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Yuki NISHIMURA @ynishimuraLv
Joined October 2024
  • Tweets 308
  • Following 24
  • Followers 63
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Yuki NISHIMURA retweeted
R. Shimada@JeN4iPasLeTemps
Jun 13
AIがこの記事は正しくておもしろいってゆってました 「幕末」の数学者たち: AIと数学｜R. Shimada @JeN4iPasLeTemps note.com/rshimada/n/n776da2f…

「幕末」の数学者たち: AIと数学｜R. Shimada

まさに黒船来航といったところでしょうか。 先月、OpenAIは内部モデルを使ってエルデシュの単位距離問題を解決したと発表しました。これは、AIが初めて数学における重要な未解決問題を解いた例であるという意味で、極めて重要な意義を持つと思います。 本記事は、今、数学界で何が起こっているのかを、数学者である筆者が私見も交えつつ解説し、まとめるものです。第一部では数学的内容を、第二部では専門家による...

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Yuki NISHIMURA retweeted
Nature Microbiology@NatureMicrobiol
Jun 12
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity dlvr.it/TT16jm #MicroSky

Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity

Nature Microbiology - The activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect...

nature.com
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Yuki NISHIMURA retweeted
Nature Microbiology@NatureMicrobiol
Jun 12
Bacteria–phage coevolution drives variation in bacterial wilt disease incidence via resistance–virulence trade-offs dlvr.it/TT16Tf #MicroSky

Bacteria–phage coevolution drives variation in bacterial wilt disease incidence via resistance–vi...

Nature Microbiology - Phage–bacteria coevolution is associated with field-specific anti-phage defence and locally adapted phage populations, resulting in phage-resistant but weakly virulent...

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Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions link.springer.com/article/10…

Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and...

Microbiome - The ecological significance of bacteriophages has been extensively investigated, while the role of archaeal viruses across different environments remains poorly understood. Here, we...

link.springer.com
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A unicellular relative links aggregative multicellularity to animal origins doi.org/10.1038/s41586-026-1…

A unicellular relative links aggregative multicellularity to animal origins

Nature - A unicellular relative links aggregative multicellularity to animal origins

nature.com
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Gene ancestries reveal diverse microbial associations during eukaryogenesis. doi.org/10.1038/s41586-026-1…

Gene ancestries reveal diverse microbial associations during eukaryogenesis

Nature - Phylogenomic reconstruction of the proteome of the last eukaryotic common ancestor sheds light on the origin of eukaryotes, indicating an important role of horizontal transfer of genes...

nature.com
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Yuki NISHIMURA retweeted
Nature Microbiology@NatureMicrobiol
Jun 9
Wall teichoic acids plug nanopores in Bacillus subtilis cell wall and regulate peptidoglycan synthesis dlvr.it/TSy60h #MicroSky

Wall teichoic acids plug nanopores in Bacillus subtilis cell wall and regulate peptidoglycan...

Nature Microbiology - In Bacillus subtilis, wall teichoic acids sustain rod shape by filling nanoscale pores in the cell wall. The presence of wall teichoic acids limits the activity of PBP1, a...

nature.com
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A protein interactome for the last eukaryotic common ancestor illuminates the biochemical basis of modern genetic diseases doi.org/10.1016/j.xgen.2026.…
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mRNAの非翻訳領域がシャペロンとして働くかも 保存された配列を持つ3'UTRが、天然変性領域を持つタンパク質の凝集などを防ぎ、活性を維持するために重要であることを発見。3'UTRが欠損するとタンパク質が適切に折り畳まれず、量や局在は変わらず活性が減少 驚きです、、 cell.com/cell/fulltext/S0092…

mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity

Highly conserved mRNA 3′ UTRs act as co-translational chaperones for intrinsically disordered regions (IDRs), preventing inter-domain misfolding and enabling biogenesis of fully active proteins.

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エンハンサーRNAからタンパク質ができる？ エンハンサーRNAは長く非コードRNAと思われいたが、その一部がタンパク質へと翻訳されること、それらがde novo(新規)遺伝子誕生に関わる可能性を報告。アルギニンに富み、細胞核内に多いとか エンハンサーからもタンパク質が、 cell.com/trends/genetics/ful…

Emergence of protein-coding enhancer RNAs in primate evolution

Enhancer RNAs (eRNAs) are short, unstable RNA polymerase II transcripts from active enhancers processed by the Integrator complex. Once considered noncoding, recent work from Vlasov et al. shows that...

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Yuki NISHIMURA retweeted
Su'etsugu@sweats_good
Jun 4
ゲノム合成と起動、デバッグでゲノムサイズ半分の大腸菌をつくり出しました 向井助教の力作、プレプリントをbioRxivにポスト Generating E. coli 0.5 controlled by a half-sized genome biorxiv.org/content/10.64898…
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爆発的細胞死「ラプトーシス」 プラナリアで、細胞が爆発する細胞死を起こし、周囲の細胞を死滅させる免疫系として働くことを発見。分泌細胞由来の細胞によって担われ、進化の初期から存在する生体防御機構である可能性。ホルモンによって制御されるらしい cell.com/cell/fulltext/S0092…

Explosive cytotoxicity of ruptoblasts bridges hormone surveillance and immune defense

Ruptoblasts are a cytotoxic glandular cell type that undergoes explosive cell death, ruptosis, releasing potent, broad-spectrum agents capable of killing nearby cells. Ruptosis is triggered by the...

cell.com
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Signatures of gene transfer in the parallel evolution of osmotrophic specialization in eukaryotes. doi.org/10.1038/s41559-026-0…

Signatures of gene transfer in the parallel evolution of osmotrophic specialization in eukaryotes

Nature Ecology & Evolution - Comparative genomics of 86 eukaryotic species reveals a shared genetic toolkit enriched in metabolic functions among osmotrophs that was shaped by early horizontal...

nature.com
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SNooPy: a statistical framework for long-read metagenomic variant calling doi.org/10.1093/nar/gkag556

SNooPy: a statistical framework for long-read metagenomic variant calling

Abstract. Current long-read single-nucleotide variant callers were designed primarily for genomic data—particularly human genomes. While some have been use

academic.oup.com
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Yuki NISHIMURA retweeted
Nature Microbiology@NatureMicrobiol
Jun 3
Functional diversity of phage sponge proteins that sequester host immune signals dlvr.it/TSrfNN #MicroSky

Functional diversity of phage sponge proteins that sequester host immune signals

Nature Microbiology - A functional screen reveals phage sponge proteins that bind Pycsar, Thoeris and CBASS signalling molecules to inhibit bacterial immunity.

nature.com
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Yuki NISHIMURA retweeted
Nature Microbiology@NatureMicrobiol
Jun 3
Mapping an ocean metabolite’s path dlvr.it/TSrfWW #MicroSky

Mapping an ocean metabolite’s path

Nature Microbiology - Seawater contains a complex tapestry of metabolites, but for most, the microorganisms and pathways that process them remain unknown. A metabolomics analysis links a particular...

nature.com
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超並列の生化学解析を可能する新手法(APB-Display) ハイドロゲルビーズに目的のタンパク質を発現させ、FACSとNGSと組み合わせることで、数万以上のタンパク質親和性を一気に解析することを可能に。タンパク質の配列と機能の相関を予測するための機械学習モデルの構築へ biorxiv.org/content/10.64898…

Amplicon/Protein Bead Display enables quantitative in vitro biochemistry at scale

Scalable methods for producing and characterizing protein libraries are essential for generating standardized datasets needed to train models linking sequence to function. Here, we present Amplicon...

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ゼロから作るDeep Learning ❻ ―LLM編 oreilly.co.jp/books/97848144…

ゼロから作るDeep Learning ❻

人気シリーズの第6弾。今回のテーマは「大規模言語モデル（LLM）」です。ChatGPTの魔法のような能力、その仕組みを自らの手で解き明かしてみませんか？ 本書では、トークナイザからTransformer、事前学習から事後学習まで、LLMを支える技術をゼロから実装します。実装の舞台となるのは、CodeBot→StoryBot→WebBotという3段階のチャットボット開発。作るほどに、見えてくる...

oreilly.co.jp
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Yuki NISHIMURA retweeted
Yuki Sudo（須藤雄気）@Rhodopsinist_YS
May 26
📣学術変革領域（A）「光グローカル」の公式Xはこちらです。 → x.com/LightGlocal

学術変革領域研究（A）「光グローカル」 2026-2030 (@LightGlocal) on X

x.com
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Yuki NISHIMURA retweeted
Susumu Yoshizawa@qo_opYoshizawa
May 30
光と生物の関係に興味のある人の集まりだったので、めちゃ楽しかったです！
Yuki Sudo（須藤雄気）@Rhodopsinist_YS
May 29
📝学術変革領域「光グローカル」の第一回領域会議＠京都キャンパスプラザに参加しました。 💡「光と生命」「光と地球」を考える上で、とても刺激的な会になりました。写真は昼の部（領域会議）と夜の部（懇親会）での写真です。 glocal-photobiology.pharm.ok…
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