iiinova — where your digital self keeps evolving

Reposted by Shoichi Sakaguchi

Antigen Evolution & Design Lab @antigenevo.bsky.social · 22/07/2026

🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st

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Reposted by Shoichi Sakaguchi

Ingrida Olendraite @ingrida.bsky.social · 11/06/2026

It's today - don't miss it - simply click on zoom link below to join, no registration needed :) but adding it to your calendar for a reminder - suggested ;) @rdrpsummit.bsky.social

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Reposted by Shoichi Sakaguchi

Ingrida Olendraite @ingrida.bsky.social · 05/06/2026

RNA virus Journal Club is back after the pause for #ViBioM2026 📚 June 11th | Thursday, 15:30 Central European Time. AmpliDiff: a tool to find discriminatory genomic regions in viral genomes of a single species! Perfect for primer design! Join, talk & discuss! Details ⬇️ @rdrpsummit.bsky.social

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Reposted by Shoichi Sakaguchi

Ingrida Olendraite @ingrida.bsky.social · 16/03/2026

RNA virus Journal Club is on! 🌳March 17th | Tuesday, 10 AM Berkeley time / 18 PM CET 🕰️ You've probably heard about the meta-virus resource? We will get to dive into metaVR database & huge viral diversity within thanks to @mattlabguy.bsky.social 🥳 All welcome! Details ⬇️ @rdrpsummit.bsky.social

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Reposted by Shoichi Sakaguchi

Ingrida Olendraite @ingrida.bsky.social · 11/02/2026

what can be better than global RNA virome and Dolja? Nothing for me.. :) Join RNA virus club (by @rdrpsummit.bsky.social ) already tomorrow: Thu, Feb 12, 11:00 AM Pacific Time (US 🇺🇸, Canada🇨🇦) (or 7pm London time 🇬🇧) for an hour with one and only Prof. Valerian Dolja (Oregon State University)

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Ingrida Olendraite @ingrida.bsky.social · 09/01/2026

Save the date for phylogenetics! RNA virus Journal Club returns ( @rdrpsummit.bsky.social ) with @evogytis.bsky.social intro to his "Baltic" - python module to visualise phylogenetic trees. January 15th (Thu) - EEST Vilnius Time 3:00 PM Join slack for updates: join.slack.com/t/rdrp-io/sh...

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Reposted by Shoichi Sakaguchi

Ingrida Olendraite @ingrida.bsky.social · 11/12/2025

It's today! December 11th Finding endogenous viral elements in genomic data 🧑‍💻 by Sebastian Lequime (University of Groningen @rug.nl ) Time: 2pm EST🇺🇸 / 8pm CET 🇪🇺 / 4am JST 🇯🇵 Join @rdrpsummit.bsky.social RNA Virus Journal Club talk & discussion: oregonstate.zoom.us/j/9164101918... #rdrpsummit

onlinelibrary.wiley.com

detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data

Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs because of their genomic integration during t...

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Reposted by Shoichi Sakaguchi

Ingrida Olendraite @ingrida.bsky.social · 04/11/2025

RNA Virus Journal Club – Upcoming Talk - this thursday (Nov 6th !) With @rdrpsummit.bsky.social - excited to announce talk and discussion with Dr Sanguu Kim about HF nanopore sequencing strategy for virology :) calendar.app.google/oyRVP6v5Tvjg... CET: 14:00–15:00, Format: 30 min + 30 min

doi.org

CLAE: A High‐Fidelity Nanopore Sequencing Strategy for Read‐Level Viral Variant Detection and Environmental RNA Virus Discovery

High-fidelity Nanopore sequencing offers a cost-effective, portable path to uncovering viral dark matter in complex environments—but suffers from severe read-length bias, low throughput, and limited ...

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Reposted by Shoichi Sakaguchi

Simon Roux @simrouxvirus.bsky.social · 13/06/2025

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

doi.org

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Reposted by Shoichi Sakaguchi

Katy Brown @thekatybrown.bsky.social · 27/05/2025

I'm thinking of organising a meeting on endogenous viral elements (RNA, DNA and retroviral) - if you'd potentially be interested, please fill out the form here - forms.gle/wrCiWMw4yXZe... - so I can gauge interest. Please RT or share with anyone maybe interested! 🧪🧬🖥️🦠 #virology #bioinformatics

forms.gle

EVE Meeting Expression of Interest

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Shoichi Sakaguchi @sho1.bsky.social · 27/05/2025

Tried PyMOL for the first time today, and thanks to ChatGPT, I could do exactly what I wanted. While there’s a trend in bioinformatics toward developing GUIs to make tools more accessible, I wonder if, in the era of AI, command-line tools might actually get you to the result faster 🤔

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Xin Hou @xinhou.bsky.social · 12/05/2025

Thanks again for the organization and invitation, and also thanks for the food, for the help and everything!! Definitely amazing to be in Lisbon to share our work!!!

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Rachel Seongeun Kim @eunbelivable.bsky.social · 12/05/2025

I cannot say anything what F stands for. I'm thrilled to present BFVD at RdRp summit, finally found right place. Thank you for organizers for inviting to this awesome meeting and city. I would appreciate any feedback and feel free to discuss in-person or cia message. Explore BFVD🧭

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Reposted by Shoichi Sakaguchi

RdRp Summit @rdrpsummit.bsky.social · 02/05/2025

Introducing our invited speaker for the session on 'Viral Dark Matter' we have Rachel Seongeun Kim from the Seoul National University!!!! The registrations for on-site & remote participation are still open! More info: RdRp.io #RdRpSummit2025

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Reposted by Shoichi Sakaguchi

Ingrida Olendraite @ingrida.bsky.social · 02/05/2025

The previous RdRp summit manifested in the consensus statement. What the second @rdrpsummit.bsky.social brings us?:)

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Shoichi Sakaguchi @sho1.bsky.social · 17/04/2025

I’m in charge of IT for #RdRpSummit2025 and will coordinate the YouTube Live streaming. I’m preparing engaging features like dynamic camera work, seamless scene transitions and incorporating remote participant’s comments into the Q&A sessions!

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Reposted by Shoichi Sakaguchi

RdRp Summit @rdrpsummit.bsky.social · 19/02/2025

The abstract submission & registration for #RdRpSummit2025 is NOW OPEN!!! 🎉🙌 Do you work on RNA virus discovery using RdRps? Are you joining the #ViBioM2025 in Portugal? Consider submitting your research in one of our sessions! More info: RdRp.io

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Reposted by Shoichi Sakaguchi

Luke Hillary @lukehillary.bsky.social · 11/02/2025

We're looking for suggestions on how to update and adapt the Minimum Information about an Uncultured Viral Genome (MIUVIG) reporting standard. What works? What needs updating? Check out the survey forms.gle/DPHvMFe8Gsdj... 🧵

forms.gle

MIUViG Update Survey

Since the development of the Minimum Information about an Uncultured Viral Genome (MIUViG) standard (Roux et al. 2019), there has been an explosion in the number of genomic data generated on unculture...

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Reposted by Shoichi Sakaguchi

RdRp Summit @rdrpsummit.bsky.social · 07/02/2025

SAVE THE DATES & plan your trip to Lisbon (for #RdRpSummit2025 & #EVBC #ViBioM) this summer accordingly! Information on registration and abstract submissions coming very very soon! 🚄✈️✨🇵🇹🌊🌉

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Shoichi Sakaguchi @sho1.bsky.social · 07/02/2025

RdRp Summit 2025 will take place on May 11-12, 2025, in Lisbon, Portugal! 🏛️✨ More details coming soon, but for now, mark your calendars! Currently working on the official logo 🎨✍️ @rdrpsummit.bsky.social #RdRpSummit2025 #Procreate

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Reposted by Shoichi Sakaguchi

Katy Brown @thekatybrown.bsky.social · 16/11/2024

I made a quick Starter Pack for scientists working on virus discovery - please reply if you’d like me to add you to the pack (or remove you) or to recommend anyone! #scisky go.bsky.app/HK1wxRb

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RdRp Summit @rdrpsummit.bsky.social · 30/04/2024

We just published a consensus statement (with 47 institutes) on advancing #RdRp-based RNA virus discovery! We sum up the challenges identified at the 1st #RdRpSummit and propose solutions to ensure greater interoperability. Here’s a summary- t.ly/Uwqge

t.ly

Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities

Improved RNA virus understanding is critical to studying animal and plant health, and environmental processes. However, the continuous and rapid RNA virus evolution makes their identification and char...

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Shoichi Sakaguchi @sho1.bsky.social · 08/04/2024

NeoRdRp2, our HMM profile for detecting RNA viruses, has been updated on GitHub! 🦠🔬 A paper detailing the improvements will be published shortly. Check out the latest version here: github.com/shoichisakag... #RNAviruses #bioinformatics

github.com

GitHub - shoichisakaguchi/NeoRdRp

Contribute to shoichisakaguchi/NeoRdRp development by creating an account on GitHub.

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