Karina Ilchenko
- Reposted by Karina Ilchenko🚨Our new article is out in #PLOS Pathogens! What drives nestedness in phages–bacteria interactions network in an agro-ecosystem? 🌱 📖 journals.plos.org/plospathogen... #Phagesky @inrae-pv.bsky.social @phimresearch.bsky.social @phagedirectory.bsky.social (Yes, that's a phage in those kinetics!)
- 🚨 New preprint! 🧬 𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect. We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps: ✅ Accurate ✅ Sensitive ✅ Easy to use 📖 www.biorxiv.org/content/10.1...
- We generated 763 𝐬𝐩𝐞𝐜𝐢𝐟𝐢𝐜 𝐩𝐫𝐨𝐭𝐞𝐢𝐧 𝐩𝐫𝐨𝐟𝐢𝐥𝐞𝐬 for most 𝐩𝐫𝐞𝐯𝐚𝐥𝐞𝐧𝐭 𝐏-𝐏 groups and described their properties: 👉 They cover both phage and plasmid functions 👉 And distinguish #P-Ps from #plasmids & #phages with high accuracy.
- 📌 𝐭𝐲𝐏𝐏𝐢𝐧𝐠'𝐬 workflow: 1️⃣ Compare proteins to 763 signature profiles 2️⃣ Process via two analytical branches 3️⃣ Assign 𝐜𝐨𝐧𝐟𝐢𝐝𝐞𝐧𝐜𝐞 𝐥𝐞𝐯𝐞𝐥𝐬 (High / Medium / Low) for simple interpretation. ✨ Currently covers the most prevalent groups (with experimentally proven members). 🚀 𝐍𝐞𝐰 𝐠𝐫𝐨𝐮𝐩𝐬 𝐜𝐚𝐧 & 𝐰𝐢𝐥𝐥 𝐛𝐞 𝐚𝐝𝐝𝐞𝐝!
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View full thread💻 Code: github.com/EpfeiferNutri/Phage-plasmids 📦 Data: doi.org/10.5281/zenodo.16616313 Huge thanks to my co-authors 🙌 @epcrocha.bsky.social, Remy A. Bonnin, and especially to my supervisor @eugenpfeifer.bsky.social! Special thanks to Marie-Agnes Petit & her team at MICALIS for deep discussions💡
