@viralemergence.org
🦠 Yale-based, NSF-funded Institute for pandemic prediction. 💻 How we do it: data, biology, AI, and team science. ⚖️ Why we do it: scientific discoveries and global health security. ➡️ See more at viralemergence.org.
A long-term dream of mine has been to bridge @viralemergence.org's work on AI/ML-driven viral risk assessment with AI/ML-driven work on drug discovery. This would make a great topic for this fellowship here at Yale! If you're interested in applying, reach out. medicine.yale.edu/biomedical-d...
We're looking for a full-stack developer! Help us build the best open data platforms for pandemic prediction in the world.
Probably a short-term contract, but if you're looking for a full-time gig, let's talk. Inquire within: www.viralemergence.org/blog/were-hi...
we're excited to share that Proceedings B has also come on board for listing PHAROS as a recommended repository for open wildlife pathogen and parasite testing data! thanks to @royalsociety.org for the support. @viralemergence.org
royalsocietypublishing.org/rspb/pages/f...
❤️ @sicb.bsky.social @sicbjournals.bsky.social
Exciting news to start 2026: for the first time ever, the PHAROS repository for wildlife disease surveillance is a journal-recommended home for your archived data!
Thanks to Integrative and Comparative Biology for taking the leap with us 🦠🔢➡️🌎💻💫 academic.oup.com/icb/pages/Ge...
🚨 Exciting new work out today led by @carolinecummings.bsky.social! Do bats host deadly viruses? Yes - but only specific bats (that just happen to be found in a lot of places!). Challenging some big ideas in the zoonosis world with data. Well done Caroline and team!!
workshop group photo
Last week, we were lucky to host an international workshop on Pandemic Risk Scenarios for the 21st Century, with generous support from PAX sapiens and @viralemergence.org. Lots of lessons learned from climate and biodiversity science on how to design useful models and imagine better futures!
🦇🦠 New preprint - in a long-term effort led by the amazing @mayajuman.bsky.social, we've shown that the ML tools developed by @viralemergence.org let us efficiently screen museum collections for pathogens with pandemic potential
🎉🔓 www.biorxiv.org/content/10.1...
Excited to share our study reporting the first Sin Nombre virus (SNV) genome sequences from the Northwestern U.S., and the first ever from a vole host.
www.biorxiv.org/content/10.1...
Honored to be featured in WSU’s “Q&A with a Graduate Student.” I talk about my path, current work, and the role of mentorship (special mention to my PI, @stephseifertphd.bsky.social) and collaboration in advancing my research goals. Full Q&A: vetmed.wsu.edu/qa-with-grad...
Figure 3 of our paper, which shows viral coinfection networks at the virus level
New preprint! 🥳🎉 We looked at viral coinfection patterns at the largest scale ever in wildlife. We found a strong association among CoVs, PMVs, and influenza A, and higher coinfection rates in wildlife trade; plus, evidence that bats accumulate persistent infections. www.biorxiv.org/content/10.1...
v1.0.0 of CoinfectionSimulator.jl is out! I think I'm starting to get a feel for coding in #JuliaLang style. You can use this simulator to model multiple directly transmitted infections in a host population, including different disease types and interactions between them. github.com/japilo/Coinf...
A table of syndromic features that best distinguish dengue, chikungunya, and Zika
Like I said: a small part of a much bigger project, which I'll let @faustobustos.bsky.social tell you about - including a much longer-term effort to figure out how to improve WHO and PAHO case definitions / syndromic surveillance / clinical treatment for very hard to distinguish endemic arboviruses.
One thing that makes this project special to me - Fausto and I adapted these algorithms from the @viralemergence.org codebase, where we've been using them to predict wildlife reservoirs of viruses like coronaviruses, hantaviruses, and paramyxoviruses. 🦇🦠🔓 www.thelancet.com/journals/lan...
Just another example among many of how NSF's investment in our Center - and specifically, in a program that uses open science and the good, ethical, runs-on-your-laptop, pre-chatbot kind of AI/ML to understand fundamental biology - has had broader benefits for public health and clinical medicine.
Paper title: "Comparison of dengue, chikungunya, and Zika among children in Nicaragua across 18 years: a single-centre, prospective cohort study" Figure beneath it shows classification rates for different diseases and the most informative variables in each model
NEW! 🚨🦠 We trained ML algorithms to identify the clinical presentations that best distinguish pediatric dengue, chikungunya, and Zika. One notable finding: afebrile dengue may be being missed. A small part of a big project led by @faustobustos.bsky.social, out now 🔓 www.thelancet.com/journals/lan...
The next release will be a major one that makes the package more Julian, as per some helpful comments by @ctrlalttim.com. I may have learned the basics of coding in Julia, but I'm still teaching myself to think beyond my R approach to scientific programs and organize my code differently.
v 0.3.0 of CoinfectionSimulator.jl is out, now with a more logical implementation of species pair interaction strength in `prep_interaction_matrix`. github.com/japilo/Coinf...
World Health Assembly
5️⃣ Since 2023, discussions about creating an "IPCC for Pandemics" have been taken up by the UN Foundation, the National Academy of Medicine, and academic orgs like Fiocruz and Verena. Now the fight heads to Geneva. If the ball doesn't start rolling at World Health Assembly 2026, expect it in 2027.
Pathways to an Intergovernmental Panel on Pandemics: lessons from the IPCC and IPBES Colin J Carlson, Christopher H Trisos, Ben Oppenheim, Shweta Bansal, Sara E Davies, Aïda Diongue-Niang, Victoria Y Fan, John D Kraemer, Rachel Golden Kroner, Lawrence O Gostin, David T S Hayman, Marion Koopmans, Torre E Lavelle, Carlos G das Neves, Zoe O’Donoghue, Laura M Pereira, Benjamin Roche, Matiangai Sirleaf, Kayla Zamanian, Carlos Zambrana-Torrelio, Alexandra L Phelan Pandemics pose a global threat to human wellbeing, justice, economies, and ecosystems and are comparable with other planetary crises such as climate change and biodiversity loss in terms of urgency and impact. The global community would benefit from a dedicated scientific synthesis body to assess pandemic risks and solutions. In this Personal View, we explore proposals for an Intergovernmental Panel on Pandemics and assess potential pathways to its creation. Learning lessons from the Intergovernmental Panel on Climate Change (IPCC) and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) might help national governments and international organisations to chart a course through important decisions about format, governance, operations, scientific scope and process, and ability to recommend policies that make the world safer.
🚨 Very, very big news. Today, a global coalition - including members of the IPCC, IPBES, and WHO expert advisors, as well as independent virologists, epidemiologists, and lawyers - started the process of creating an "IPCC for Pandemics."
🔓 www.thelancet.com/journals/lan...
🧵 Five things to know 👉
👋 We’re still collecting responses!! We’d love your input if you’re in an adjacent field — already seeing some super cool questions that make me so excited for the workshop.
Newest software stuff from team @viralemergence.org and maybe the most widely-useful thing we've developed? Huge congrats to Alexander and Steph, this is such an amazing bioinformatics tool. (Just wait until you see what they're doing with it!)
This is a really great project led by two PhD students in our group, and I can already tell it's going to lead to a really fun workshop. Consider participating if you're a virologist / disease ecologist / something more like that than not like that!
🚨 Our team just released a reproducible Docker pipeline for RNAseq assembly and annotation designed for nonmodel organisms!
We're using it to explore how bats manage viral infections, but it's built for broad utility in wildlife transcriptomics. @viralemergence.org
www.biorxiv.org/content/10.1...
🚨 New publication out today. Bats are over 1480 species. In this latest article, we discuss the diversity within bats and their immune systems. Elegantly led by the Becker and Frank laboratories.
nyaspubs.onlinelibrary.wiley.com/doi/10.1111/...
@danjbecker.bsky.social @bat-lady.bsky.social
🦠🌿🐦🧪 How can biodiversity monitoring help global efforts in disease surveillance?
With ✨ fantastic ✨ colleagues from @viralemergence.org and the @geobon.org working group on One Health, we try to identify three key lessons for the future.
🧵 A short thread!
academic.oup.com/bioscience/a...
Check out our new paper describing a wildlife disease data standard!
Do you study wildlife disease? Don't just share your sequences - share your testing data! We've developed a minimum data standard and an R package to help you, and wrote a little how-to-share-data handbook for disease ecology and One Health surveillance projects 🦇🦟🦠🗺️🔢
www.nature.com/articles/s41...
Virus researchers! Please consider participating in this project - it would be a huge help to our lab, and we think it'll lead to some really exciting synthesis. Plus, you'll get an invitation to participate in a workshop later in the project! 🦠😷
All of this AND food systems are the #1 driver of pandemic risk! www.nature.com/articles/s44...