@akifoss.bsky.social
Viruses - Evolution - Bioinformatics Berlin // Robert Koch Institute
🚨 New Perspective in Nature Water 🚰💻
"Augmenting wastewater epidemiology with machine learning" 🧠🌍
A huge interdisciplinary collab w/ amazing colleagues @rki.de & beyond! 🙌
Special thx to lead author PhD student Eva & shared last Christopher for this effort!
🔗 www.nature.com/articles/s44...
🚀 Excited to share our NatComm paper on varVAMP – a open-source tool for degenerate primer design in viral genome seq & qPCR!
🔬 Supports diverse viruses SC2, HEV, Polio ...
🤝 Built in collaboration with amazing virus experts
🔗 github.com/jonas-fuchs/varVAMP
🧬 nature.com/articles/s41467-025-60175-9
What can wastewater tell us about viruses? 💩🚽🧬📈
During the COVID-19 pandemic many labs turned to wastewater monitoring to detect viruses. However, Prof White's group @unswbabs.bsky.social has been using wastewater for over 10 years to monitor circulating norovirus 🤮. 🧵
doi.org/10.1080/2374...
This approach enabled us to infer a mechanistic model of behaviour change for the 2022 Mpox outbreak in Berlin. You can preprint here: www.researchsquare.com/article/rs-6... 5/5
02.06.2025 19:25 — 👍 1 🔁 1 💬 0 📌 0
Very pleased to see our latest work on sampling of spreading processes on adaptive temporal network published at @plos.org Complex Systems!
Read more at doi.org/10.1371/jour... or find some information below
1/5🧵
"Roughly 1,500 babies have been born HIV-positive every day since January 21, because Musk cut off their mothers’ medication." prospect.org/power/2025-0...
30.05.2025 13:15 — 👍 6037 🔁 3043 💬 185 📌 339
Nature research paper: SARS-CoV-2 evolution on a dynamic immune landscape
https://go.nature.com/4aCPDem
You might be wondering why we haven't updated outbreak.info for months.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Happy to share this interview with Weijie Zhao from NSR at #OxfordUniversityPress. It covers questions I’m often asked—why I chose Korea, AlphaFold2, my unconventional journey into academia, and research insights. Thanks again for the fun conversation.
📄 academic.oup.com/nsr/article/...
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
27.05.2025 11:53 — 👍 13 🔁 21 💬 1 📌 3
Very glad to have participated in #ViBioM2025 and an honor to be in this panel! An amazing week of talks, posters, and discussing with colleagues at IHMT NOVA in Lisbon. Huge thanks to the @evbc.bsky.social and everyone in the organizing committee ✨😊
#VirusBioinformatics #IHMT #EVBC
What a week in Lisbon! 🇵🇹 ViBioM 2025 brought 150+ virus bioinformaticians from 34 countries to explore viral evolution, ML tools, & taxonomy challenges. 🌱 All plant-based thanks to @desafiovegetariano! Huge thanks to organizers, speakers, and community! #ViBioM2025 #Viromics
19.05.2025 08:05 — 👍 21 🔁 9 💬 0 📌 0We just succeeded in formally linking a specific rodent species - the otherwise charming fire-footed rope squirrel - to the onset of a mpox outbreak in a primate species - sooty mangabeys. Here Kai’s report on the preprint we released yesterday 1/2
09.04.2025 06:24 — 👍 14 🔁 7 💬 1 📌 2
The Department of Health and Human Services (HHS) is being decimated right now. Mass layoffs happening across agencies (NIH, FDA, CDC etc).
Some employees found out by security badge being denied. Others got email.
Line outside Health Resources and Services Administration this AM shared with me:
RFK, Jr. Laying Off the entire OIDP - Office Of Infectious Disease And HIV/AIDS Policy
Problem is: general public not aware of what OIDP stands for, let alone what it does - and why this vision, strategy and organization is crucial
Here's just a small segment of what OIDP:
🧵
Very happy to share this work on #SARS-CoV-2 dynamics!✨
Model based on immunity & cross-neutralization, considering the variants' infection history of the population. @martinhoelzer.bsky.social and other colleagues at #RKI and #FUBerlin, congrats to all!
