iiinova — where your digital self keeps evolving

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Colin Carlson @colincarlson.bsky.social · 02/02/2026

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...

medicine.yale.edu

Yale University and Boehringer Ingelheim Biomedical Data Science Fellowship Program

Yale University, in partnership with Boehringer Ingelheim, one of the world’s leading pharmaceutical companies, launched in 2021 a Biomedical Data Science

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Verena @viralemergence.org · 17/01/2026

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...

viralemergence.org

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...

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Daniel Becker @danjbecker.bsky.social · 15/01/2026

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...

royalsocietypublishing.org

For Authors | Proceedings B | The Royal Society

For Authors | Proceedings B | The Royal Society Information for authors   Presubmission enquiries ...

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Verena @viralemergence.org · 05/01/2026

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...

academic.oup.com

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

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Colin Carlson @colincarlson.bsky.social · 30/10/2025

🚨 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!!

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 22/09/2025

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!

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Ricardo Rivero H. 💻🧬 @ricardoriveroh.bsky.social · 13/09/2025

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...

vetmed.wsu.edu

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...

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Colin Carlson @colincarlson.bsky.social · 10/09/2025

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...

Figure 3 of our paper, which shows viral coinfection networks at the virus level

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Dr. July Pilowsky @pilowsky.me · 14/08/2025

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...

github.com

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...

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Colin Carlson @colincarlson.bsky.social · 06/08/2025

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.

A table of syndromic features that best distinguish dengue, chikungunya, and Zika

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Colin Carlson @colincarlson.bsky.social · 06/08/2025

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...

thelancet.com

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...

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Colin Carlson @colincarlson.bsky.social · 06/08/2025

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.

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Colin Carlson @colincarlson.bsky.social · 06/08/2025

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...

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

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Dr. July Pilowsky @pilowsky.me · 30/07/2025

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.

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Colin Carlson @colincarlson.bsky.social · 17/07/2025

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.

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Colin Carlson @colincarlson.bsky.social · 17/07/2025

🚨 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 👉

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.

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Hailey Robertson @haileyrobertson.bsky.social · 16/07/2025

👋 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.

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Colin Carlson @colincarlson.bsky.social · 14/07/2025

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!)

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Colin Carlson @colincarlson.bsky.social · 16/07/2025

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!

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Steph N. Seifert, PhD @stephseifertphd.bsky.social · 14/07/2025

🚨 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...

biorxiv.org

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...

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Timothée Poisot @ctrlalttim.com · 30/06/2025

🦠🌿🐦🧪 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...

academic.oup.com

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

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Collin Schwantes @collin-schwantes.bsky.social · 23/06/2025

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

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 23/06/2025

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...

nature.com

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

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

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Colin Carlson @colincarlson.bsky.social · 17/06/2025

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! 🦠😷

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Hailey Robertson @haileyrobertson.bsky.social · 17/06/2025

🧬🦠🌍 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...

airtable.com

Airtable | Everyone's app platform

Airtable is a low-code platform for building collaborative apps. Customize your workflow, collaborate, and achieve ambitious outcomes. Get started for free.

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Colin Carlson @colincarlson.bsky.social · 17/06/2025

A brief update on this today: we are still down $1.25m in our final year, and down a still-unknown amount - could be less, could be $2.5m more - starting in September. No one has stepped in to save us. If you are a philanthropy looking to take action, we still need your help. 🫂

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Ricardo Rivero H. 💻🧬 @ricardoriveroh.bsky.social · 16/06/2025

If you’re at @eeid2025.bsky.social Come see my poster tomorrow, and let’s talk about viral evolution!

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Colin Carlson @colincarlson.bsky.social · 10/06/2025

Last year, I helped organize a workshop hosted by Fiocruz and the National Academy of Medicine to consider an "IPCC for pandemics" and explore the intersection of climate change and pandemic risk. You can read the proceedings now 🎉🇧🇷 nam.edu/perspectives...

NAM Discussion Proceedings: Pandemic risk assessment and its intersection with climate change

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Colin Carlson @colincarlson.bsky.social · 10/06/2025

This important commentary from Victor Dzau (NAM/GPMB), Lourdes Oliveira Aguiar (Fiocruz), and Joy Phumaphi (GPMB) also outlines the case for a new channel for scientific assessment, synthesis, and policy advice on pandemic risk (e.g., an "IPCC for pandemics") nam.edu/perspectives...

nam.edu

The Imperative of a Global Pandemic Risk Assessment Framework - NAM

In just two decades, the world has faced a relentless barrage of deadly infectious disease outbreaks— SARS in 2002, H1N1 in 2009, Ebola in 2014, Zika in 2016,

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Verena @viralemergence.org · 02/06/2025

An update from the team on the uncertain future of our program and the impact of NSF budget cuts. Please share and reach out 🦠

Some difficult news from the team:

In NSF's FY25-26 Budget Request to Congress, we learned that our program will take a whopping 50% cut - meaning that in September, we'll be $1.25m short of an operating budget that currently supports a cohort of seven PhD students, four postdocs, and three full-time staff.

Verena is one of the largest and last pandemic prevention-focused programs in the United States: since 2020, we've supported the training of over 60 postdocs, graduate students, and undergraduates. Our researchers have established unique laboratory resources for studying animal immune systems, and discovered new antiviral immune adaptations in bats; developed risk assessment algorithms for wildlife and livestock viruses, and diagnostic algorithms for viruses like dengue, Ebola, and Zika; and quantified the effects of climate change, deforestation, and factory farming on spillover risk. Everything we develop is 100% open source, and our data has supported the research of nearly 150 external researchers in 21 countries to date.

We have three months to make up our budget shortfall. Every dollar spent on Verena supports not just our team, but the community of researchers who use our data, code, and resources. You can help us by sharing this post, and reaching out if you're able to support a unique and vulnerable program. Or just head over to viralemergence.org, and take a look at what we do. 🦟 🦇 🦠

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Cole Brookson @colebrookson.bsky.social · 02/06/2025

It's hard to overstate how devastating these cuts will be for our incredible group of people working on these important questions.

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Dr. July Pilowsky @pilowsky.me · 02/06/2025

I’m one of those four postdocs. Fight the budget cuts, for the sake of pandemic prevention.

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Verena @viralemergence.org · 02/06/2025

An update from the team on the uncertain future of our program and the impact of NSF budget cuts. Please share and reach out 🦠

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 08/05/2025

Some coverage of our recent work on Oropouche virus. Big lingering questions: Where are these midges? Are we at risk in the United States? Is climate change contributing to bigger epidemics? ysph.yale.edu/news-article...

ysph.yale.edu

Oropouche is spread by midges, not mosquitoes

In a new study, Yale researchers conclude that Oropouche fever is spread chiefly by biting insects called midges, while mosquitoes are unlikely to play much of

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Colin Carlson @colincarlson.bsky.social · 02/05/2025

I talked to Nature about the latest development at NSF, which is a five-alarm fire for American science. The scale of immediate impact is massive. We narrowly escaped this affecting @viralemergence.org for now, but will have to shut down in a few months if this stays. www.nature.com/articles/d41...

nature.com

Exclusive: NSF stops awarding new grants and funding existing ones

US science funder also plans to screen grant applications for compliance with ‘agency priorities’.

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Colin Carlson @colincarlson.bsky.social · 30/04/2025

What does this mean in practical terms? We don't have a great handle on how Oropouche virus is maintained in nature (more on this later...) or whether it could spread in the United States - especially when this is all the data we have on where the midge vectors are found.

Occurrence data map from GBIF for Culicoides paraensis, showing a big hole in most of Brazil and just a couple scattered points in North America.

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Colin Carlson @colincarlson.bsky.social · 30/04/2025

Turns out, that's only seven studies between 1961 and 2024. Still, a fair bit of work to extract the data, summarize it, make sense of methodological differences, and come to a conclusion about public health risks. Our open data initiatives can save us some time on #1 and #2 before outbreaks start.

Fig 3. Experimental vector origin location and collection year. a) Map and b) table of the origin of each vector used in experimental vector competence publications. World map created in BioRender. c) The vector collection year of each colony/strain of species (line) relative to the corresponding publication year (circle/hexagon). Vectors without a collection year stated in the publication are shown as hexagons without a corresponding line.

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Colin Carlson @colincarlson.bsky.social · 30/04/2025

🦟🦠 NEW! We looked at every experiment going back to the 1960s, and found that mosquitoes are almost certainly not primary or secondary vectors of Oropouche virus - a common claim in both the scientific literature and public health communication. #EpiSky #IDSky 😷🧪 journals.plos.org/plosntds/art...

journals.plos.org

Vector competence for Oropouche virus: A systematic review of pre-2024 experiments

Oropouche virus has recently become an urgent threat to public health in Central and South America. OROV is mainly transmitted by biting midges; however, some public health agencies and scientific sou...

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Colin Carlson @colincarlson.bsky.social · 28/04/2025

Hey disease ecologists: We're still doing that open data thing. A few months ago, we hired two amazing data scientists, and they'd love to work with you to help you use this data standard (and a new R package!!) to get your data into a FAIR repository. Please reach out if you want to work with us!

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Verena @viralemergence.org · 28/04/2025

Updated preprint: "A minimum data standard for wildlife disease research and surveillance." With: ✏️ A new version of the standard 💻 A new R package to help you format your data 🦇 A retrospective mini-study of data sharing rates Preprint here: ecoevorxiv.org/repository/v... Got data? Reach out! 🦠🧪

ecoevorxiv.org

A minimum data standard for wildlife disease research and surveillance

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Verena @viralemergence.org · 28/04/2025

Public health journalists: We have a new paper coming on April 30! Currently under embargo, but the headline is "Oropouche virus is probably transmitted by midges, not mosquitoes - but it's been horribly understudied for decades." Ping us if you're keen!

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PLOS Biology @plosbiology.org · 22/04/2025

Research on the #bat innate #ImmuneResponse to pathogens is hindered by a lack of lab reagents. @fviromics.bsky.social @stephseifertphd.bsky.social @virology.bsky.social &co generate new bat #CellLines, enabling studies on viral susceptibility & immune responses @plosbiology.org 🧪 plos.io/4jkXukf

Top left: Primary cells were isolated from brain, lung, kidney, liver, and spleen of a single C. perspicillata bat. Bottom left: CaPsm-K primary and immortalized cells were transfected with 10 μg of poly (I:C) chemically labeled with rhodamine (pIC-Rho) for 16 h. Following fixation, cells were stained with antibodies against GAPDH and DAPI and visualized by confocal microscopy. Scale bars represent 25 μm. Right: Clonal transduced kidney cells infected with Seoul virus (SEOV) were monitored by end-point microscopy for Seoul nucleocapsid protein.

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Colin Carlson @colincarlson.bsky.social · 28/03/2025

The first really big comparative immunology study from @viralemergence.org - some bat cells can be infected with Zika virus, others can't, and we're getting to the bottom of why. First step in a long journey to understand how some bats are different, and what that means for human health!

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Steph N. Seifert, PhD @stephseifertphd.bsky.social · 28/03/2025

Are bats tolerant of all viruses? With a comparative -omics approach, we show that Egyptian fruit bat cells show both antiviral and pro-inflammatory immune responses to infection with Zika virus while our Jamaican fruit bat cells are not susceptible. www.biorxiv.org/content/10.1...

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