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 Hiring! — Verena

The Verena Institute is looking for a full stack developer or full stack development team (hereafter, the “Supplier”) to assist with the maintenance, documentation, and development of the Pathogen H...

viralemergence.org

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...

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...

General_Instructions

Instructions for Authors Authors who publish their papers under our open access model or who are NIH-funded will have their paper automatically depos

academic.oup.com

🚨 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!!

Communications Biology@commsbio.nature.com · 9mo ago

just in time for #batweek --Phylogenetic and ML analyses show that viral epidemic potential is not uniform among bats: virulence, transmissibility, and death burden cluster within distinct clades.🦇@carolinecummings.bsky.social @colincarlson.bsky.social @viralemergence.org go.sn.pub/acnbg1

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...

Museum collections and machine learning guide discovery of novel coronaviruses and paramyxoviruses

Natural history museum collections are valuable but underutilized resources for viral discovery, offering opportunities to test hypotheses about viral occurrence across space, time, and taxonomic grou...

biorxiv.org

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...

First Sin Nombre virus (Orthohantavirus sinnombreense) genome sequences from the Northwestern United States

We report the first Sin Nombre virus (SNV) genome sequences from the Northwestern United States and the first SNV sequences recovered from voles. Analysis of samples collected from 189 individual rode...

biorxiv.org

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...

Q&A with graduate student Ricardo Rivero

WSU graduate student Ricardo Rivero is working to uncover the rules that govern how viruses evolve — insights that could one day help predict viral behavior and guide public health responses. A PhD st...

vetmed.wsu.edu

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...

Release v1.0.0 · japilo/CoinfectionSimulator.jl

This version is more Julian in structure, and uses abstract types to manage simulation parameters, host populations, and disease strains. The simulations are more broken down into a network of help...

github.com

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...

Optimising predictive models to prioritise viral discovery in zoonotic reservoirs

Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guid...

thelancet.com

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.

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...

Release v0.3.0 · japilo/CoinfectionSimulator.jl

Version 0.3.0 has improved implementation of interaction strengths in prep_interaction_matrix. Previously, interaction_strength determined the standard deviation of draws from a normal distribution...

github.com

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.

🚨 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.

The Carlson Lab @ Yale@carlsonlab.bsky.social · last yr.

Viral -ologists of all kinds - molecular, ecological, evolutionary - if you haven't yet, consider joining our horizon scan study and help us identify 100 questions that are guiding where your field is going! Fill in the survey and get an invite to a workshop: 📝 airtable.com/appTW4ZoSFjR...

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!)

Steph N. Seifert, PhD@stephseifertphd.bsky.social · last yr.

🚨 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...

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!

The Carlson Lab @ Yale@carlsonlab.bsky.social · last yr.

Viral -ologists of all kinds - molecular, ecological, evolutionary - if you haven't yet, consider joining our horizon scan study and help us identify 100 questions that are guiding where your field is going! Fill in the survey and get an invite to a workshop: 📝 airtable.com/appTW4ZoSFjR...

🚨 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...

TATAT: a containerized software for generating annotated coding transcriptomes from raw RNA-seq data

Motivation: Many transcriptome creation workflows are not standardized, are difficult to install or share, prone to breaking as dependencies update or cease to be maintained and are resource intensive...

biorxiv.org

🚨 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

NYAS Publications

Bats are recognized to have distinct immune systems from other vertebrates that may allow them to host virulent pathogens without showing disease. However, these flying mammals are also incredibly di...

nyaspubs.onlinelibrary.wiley.com

🦠🌿🐦🧪 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...

Biodiversity science and biosurveillance are fellow travelers

The failure to meet the Aichi targets to alleviate global biodiversity decline (Nature 2020) was a wake-up call to the biodiversity monitoring community (T

academic.oup.com

Check out our new paper describing a wildlife disease data standard!

The Carlson Lab @ Yale@carlsonlab.bsky.social · last yr.

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...

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...

A minimum data standard for wildlife disease research and surveillance - Scientific Data

Scientific Data - A minimum data standard for wildlife disease research and surveillance

nature.com

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! 🦠😷

Hailey Robertson@haileyrobertson.bsky.social · last yr.

🧬🦠🌍 What are the big, cross-scale questions shaping the ecology and evolution of emerging viruses? @torrelavelle.bsky.social and I are building a list of 100 questions + want your input. Help map the future of EEID — fill out & share our short survey! 🔗 airtable.com/appTW4ZoSFjR...

All of this AND food systems are the #1 driver of pandemic risk! www.nature.com/articles/s44...

Pathogens and planetary change - Nature Reviews Biodiversity

This Review explores the relationship between emerging infectious diseases and biodiversity loss, and how both are connected to global environmental changes in the Anthropocene.

nature.com

Richard Waite@waiterich.bsky.social · last yr.

What is common knowledge in your field, but shocks outsiders? Food systems are the #2 contributor to climate change, the #1 driver of deforestation, the #1 driver of biodiversity loss on land, and the #1 user of freshwater. (It follows that food systems contain many solutions to these problems.)

🧬🦠🌍 What are the big, cross-scale questions shaping the ecology and evolution of emerging viruses? @torrelavelle.bsky.social and I are building a list of 100 questions + want your input. Help map the future of EEID — fill out & share our short survey! 🔗 airtable.com/appTW4ZoSFjR...

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