域に生息する近縁なアオサ属（Ulva）緑藻をRNA-seqで比較し、低塩分環境への適応に関わる候補遺伝子を同定。これらの藻類が低塩分環境に耐えるしくみの手がかりを得た。"
   }
  },
  {
   "n": 38,
   "citation": "Yonezawa K., Mori T., Shigeno S., Ogura A. “DASE: Condition-specific differential alternative splicing variants estimation method without reference genome sequence, and its application to non-model organisms”, 2016, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 324-329",
   "year": 2016,
   "doi": "https://doi.org/10.1109/BIBM.2016.7822540",
   "url": null,
   "topics": [
    "genome-tools"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Introduces DASE, a method to estimate condition-specific differential alternative splicing variants from RNA-seq data without a reference genome sequence, and applies it to non-model organisms for which annotated exon/intron information is unavailable.",
    "ja": "参照ゲノム配列を使わずにRNA-seqデータから条件特異的な選択的スプライシング変異体を推定する手法DASEを提案。エクソン・イントロン情報がそろわない非モデル生物への応用を示した。"
   }
  },
  {
   "n": 39,
   "citation": "R Minei, T Mori, A Ogura, “Brain transcriptome analysis of predator-specific stress response in Rana pirica”, 2016, GENES & GENETIC SYSTEMS 91 (6), 353-353",
   "year": 2016,
   "doi": null,
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "A conference report on brain transcriptome analysis of the frog Rana pirica, examining how gene expression in the brain changes in response to predator-specific stress as part of predator-induced plasticity.",
    "ja": "カエルRana piricaの脳トランスクリプトーム解析に関する学会報告。捕食者誘導性の可塑性の一環として、捕食者特有のストレスに応じて脳内の遺伝子発現がどう変化するかを調べた。"
   }
  },
  {
   "n": 40,
   "citation": "Komiyama T., Lin M., Ogura A. “aCGH Analysis to Estimate Genetic Variations among Domesticated Chickens”, 2016, BioMed Research International, 2016:1794329",
   "year": 2016,
   "doi": "https://doi.org/10.1155/2016/1794329",
   "url": null,
   "topics": [
    "genome-tools"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using array comparative genomic hybridization, the study compared whole genomes of six chicken breeds bred for cultural purposes such as fighting or long-crowing. It identified 782 regions shaped by human selection, and found the diversified genes differed from those in food breeds like broilers and layers.",
    "ja": "闘鶏や長鳴きなど文化的な目的で改良された6品種のニワトリの全ゲノムをアレイCGH法で比較し、人為選択の痕跡を示す782の領域を同定した。多様化した遺伝子は、ブロイラーや採卵鶏など食用品種のものとは異なることも明らかになった。"
   }
  },
  {
   "n": 41,
   "citation": "Koga H., Fujitani H., Morino Y., Miyamoto N., Tsuchimoto J., Shibata TF., Nozawa M., Shigenobu S., Ogura A., Tachibana K., Kiyomoto M., Amemiya S., Wada H. “Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton”, 2016, PloS One, 11(2):e0149067",
   "year": 2016,
   "doi": "https://doi.org/10.1371/journal.pone.0149067",
   "url": null,
   "topics": [
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Comparing Alx gene expression across echinoderm classes, the study found that alx1, known for sea urchin skeleton formation, was barely expressed in skeleton-lacking starfish larvae. Forcing its expression activated part of the skeletogenic program but not a full skeleton, showing alx1 is necessary but not sufficient for larval skeleton evolution.",
    "ja": "棘皮動物の各綱でAlx遺伝子の発現を比較し、ウニの骨格形成に関わるalx1が、骨格を持たないヒトデ幼生ではほとんど発現しないことを示した。alx1を強制発現させると骨格形成プログラムの一部が動くが完全な骨格はできず、幼生骨格の進化にalx1は必要だが十分ではないと結論づけた。"
   }
  },
  {
   "n": 42,
   "citation": "Miyake M., Nomura A., Ogura A., Takehana K., Kitahara Y., Takahara K., Tsugawa K., Miyamoto C., Miura N., Sato R., Kurahashi K., Harding HP., Oyadomari M., Ron D., Oyadomari S. “Skeletal muscle-specific eukaryotic translation initiation factor 2α phosphorylation controls amino acid metabolism and fibroblast growth factor 21-mediated non-cell-autonomous energy metabolism”, 2015, FASEB Journal, 30(2):798-812",
   "year": 2015,
   "doi": "https://doi.org/10.1096/fj.15-275990",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "In transgenic mice, the study showed that phosphorylation of the translation factor eIF2alpha in skeletal muscle activates the integrated stress response, boosting amino acid metabolism and, unexpectedly, inducing secretion of the myokine FGF21. This links muscle stress signaling to whole-body energy metabolism and protection against obesity.",
    "ja": "遺伝子改変マウスを用い、骨格筋で翻訳因子eIF2αがリン酸化されると統合的ストレス応答が起こり、アミノ酸代謝が活性化するとともに、意外にも筋肉ホルモンFGF21の分泌が誘導されることを示した。筋肉のストレス応答が全身のエネルギー代謝や肥満抑制につながることを明らかにした。"
   }
  },
  {
   "n": 43,
   "citation": "Yoshida MA., Ogura A., Ikeo K., Shigeno S., Moritaki T., Winters GC., Kohn AB., Moroz LL. “Molecular Evidence for Convergence and Parallelism in Evolution of Complex Brains of Cephalopod Molluscs: Insights from Visual Systems”, 2015, Integrative and Comparative Biology, 55(6):1070-83",
   "year": 2015,
   "doi": "https://doi.org/10.1093/icb/icv049",
   "url": null,
   "topics": [
    "cephalopod-eye",
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Deep sequencing of eye transcriptomes from pygmy squid and chambered nautilus revealed three modes of genomic innovation behind cephalopods' vertebrate-like brains and eyes: recruitment of new genes, co-option of existing genes, and gene duplication. Massive gene recruitment underlay the shift from nautilus' pinhole eye to the squid camera eye.",
    "ja": "ヒメイカとオウムガイの眼のトランスクリプトームを大規模解析し、脊椎動物に似た頭足類の脳と眼を生んだ3つのゲノム革新(新規遺伝子の動員、既存遺伝子の転用、遺伝子重複)を示した。オウムガイのピンホール眼からイカのカメラ眼への進化には、大規模な遺伝子の動員が関わっていた。"
   }
  },
  {
   "n": 44,
   "citation": "Kamijyo A., Yura K., Ogura A. “Distinct evolutionary rate in the eye field transcription factors found by estimation of ancestral protein structure”, 2014, Gene, 555(2):73-9",
   "year": 2015,
   "doi": "https://doi.org/10.1016/j.gene.2014.10.003",
   "url": null,
   "topics": [
    "cephalopod-eye",
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "By reconstructing ancestral sequences and 3D structures of seven conserved eye-field transcription factors, the study traced their evolution across animal phyla. DNA-binding domains were consistently the most conserved, but evolutionary rates varied among and within factors, with the network-central gene rx1 evolving faster than the others.",
    "ja": "眼の発生を担う保存された7つの転写因子について、祖先配列と立体構造を推定し、動物門を越えた進化を追跡した。DNA結合ドメインは常に最も保存されていたが、進化速度は因子間・因子内で一様ではなく、ネットワークの中心に位置するrx1が他より速く進化していた。"
   }
  },
  {
   "n": 45,
   "citation": "Shigeno S., Ogura A., Mori T., Toyohara H., Yoshida T., Tsuchida S., Fujikura K. “Sensing deep extreme environments: the receptor cell types, brain centers, and multi-layer neural packaging of hydrothermal vent endemic worms”, 2014, Frontiers in Zoology, 11(1):82",
   "year": 2014,
   "doi": "https://doi.org/10.1186/s12983-014-0082-9",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using immunocytochemistry, ultrastructure, and neural tracing, the study examined the sensory cells and brain of alvinellid worms endemic to deep-sea hydrothermal vents. It found mitochondria-rich sensory cells, insect-like mushroom-body neural clusters, and neurons wrapped in multiple membranes, suggesting enhanced protection against the vents' oxidative stress.",
    "ja": "深海熱水噴出孔に固有のアルビネラ科ゴカイの感覚細胞と脳を、免疫染色・微細構造・神経トレースで調べた。ミトコンドリアに富む感覚細胞や昆虫に似たキノコ体状の神経塊に加え、複数の膜に包まれた神経細胞を見いだし、熱水環境の酸化ストレスから神経を守る仕組みではないかと考察した。"
   }
  },
  {
   "n": 46,
   "citation": "Hayashi K., Kawai YL., Yura K., Yoshida MA., Ogura A., Hata K., Nakabayashi K., Okamura K. “Complete genome sequence of the mitochondrial DNA of the sparkling enope squid, Watasenia scintillans”, 2014, Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis, 27(3):1842-3",
   "year": 2014,
   "doi": "https://doi.org/10.3109/19401736.2014.971251",
   "url": null,
   "topics": [
    "cephalopod-eye",
    "genome-tools"
   ],
   "themes": [
    "evolution",
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The study determined the complete 20,089 bp mitochondrial genome of the deep-sea bioluminescent sparkling enope squid, Watasenia scintillans, from a single female using Illumina sequencing. From the read depths it also estimated about 108 mitochondria per brain cell, a haploid genome size of 4.78 Gb, and six heteroplasmy sites.",
    "ja": "深海の発光性のホタルイカ(Watasenia scintillans)の雌1個体から、イルミネーラの次世代シークエンサーで全長20,089塩基対のミトコンドリアゲノムを決定した。リード深度から脳細胞あたり約108個のミトコンドリア、半数体ゲノムサイズ4.78 Gb、6か所のヘテロプラスミー部位も推定した。"
   }
  },
  {
   "n": 47,
   "citation": "Yoshida MA., Yamada L., Ochi H., Iwata Y., Tamura-Nakano M., Sawada H., Sauer WHH., Ogura A., Hirohashi N. “Integrative omics analysis reveals differentially distributed proteins in dimorphic euspermatozoa of the squid, Loligo bleekeri”, 2014, Biochemical and Biophysical Research Communications, 450(3):1218-24",
   "year": 2014,
   "doi": "https://doi.org/10.1016/j.bbrc.2014.04.076",
   "url": null,
   "topics": [
    "cephalopod-eye"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "In the squid Loligo bleekeri, large 'consort' and small 'sneaker' males produce differently shaped sperm. Combining RNA-seq and proteomics, the study found sperm-type-biased proteins: dynein heavy chains enriched in sneaker sperm and energy-metabolism enzymes in consort sperm, suggesting the dimorphic sperm traits arise from altered intracellular components.",
    "ja": "ヤリイカ(Loligo bleekeri)では大型の「本命」雄と小型の「こそこそ」雄が形の異なる精子をつくる。RNA-seqとプロテオーム解析から、こそこそ型精子ではダイニン重鎖が、本命型精子ではエネルギー代謝酵素が多いなど型ごとに偏るタンパク質を見いだし、精子の二型が細胞内成分の違いから生じることを示した。"
   }
  },
  {
   "n": 48,
   "citation": "Yoshida MA., Yura K., Ogura A. “Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants”, 2014, Scientific Reports, 4:4256",
   "year": 2014,
   "doi": "https://doi.org/10.1038/srep04256",
   "url": null,
   "topics": [
    "cephalopod-eye",
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "Examining Pax-6 in squid, the study found five splicing variants of a single Pax-6 gene, with no gene duplication as seen in insects. The variants showed distinct spatial and temporal expression during development, suggesting cephalopods evolved eye-controlling Pax-6 variants independently of the four variants used in vertebrates.",
    "ja": "イカのPax-6遺伝子を調べ、昆虫のような遺伝子重複はなく、単一のPax-6から5種類のスプライシング変異体が生じることを見いだした。各変異体は発生過程で異なる時空間発現を示し、頭足類は脊椎動物の4変異体とは独立にPax-6の変異体を獲得して眼の進化に用いたことが示唆された。"
   }
  },
  {
   "n": 49,
   "citation": "Hall NE., Hanzak J., Allcock AL., Cooke IR., Ogura A., Strugnell JM. “The complete mitochondrial genome of the pygmy squid, Idiosepius (Cephalopoda: Decapodiformes): the first representative from the family Idiosepiidae”, 2014, Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis, 27(1):5-6",
   "year": 2014,
   "doi": "https://doi.org/10.3109/19401736.2013.865180",
   "url": null,
   "topics": [
    "cephalopod-eye",
    "genome-tools"
   ],
   "themes": [
    "evolution",
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The study reported the first complete mitochondrial genome from the squid family Idiosepiidae, sequencing the 16,183 bp mtDNA of the pygmy squid Idiosepius. It identified all conserved metazoan mitochondrial genes plus a 1,018 bp non-coding region, and found the gene order most closely resembled that of the bobtail squid Semirossia.",
    "ja": "ヒメイカ科として初めて、ミミイカダマシ(Idiosepius)の全長16,183塩基対のミトコンドリアゲノムを解読した。動物に共通する保存遺伝子すべてに加えて1,018塩基対の非コード領域を同定し、その遺伝子配置はダンゴイカ類のSemirossiaに最も近いことを示した。"
   }
  },
  {
   "n": 50,
   "citation": "Sousounis K., Ogura A., Tsonis PA. “Transcriptome analysis of Nautilus and pygmy squid developing eye provides insights in lens and eye evolution”, 2013, PloS One, 8(10):e78054",
   "year": 2013,
   "doi": "https://doi.org/10.1371/journal.pone.0078054",
   "url": null,
   "topics": [
    "cephalopod-eye",
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using RNA sequencing of developing eyes from Nautilus (pinhole eye) and pygmy squid (camera eye), the study compared their transcriptomes. Eye morphogenesis genes were broadly conserved, photoreceptor genes tracked the invertebrate/vertebrate split, and gene duplications, including in NF1, hinted at previously unsuspected roles in mollusc lens evolution.",
    "ja": "ピンホール眼を持つオウムガイとカメラ眼を持つヒメイカの発生中の眼をRNAシークエンスで比較した。眼の形態形成遺伝子は広く保存され、光受容体遺伝子は無脊椎/脊椎動物の違いを反映し、NF1などの遺伝子重複が軟体動物のレンズ進化における未知の役割を示唆した。"
   }
  },
  {
   "n": 51,
   "citation": "Ogura A., Yoshida MA., Moritaki T., Okuda Y., Sese J., Shimizu KK., Sousounis K., Tsonis PA. “Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus”, 2013, Scientific Reports, 3:1432",
   "year": 2013,
   "doi": "https://doi.org/10.1038/srep01432",
   "url": null,
   "topics": [
    "cephalopod-eye",
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "RNA-seq of developing eyes in Nautilus and pygmy squid showed that although most upstream eye-development genes were expressed in both, the gene six3/6 and its downstream lens and crystallin genes were not expressed in Nautilus. Since six3/6 pathways are conserved across other molluscs, its loss likely drove Nautilus' primitive pinhole eye.",
    "ja": "オウムガイとヒメイカの発生中の眼のRNA-seqから、多くの上流の眼発生遺伝子は両者で発現する一方、レンズ形成に関わるsix3/6とその下流のクリスタリン遺伝子群がオウムガイでは発現しないことを示した。six3/6経路は他の軟体動物で保存されており、その喪失がオウムガイのピンホール眼進化を招いたと示唆した。"
   }
  },
  {
   "n": 52,
   "citation": "Asato R., Yoshida S., Ogura A., Nakama T., Ishikawa K., Nakao S., Sassa Y., Enaida H., Oshima Y., Ikeo K., Gojobori T., Kono T., Ishibashi T. “Comparison of gene expression profile of epiretinal membranes obtained from eyes with proliferative vitreoretinopathy to that of secondary epiretinal membranes”, 2013, PloS One, 8(1):e54191",
   "year": 2013,
   "doi": "https://doi.org/10.1371/journal.pone.0054191",
   "url": null,
   "topics": [
    "cephalopod-eye"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The team built cDNA/EST libraries to profile genes expressed in epiretinal membranes from eyes with proliferative vitreoretinopathy (PVR) versus less-aggressive secondary membranes. Cell-adhesion genes were prominent, and soluble CD44 and VCAM-1 were elevated, supporting the view that PVR membranes are an aberrant wound-healing response.",
    "ja": "増殖性硝子体網膜症（PVR）に伴う網膜前膜と、より軽度の二次性前膜で発現する遺伝子をcDNAライブラリで比較した。細胞接着関連遺伝子が目立ち、可溶型CD44やVCAM-1の上昇も確認され、PVR前膜が異常な創傷治癒反応であるとの説を裏付けた。"
   }
  },
  {
   "n": 53,
   "citation": "Fukuzaki M., Yoshida M., Ogura A., Sese J. “Systematic measurement of missmatch effect for designing inter-species microarray”, 2012, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 478-481",
   "year": 2012,
   "doi": "https://doi.org/10.1109/BIBM.2012.6392729",
   "url": null,
   "topics": [
    "genome-tools"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "To design microarrays that measure gene expression across species with a single probe per orthologous gene, the authors systematically tested mutated probes. Mutations near the probe 3'-end barely affected signal while 5'-end mutations lowered it, and they built a human/rat/mouse array covering 6,683 genes.",
    "ja": "複数種の遺伝子発現を1プローブで測る種間比較マイクロアレイを設計するため、変異を入れたプローブを系統的に検証した。3'末端側の変異は信号にほぼ影響しないが5'末端側は低下させることを見いだし、ヒト・ラット・マウス6,683遺伝子を対象とするアレイを構築した。"
   }
  },
  {
   "n": 54,
   "citation": "Albertin CB., Bonnaud L., Brown CT., Crookes-Goodson WJ., da Fonseca RR., Di Cristo C., Dilkes BP., Edsinger-Gonzales E., Freeman RM., Hanlon RT., Koenig KM., Lindgren AR., Martindale MQ., Minx P., Moroz LL., Nödl MT., Nyholm SV., Ogura A., Pungor JR., Rosenthal JJ., Schwarz EM., Shigeno S., Strugnell JM., Wollesen T., Zhang G., Ragsdale CW. “Cephalopod genomics: A plan of strategies and organization”, 2012, Standards in Genomic Sciences, 7(1):175-88",
   "year": 2012,
   "doi": "https://doi.org/10.4056/sigs.3136559",
   "url": null,
   "topics": [
    "cephalopod-eye"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "This white paper from the CephSeq Consortium, formed at a 2012 international meeting, sets out strategies and an organizational plan for sequencing cephalopod (squid and octopus) genomes, selecting priority species and coordinating the community to address the field's lack of genomic resources.",
    "ja": "2012年の国際会議で発足したCephSeqコンソーシアムによる提言書。頭足類（イカ・タコ）のゲノム解読を進めるための戦略と組織体制を示し、優先的に解読すべき種の選定や研究コミュニティの連携方針をまとめた。"
   }
  },
  {
   "n": 55,
   "citation": "Ogura A., Lin M., Shigenobu Y., Fujiwara A., Ikeo K., Nagai S. “Effective gene collection from the metatranscriptome of marine microorganisms”, 2011, BMC Genomics, 12(Suppl 3):S15",
   "year": 2011,
   "doi": "https://doi.org/10.1186/1471-2164-12-S3-S15",
   "url": null,
   "topics": [
    "symbiosis-virus"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The study developed a normalized metatranscriptomic method and applied it to marine microbes from Hiroshima Bay, comparing normalized and non-normalized libraries. Normalization increased the number of unique genes, functional categories and taxonomic richness recovered, improving gene collection for comparative transcriptomics.",
    "ja": "環境サンプルの発現遺伝子を集めるため、正規化を用いたメタトランスクリプトーム手法を開発し、広島湾の海洋微生物に適用した。正規化により得られるユニーク遺伝子や機能カテゴリ、分類群の多様性が増え、比較解析の基盤づくりに有効と示した。"
   }
  },
  {
   "n": 56,
   "citation": "Yoshida MA., Ogura A. “Genetic mechanisms involved in the evolution of the cephalopod camera eye revealed by transcriptomic and developmental studies”, 2011, BMC Evolutionary Biology, 11:180",
   "year": 2011,
   "doi": "https://doi.org/10.1186/1471-2148-11-180",
   "url": null,
   "topics": [
    "cephalopod-eye",
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Combining transcriptomics with developmental analysis across six molluscs, the study probed how cephalopods evolved a camera eye resembling that of vertebrates. It identified 156 genes under positive selection in the cephalopod lineage and 1,571 shared with vertebrate camera eyes, implicating both expression and sequence changes.",
    "ja": "6種の軟体動物のトランスクリプトームと発生解析から、頭足類が脊椎動物に似たカメラ眼を進化させた仕組みを探った。頭足類系統で正の選択を受けた156遺伝子と、脊椎動物のカメラ眼と共通する1,571遺伝子を同定し、発現と配列の両変化の関与を示した。"
   }
  },
  {
   "n": 57,
   "citation": "Yoshida MA., Ishikura Y., Moritaki T., Shoguchi E., Shimizu KK., Sese J., Ogura A. “Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation”, 2011, Gene, 483(1-2):63-71",
   "year": 2011,
   "doi": "https://doi.org/10.1016/j.gene.2011.05.027",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using partial shotgun sequencing of pygmy squid, nautilus and scallop, the authors compared molluscan genome structure. They quantified repetitive-element content and estimated genome sizes, and found large-scale gene duplication after divergence from the limpet, with lineage-specific repeat and gene-family expansions.",
    "ja": "ヒメイカ・オウムガイ・ホタテのショットガン配列から軟体動物のゲノム構造を比較した。反復配列の割合やゲノムサイズを推定し、カサガイとの分岐後に大規模な遺伝子重複が起きたこと、系統ごとに反復配列や遺伝子ファミリーが増えたことを示した。"
   }
  },
  {
   "n": 58,
   "citation": "福崎睦美, 吉田真明, 小倉淳, *瀬々潤 “比較トランスクリプトーム向けマイクロアレイの設計” IPSJ SIG Technical Report, 2011, Vol.2011-BIO-24 No.10 1-6",
   "year": 2011,
   "doi": null,
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "This Japanese technical report addresses the design of DNA microarrays for comparative transcriptomics, aiming to measure gene expression across multiple species. It is an earlier report in the same line of work as the authors' inter-species microarray studies.",
    "ja": "複数種の遺伝子発現を測る比較トランスクリプトーム向けマイクロアレイの設計手法を論じた国内学会の技術報告。著者らの種間マイクロアレイ研究につながる初期の報告である。"
   }
  },
  {
   "n": 59,
   "citation": "小中佳子, 福崎睦美, 吉田真明, 小倉淳, *瀬々潤 “頻出パターン解析による重複遺伝子の同定 手法” IPSJ SIG Technical Report, 2010, Vol.2010-BIO-23 No.18 1-8",
   "year": 2010,
   "doi": null,
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "This Japanese technical report proposes a method for identifying duplicated genes using frequent-pattern (pattern-mining) analysis, applying data-mining techniques to detect gene duplications from sequence or expression data.",
    "ja": "頻出パターン解析（データマイニング手法）を用いて重複遺伝子を同定する手法を提案した国内学会の技術報告。配列や発現データから遺伝子の重複を検出することを目指している。"
   }
  },
  {
   "n": 60,
   "citation": "Ogura A., Yoshida MA., Fukuzaki M., Sese J. “In vitro homology search array comprehensively reveals highly conserved genes and their functional characteristics in non-sequenced species”, 2010, BMC Genomics, 11(Suppl 4):S9",
   "year": 2010,
   "doi": "https://doi.org/10.1186/1471-2164-11-S4-S9",
   "url": null,
   "topics": [
    "genome-tools"
   ],
   "themes": [
    "infobiology"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The authors developed an 'in vitro homology search' microarray, using probes for human single-copy genes and hybridizing squid mRNA to it. About 68% of probes detected squid homologs, showing the method can find conserved genes in species without sequenced genomes.",
    "ja": "ヒトの単一コピー遺伝子のプローブにイカのmRNAを反応させる「in vitro相同性検索」アレイを開発した。約68%のプローブでイカの相同遺伝子を検出し、ゲノム未解読の種でも保存遺伝子を見つけられる手法だと示した。"
   }
  },
  {
   "n": 61,
   "citation": "Chapman JA., Kirkness EF., Simakov O., Hampson SE., Mitros T., Weinmaier T., Rattei T., Balasubramanian PG., Borman J., Busam D., Disbennett K., Pfannkoch C., Sumin N., Sutton GG., Viswanathan LD., Walenz B., Goodstein DM., Hellsten U., Kawashima T., Prochnik SE., Putnam NH., Shu S., Blumberg B., Dana CE., Gee L., Kibler DF., Law L., Lindgens D., Martinez DE., Peng J., Wigge PA., Bertulat B., Guder C., Nakamura Y., Ozbek S., Watanabe H., Khalturin K., Hemmrich G., Franke A., Augustin R., Fraune S., Hayakawa E., Hayakawa S., Hirose M., Hwang JS., Ikeo K., Nishimiya-Fujisawa C., Ogura A., Takahashi T., Steinmetz PR., Zhang X., Aufschnaiter R., Eder MK., Gorny AK., Salvenmoser W., Heimberg AM., Wheeler BM., Peterson KJ., Böttger A., Tischler P., Wolf A., Gojobori T., Remington KA., Strausberg RL., Venter JC., Technau U., Hobmayer B., Bosch TC., Holstein TW., Fujisawa T., Bode HR., David CN., Rokhsar DS., Steele RE. “The dynamic genome of Hydra”, 2010, Nature, 464(7288):592-6",
   "year": 2010,
   "doi": "https://doi.org/10.1038/nature08830",
   "url": null,
   "topics": [
    "symbiosis-virus"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "This Nature paper reports the genome of the freshwater cnidarian Hydra magnipapillata and compares it with other animals. It reveals shaping by transposable-element bursts, horizontal gene transfer and trans-splicing, and sheds light on the evolution of epithelia, contractile tissue and the neuromuscular junction.",
    "ja": "淡水産刺胞動物ヒドラのゲノムを解読し、他の動物と比較したNature論文。転移因子の増加、水平伝播、トランススプライシングによってゲノムが形づくられたことを明らかにし、上皮や収縮組織、神経筋接合部の進化に光を当てた。"
   }
  },
  {
   "n": 62,
   "citation": "Yoshida S., Ogura A., Ishikawa K., Yoshida A., Kohno R., Yamaji Y., Ikeo K., Gojobori T., Kono T., Ishibashi T. “Gene expression profile of fibrovascular membranes from patients with proliferative diabetic retinopathy”, 2009, British Journal of Ophthalmology, 94(6):795-801",
   "year": 2009,
   "doi": "https://doi.org/10.1136/bjo.2009.167072",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "To profile genes active in the fibrovascular membranes that form in proliferative diabetic retinopathy, the team built a cDNA/EST library from surgically removed membranes, assembling 625 gene clusters. The resulting expression profile is a resource for studying how these damaging membranes develop.",
    "ja": "増殖糖尿病網膜症で生じる線維血管膜で働く遺伝子を調べるため、手術で摘出した膜からcDNAライブラリを作成し625の遺伝子クラスターを得た。得られた発現プロファイルは、この病的な膜の形成機構を研究する基盤資料となる。"
   }
  },
  {
   "n": 63,
   "citation": "Landry CR., Castillo-Davis CI., Ogura A., Liu JS., Hartl DL. “Systems-level analysis and evolution of the phototransduction network in Drosophila”, 2007, Proceedings of the National Academy of Sciences of the United States of America, 104(9):3283-8",
   "year": 2007,
   "doi": "https://doi.org/10.1073/pnas.0611402104",
   "url": null,
   "topics": [
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "Using the well-characterized Drosophila phototransduction network, the study measured gene-expression variation within and between D. melanogaster and D. simulans. Expression was largely conserved, but the light-channel gene TRPL showed excess divergence, suggesting natural selection shaped this difference with functional consequences for vision.",
    "ja": "解析が進んだショウジョウバエの光情報伝達ネットワークを用い、近縁2種の種内・種間で遺伝子発現の変動を測定した。発現はおおむね保存されていたが、光チャネル遺伝子TRPLは種間の差が大きく、視覚に影響する自然選択の関与が示唆された。"
   }
  },
  {
   "n": 64,
   "citation": "Choy KW., Wang CC., Ogura A., Lau TK., Rogers MS., Ikeo K., Gojobori T., Tang LY., Lam DSC., Chung TKH., Pang CP. “Molecular characterization of the developmental gene in eyes: through data-mining on integrated transcriptome databases”, 2006, Clinical Biochemistry, 39(3):224-30",
   "year": 2006,
   "doi": "https://doi.org/10.1016/j.clinbiochem.2005.12.005",
   "url": null,
   "topics": [
    "cephalopod-eye"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using integrated transcriptome databases and gene-ontology tools, the team mined expressed sequence tags from human fetal eyes to identify candidate genes for ocular development, comparing expression across tissues and species and highlighting the strengths and limits of each data-mining platform.",
    "ja": "統合トランスクリプトームデータベースと遺伝子オントロジー解析を用いて、ヒト胎児眼のESTから眼の発生に関わる候補遺伝子を探索した。組織間・種間で発現を比較し、各データマイニング手法の長所と限界を示した。"
   }
  },
  {
   "n": 65,
   "citation": "Choy KW., Wang CC., Ogura A., Lau TK., Rogers MS., Ikeo K., Gojobori T., Lam DSC., Pang CP. “Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes”, 2005, Physiological Genomics, 25(1):9-15",
   "year": 2005,
   "doi": "https://doi.org/10.1152/physiolgenomics.00121.2005",
   "url": null,
   "topics": [
    "cephalopod-eye"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The authors built a cDNA library from human fetal eyes at 9-14 weeks of gestation and annotated 15,809 ESTs, identifying 5,534 gene clusters including novel sequences and known retinal-disease genes, and compared them across eight species to support gene discovery and evolutionary analysis.",
    "ja": "妊娠9〜14週のヒト胎児眼からcDNAライブラリを作製し、15,809件のESTを注釈付けして5,534の遺伝子クラスターを同定した。新規配列や既知の網膜疾患遺伝子を含み、8種との比較により遺伝子探索と進化解析の基盤を提供した。"
   }
  },
  {
   "n": 66,
   "citation": "Ogura A., Ikeo K., Gojobori T. “Estimation of ancestral gene set of bilaterian animals and its implication to dynamic change of gene content in bilaterian evolution”, 2005, Gene, 345(1):65-71",
   "year": 2005,
   "doi": "https://doi.org/10.1016/j.gene.2004.11.036",
   "url": null,
   "topics": [
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "By comparing over a million genes, the study estimated the ancestral gene sets of bilaterian animals and of the plant-animal-fungi split, finding a 2.7-fold increase in gene clusters between these points and showing that living animals both retained and lost large numbers of ancestral genes during evolution.",
    "ja": "100万を超える遺伝子を比較し、左右相称動物と植物・動物・菌類の分岐点における祖先遺伝子セットを推定した。この間に遺伝子クラスターが約2.7倍に増え、現生動物は祖先遺伝子を多数保持する一方で多数を失ってきたことを示した。"
   }
  },
  {
   "n": 67,
   "citation": "Ogura A., Ikeo K., Gojobori T. “Comparative analysis of gene expression for convergent evolution of camera eye between octopus and human”, 2004, Genome Research, 14(8):1555-61",
   "year": 2004,
   "doi": "https://doi.org/10.1101/gr.2268104",
   "url": null,
   "topics": [
    "cephalopod-eye",
    "evolution"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": true,
   "summary": {
    "en": "To probe the convergent evolution of camera eyes in octopus and human, the team sequenced octopus-eye ESTs and compared gene expression with the human eye. About 69% of genes were shared, and most already existed in the bilaterian ancestor, suggesting conserved genes and similar expression underlie this convergence.",
    "ja": "タコとヒトのカメラ眼が独立に進化した収斂進化の仕組みを探るため、タコ眼のESTを解読しヒト眼と発現を比較した。約69%の遺伝子が共通し、その多くは左右相称動物の共通祖先に既に存在しており、保存された遺伝子と類似した発現が収斂の基盤である可能性を示した。"
   }
  },
  {
   "n": 68,
   "citation": "Nishida H., Ogura A., Yokota A., Yamaguchi I., Sugiyama J. “Group I intron located in PR protein homologue gene in Youngia japonica”, 2000, Bioscience, Biotechnology, and Biochemistry, 64(3):606-9",
   "year": 2000,
   "doi": "https://doi.org/10.1271/bbb.64.606",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "The study identified a group I intron in the wild plant Youngia japonica, located within a pathogenesis-related (miraculin homologue) protein gene. Evidence suggested the intron had been horizontally transferred from Protomyces inouyei, a fungus that infects the plant.",
    "ja": "雑草オニタビラコ（Youngia japonica）から、病原関連タンパク質（ミラクリン相同）遺伝子内に位置するグループIイントロンを同定した。このイントロンは、この植物に寄生する菌類Protomyces inouyeiから水平伝播した可能性が示された。"
   }
  },
  {
   "n": 69,
   "citation": "Zimmer T., Ogura A., Takewaka T., Zimmer RM., Ohta A., Takagi M. “Gene regulation in response to overexpression of cytochrome P450 and proliferation of the endoplasmic reticulum in Saccharomyces cerevisiae”, 2000, Bioscience, Biotechnology, and Biochemistry, 64(9):1930-6",
   "year": 2000,
   "doi": "https://doi.org/10.1271/bbb.64.1930",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "Using mRNA differential display in baker's yeast, the study identified genes up- and down-regulated when cytochrome P450 is overexpressed and the endoplasmic reticulum proliferates. Two strongly induced genes required P450 membrane integration but were not essential for its overproduction.",
    "ja": "出芽酵母でmRNAディファレンシャルディスプレイを用い、シトクロムP450の過剰発現と小胞体増殖に伴って発現が変動する遺伝子を同定した。強く誘導される2遺伝子はP450の膜組込みを必要としたが、P450の過剰生産自体には必須ではなかった。"
   }
  },
  {
   "n": 70,
   "citation": "Zimmer T., Ogura A., Ohta A., Takagi M. “Misfolded membrane-bound cytochrome P450 activates KAR2 induction through two distinct mechanisms”, 1999, Journal of Biochemistry, 126(6):1080-9",
   "year": 1999,
   "doi": "https://doi.org/10.1093/oxfordjournals.jbchem.a022553",
   "url": null,
   "topics": [
    "genomics"
   ],
   "themes": [
    "evolution"
   ],
   "type": "journal",
   "selected": false,
   "summary": {
    "en": "In baker's yeast, the study showed that misfolded membrane-bound cytochrome P450 induces the chaperone gene KAR2 through two distinct promoter elements: the heat-shock element (responding to the cytosolic domain) and the unfolded-protein-response element (responding to the membrane-integrated mutant), revealing parallel stress pathways.",
    "ja": "出芽酵母において、誤って折りたたまれた膜結合型シトクロムP450がシャペロン遺伝子KAR2を、熱ショックエレメント（細胞質側ドメインに応答）と小胞体ストレス応答エレメント（膜組込み型変異体に応答）という2つの異なるプロモーター要素を介して誘導することを示し、並行するストレス経路の存在を明らかにした。"
   }
  }
 ],
 "books": [
  {
   "n": 71,
   "citation": "小坂浩司, 小松和也, 大熊那夫紀, 八尾英也, 山内仁, 木俣光正, 野村幹弘, 熊野淳夫, 今野大輝, 大河佑貴, 小倉淳, 吉村和就 “水処理・水ビジネスの技術と市場2025”, 2025, ISBN 978-4-7813-1860-8",
   "year": 2025,
   "doi": null,
   "url": "http://www.cmcbooks.co.jp/products/detail.php?product_id=115845"
  },
  {
   "n": 72,
   "citation": "Ogura A. “AI and ML-Driven Strategies for Drug Repurposing: Techniques, Applications, and Challenges,” in “Applied Artificial Intelligence for Drug Discovery”, 2025, Springer Nature",
   "year": 2025,
   "doi": null,
   "url": "https://link.springer.com/chapter/10.1007/978-3-031-98022-0_23"
  },
  {
   "n": 73,
   "citation": "小倉淳 “藻類による二酸化炭素回収・固定化と有用物質生産”, 2025, ISBN 978-4-7813-1857-8",
   "year": 2025,
   "doi": null,
   "url": "https://www.cmcbooks.co.jp/products/detail.php?product_id=115819"
  },
  {
   "n": 74,
   "citation": "小倉淳, 田端裕正 “藻類培養技術 屋内外大量生産・各種処理評価／トラブル対応・商業化 に向けた取り組み”, 2021, ISBN 978-4-86502-219-3",
   "year": 2021,
   "doi": null,
   "url": "https://johokiko.co.jp/publishing/BC211001.php"
  },
  {
   "n": 75,
   "citation": "*Ogura A. “Genome and transcriptome-wide researches of brain evolution”, 2017, Brain Evolution by Design, Springer, ISBN 978-4-431-56469-0 ～",
   "year": 2017,
   "doi": null,
   "url": "https://link.springer.com/book/10.1007/978-4-431-56469-0"
  },
  {
   "n": 76,
   "citation": "*Ogura A. “Metatranscriptome” Genome Analysis: Current Procedures and Applications, 2014, Horizon press, ISBN:978-1908230294",
   "year": 2014,
   "doi": null,
   "url": "http://www.caister.com/genomeanalysis"
  },
  {
   "n": 77,
   "citation": "*Ogura A. “Evolutionary genomics for eye diversification” Evolutionary Biology, 2010, Springer Verlag, pp 179-186, ISBN:978-3642433818",
   "year": 2010,
   "doi": null,
   "url": "https://link.springer.com/chapter/10.1007/978-3-642-12340-5_11"
  },
  {
   "n": 78,
   "citation": "*Ogura A. Translation of “Section B, Data acquisition (pp.9~27)” in “Instant Notes in Bioinformatics”, 2003, Springer 総説",
   "year": 2003,
   "doi": null,
   "url": null
  }
 ],
 "reviews": [
  {
   "n": 79,
   "citation": "小倉淳 “昆虫食：未来の食料資源”, 昆虫と自然 2024年8月号 特集・昆虫の利用・昆虫と食",
   "year": 2024,
   "doi": null,
   "url": "http://hokuryukan-ns.co.jp/cms/books/%E6%98%86%E8%99%AB%E3%81%A8%E8%87%AA%E7%84%B6-2024%E5%B9%B4%EF%BC%98%E6%9C%88%E5%8F%B7-%E7%89%B9-%E9%9B%86%E3%83%BB%E6%98%86%E8%99%AB%E3%81%AE%E5%88%A9%E7%94%A8%E3%83%BB%E6%98%86%E8%99%AB%E3%81%A8/"
  },
  {
   "n": 80,
   "citation": "小倉淳 “藻類を用いたマイクロプラスチック除去技術”, 月間プラスチックス 2022年11月号",
   "year": 2022,
   "doi": null,
   "url": null
  },
  {
   "n": 81,
   "citation": "小倉淳 “昆虫が支える循環型食糧システムの開発を目指して”, 食品と開発 2022年11月号",
   "year": 2022,
   "doi": null,
   "url": null
  },
  {
   "n": 82,
   "citation": "小倉淳, 田端裕正 “微細藻類を用いたマイクロプラスチックの除去・回収技術” 環境浄化技術 2022年3・4月号",
   "year": 2022,
   "doi": null,
   "url": "https://jglobal.jst.go.jp/detail?JGLOBAL_ID=202202221519069412"
  },
  {
   "n": 83,
   "citation": "由良敬, 鈴木丈詞, 渡邉 崇人, 小倉淳, 朝日透, 生田和正, 霜田政美, 森岡伸介, 佐藤秀, 中村龍 平 “昆虫を活用した新たな食料生産システムの構築” JATAFFジャーナル９巻６号特集「食のフロ ンティアとパラダイムシフト」",
   "year": 2021,
   "doi": null,
   "url": null,
   "month": 6
  },
  {
   "n": 84,
   "citation": "滋野修一, 小倉淳, 坪内泰志, 森司 “深海の熱水極限環境に適応した動物たち” 生物の科学 遺 伝, 2016, 70(3), 189-193",
   "year": 2016,
   "doi": null,
   "url": null
  },
  {
   "n": 85,
   "citation": "小倉淳 “頭足類の比較ゲノムプラットフォームの展望” 比較生理生化学会誌, 2013, 30(1) 3-10 PRESENTATIONS INVITED TALKS",
   "year": 2013,
   "doi": null,
   "url": "https://www.jstage.jst.go.jp/article/hikakuseiriseika/30/1/30_3/_article/-char/ja"
  },
  {
   "n": 100,
   "year": 2025,
   "doi": null,
   "url": "https://www.midorishobo.co.jp/SHOP/2292511.html",
   "citation": "小倉淳 “養殖ビジネス 2025年11月号（寄稿）”, 緑書房, 2025",
   "month": 11
  }
 ]
}