iiinova — where your digital self keeps evolving

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Colin Carlson @colincarlson.bsky.social · 09/09/2026

🚨 NEW: Biodiversity monitoring can guide surveillance for emerging pathogens. In a new PLOS Ecosystems study led by @mdcatchen.bsky.social, we present computational algorithms to select surveillance sites that capture the most actionable data. Out now: dx.plos.org/10.1371/jour...

Fig 3. The case study for South Korea.

(A): Bivariate plot of dose (increasing green) and dose uncertainty (increasing blue). (B): Bivariate plot of dose (increasing green) and prevalence uncertainty (increasing orange; measured as the sum of estimated variance from kriging across each host-virus pair). (C): The spatial strata for which occurrence, prevalence, and both forms of sampling should occur (see main text for how these are computed). (D): The priority scores for regions where discovery sampling is a priority (increasingly blue) and prevalence sampling is the priority (increasingly purple) in their respective strata. (E): The total priority map with sites selected using Balanced Acceptance Sampling. The marker shape of each site corresponds to the type of sampling that should occur there, based on the stratum in (C) that each point falls within. Administrative boundaries come from GADM.

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Colin Carlson @colincarlson.bsky.social · 23/03/2026

‼️ New preprint: By solving a paradox in graph theory, we show that specialist symbionts constrain ecosystem structure, drive biodiversity, and face high extinction risk. With @jbyoder.org and @ctrlalttim.com: 🎉 Specialists drive biodiversity scaling in symbiotic relationships

Sublinear and linear scaling coexist in bipartite graphs

Real ecological networks are constrained by the presence of specialists

Coextinction risk is driven by host extinction risk - but especially high for specialists

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Colin Carlson @colincarlson.bsky.social · 05/03/2026

NEW PREPRINT! 🦠⚖️🌡️ The Pandemic Agreement is the first global health treaty to name climate change, and behind the scenes, the UNFCCC was a source of both inspiration and conflict. Cristina Arnés-Sanz and team tracked climate issues through three years of negotiations: papers.ssrn.com/sol3/papers....

Climate change in the WHO Pandemic Agreement negotiations: a qualitative study. Graph shows the evolution of different topics over different articles.

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 09/02/2026

New work in progress on primate reservoirs of arboviruses - when do they actually matter for transmission? and where will climate change take them - on display at the Vector-Borne and Zoonotic Diseases Symposium last Friday!

Cecilia Sanchez presents a slide showing geographic gaps in sampling effort

Hailey Robertson presents on arbovirus enzootic cycles

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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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Colin Carlson @colincarlson.bsky.social · 15/01/2026

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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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 · 23/12/2025

NEW!🦠🌡️ : What makes a "dengue year" like 2023-24? It's hard to pin down an answer unless you can homogenize out all the spatial variation and temporal trends. But once you do, the answer is pretty clean: dengue years are hot years. Last one of the year (unless...?) 👉 www.medrxiv.org/content/10.6...

Graph showing temperature anomaly and other covariates' effects on "RISc" score globally and by region

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 25/09/2025

🚨 We're about to start reviewing applications, but there's still time to reach out for our postdoc position on climate change impact attribution! If you have experience with attribution science or climate epidemiology, and want to help us launch the Global Burden of Climate Change Study, reach out!

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Colin Carlson @colincarlson.bsky.social · 22/09/2025

Believe it or not, @alexandraphelan.bsky.social and I started talking about the concept for this workshop 5? 6? years ago, so it was absolutely amazing to finally pull this off with exactly the right people, especially in a year when it feels like we're taking a lot of L's on actionable science 🥰

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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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Torre Lavelle @torrelavelle.bsky.social · 17/09/2025

Check it out! New work in which we undertake the first systematic look at the science of health impact attribution, plus a great thread by @colincarlson.bsky.social below on attribution science and what we tried to accomplish with this study.

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Colin Carlson @colincarlson.bsky.social · 17/09/2025

🚨 NEW: Climate change is already causing 30,000 deaths per year - a global annual economic loss of $100-350B USD - but the true damage is probably 10x higher. Out TODAY in Nature Climate Change: the first systematic look at the science of "health impact attribution" 🔓 www.nature.com/articles/s41...

"Health losses attributed to anthropogenic climate change," a brief communication in the journal Nature Climate Change. There's a map showing regions of the world, and pie charts of relevant studies as they apply to different health impacts like "heat-related deaths" and "maternal and child health"

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Juliana Taube @julianataube.bsky.social · 12/09/2025

3️⃣ During the pandemic & at baseline, younger adults, men, & Hispanic & Black individuals have more contacts & are at greater disease risk These geographic & social differences in risk can help target public health resources & surveillance 📢 /11

Figure showing contact by age, gender, race or ethnicity, and setting during the pandemic and at baseline

(A) Mean pandemic and baseline non-household contact rate by age. Each point represents a county-age category. Analysis was limited to counties with five or more responses per age category per week. Contact decreases with age.

(B) Mean pandemic and baseline non-household contact rate by gender. Each point represents a county-gender category. Analysis was limited to counties with five or more responses per gender category
per week. Contact is higher in men than women.

(C) Mean pandemic and baseline non-household contact rate by race or ethnicity. Each point represents a state-race or ethnicity category. Analysis was limited to states with ten or more responses
per race or ethnicity category per week. All racial and ethnic categories are non-Hispanic unless labelled otherwise. Other denotes individuals who reported their race as American Indian or Alaska Native, Native Hawaiian or Pacific Islander, or other, or as falling in multiple categories. Contact is lowest in Asian respondents, and highest in individuals reporting other or multiple race categories.

(D) Mean pandemic and baseline non-household contact rate by setting. Each point represents a county-setting. Analysis was
limited to counties with ten or more responses per setting per week. Contact is highest at work, followed by shopping, then social settings.

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Juliana Taube @julianataube.bsky.social · 12/09/2025

2️⃣ Contact patterns vary across US counties regardless of disease 🌎 Based on population density, we expected urban counties 🏙️ to have higher contact rates than rural ones 🚜 This is true at baseline, but not during the pandemic, when urban areas were more responsive to gathering restrictions /10

Figure showing spatial heterogeneity and urban–rural gradient of pandemic and estimated non-pandemic contact

(A) Mean number of non-household contacts per person per day for each county relative to the national mean (8⋅7 contacts per person per day) during the COVID-19
pandemic (Oct 1, 2020, to April 30, 2021). There was high spatial heterogeneity in contact, even within states, which was fairly consistent across time. Counties shaded in grey did not have a sufficient sample size to estimate contact.

(B) Map of inferred mean number of non-household contacts per person per day for
each county relative to the national mean (10⋅9 contacts per person per day) in a non-pandemic scenario. Spatial heterogeneity in contact remains high, although which counties have values above and below the national mean has shifted compared with the pattern observed during the COVID-19 pandemic.

(C) The mean contact rate (non-household contacts) for each county decreases with increasing urbanicity during the pandemic, but increases with urbanicity during inferred non-pandemic times.
Only counties with ten or more responses per week each week (from Oct 1, 2020, to April 30, 2021) are included. NCHS class describes the urbanicity of the county, with 1 indicating a large central metropolitan area and 6 representing rural, non-core areas. NCHS=National Center for Health Statistics.

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Juliana Taube @julianataube.bsky.social · 12/09/2025

1️⃣ Early in the pandemic, contact varied over time 📆 However, contact and COVID-19 incidence were anti-correlated during this period (when disease went ⬆️, contacts went ⬇️) Thus, after controlling for disease, there was no longer any systematic variation in contact over time /8

Figure showing contact dynamics observed over time during the COVID-19 pandemic and estimated non-pandemic contact dynamics, by county

(A) Mean number of daily non-household contacts for individual counties over time during the COVID-19 pandemic. Contact is presented as a Z score relative to each
county’s mean to allow comparison between time series despite the large range of mean contact values across counties. Each line represents a county and is coloured by mean contact relative to the national mean. The black line shows the Z score of the centred 3-week rolling average of national COVID-19 case incidence for context.
Counties had similar contact dynamics over time: most counties had higher contact during the summer of 2020, and all had lower contact during the winter of 2020–21. Counties in which contact decreased in the summer of 2020 were typically in states that had a higher incidence of COVID-19 during that time.

(B) Mean contact rate (non- household contacts) in the absence of disease (baseline; slate) was effectively constant over time, compared with observed contact during the pandemic (teal), across a diverse set of counties. We controlled for disease using a linear regression model that predicts contact from national case incidence, state and county policy data, and county vaccination coverage. This analysis is restricted to Oct 1, 2020, to April 30, 2021, to encompass a full wave of COVID-19. Shaded areas represent 1 SD above and below the fitted contact value or estimated non-pandemic value.

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Juliana Taube @julianataube.bsky.social · 12/09/2025

Our paper on US contact patterns is now published in The Lancet Digital Health! doi.org/10.1016/j.la... Thanks to my brilliant coauthors @zsusswein.bsky.social, @vcolizza.bsky.social, & @bansallab.bsky.social for their help with this project. Read on for an overview of our findings... 🧵

Screenshot of the paper titled "Characterising non-household contact patterns relevant to respiratory transmission in the USA: analysis of a cross-sectional survey"

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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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Colin Carlson @colincarlson.bsky.social · 27/08/2025

We're hiring! We have funding for a 1-year (to start with, but hopefully longer) postdoc working on climate change impacts on health broadly, and helping us launch gbcc.study. Strong skills in epi methods or attribution science needed. Can potentially be remote. Please share!

gbcc.study

The Global Burden of Climate Change Study

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 19/08/2025

We may have a one-year postdoctoral position opening! We're looking for someone with experience in attribution science OR very strong skills in climate epidemiology to come help us launch a Global Burden of Climate Change Study. Remote possible for the right person; aim to raise $ for a second year.

The Global Burden of Climate Change Study Working Group

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 19/08/2025

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Karolina Heyduk @kheyduk.bsky.social · 19/08/2025

Our "Joshua tree is CAM" paper is finally out: nph.onlinelibrary.wiley.com/doi/10.1111/... Data collection started back in 2021, when we saw weird results in some RNAseq that made me stop and wonder if Joshua trees, long thought to be C3, were actually...CAM!

nph.onlinelibrary.wiley.com

Cryptic CAM photosynthesis in Joshua tree (Yucca brevifolia, Y. jaegeriana)

Joshua trees are long-lived perennial monocots native to the Mojave Desert in North America. Composed of two species, Yucca brevifolia and Y. jaegeriana (Asparagaceae), Joshua trees are imperiled by...

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 18/08/2025

We had a great time at #ESA2025! Disclaimer: Ekiben sandwich not included in conference registration or ESA membership

Hailey Robertson presenting about the role of primates in arbovirus sylvatic maintenance

Collin Schwantes presenting about how to make an effective data management plan

Colin Carlson presenting about scaling in host-virus networks

The Ekiben neighborhood bird (fried chicken) and tofu brah (fried tofu sandwich with a cool sort of carrot slaw) and a yuzu white peach soda

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John Holbein @johnholbein1.bsky.social · 18/08/2025

"Conditional cash transfer could substantially contribute towards reducing AIDS-related inequalities and achieving the AIDS-related Sustainable Development Goal."

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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 08/08/2025

I am really excited to be a part of this team. We took our time writing this, putting a lot of thought into how our journeys as #NativesInSTEM were affected by different aspects of Universities and looking for commonalities across the world. I hope folks in academia appreciate this work.

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

This was just a fun side quest, but if our lab thought about this more in the future, I'd want to revisit some of the ideas from this 2020 preprint - rare or unique clinical presentations can improve syndromic surveillance for emerging diseases among endemic ones www.medrxiv.org/content/10.1...

Graphs with beautiful paint-drippy colors showing that after a certain number of cases it becomes easy to correctly classify different diseases with similar clinical presentations

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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

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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Prof Sam Illingworth @samillingworth.com · 03/08/2025

🌍 Green gains, blue losses From 2003–2021, plants on land grew more, but ocean productivity declined, likely due to climate warming. Land is boosting Earth’s carbon uptake, but oceans are showing signs of stress. 🔗 www.nature.com/articles/s41... #ClimateCrisis #SciComm 🧪

nature.com

Contrasting biological production trends over land and ocean - Nature Climate Change

The authors jointly assess the changes in land and ocean net primary production from 2003 to 2021. They show contrasting trends, with overall planetary increases (0.11 ± 0.13 PgC yr−1) driven by terre...

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College of Health Solutions at Arizona State University @asuhealthsolutions.bsky.social · 01/08/2025

In summer, Phoenix faces dual crises: extreme heat and drug overdoses. Our latest #HealthTalks examines how those two are connected. 💻 Hear from physicians Pope Moseley and David Sklar and substance-use researcher Raminta Daniulaityte, all @asuhealthsolutions.bsky.social faculty: ow.ly/F4RF50WyOOx

The words Health Talks appear in large black type to the right of a gold polygon that has 8
points. Below, on a gold background, appear the words, College of Health Solutions. At left, type reads, "Too Hot to Handle: Extreme Heat and Drug-Related Risks."

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Jo Rhodes @drjorhodes.com · 29/07/2025

A little holiday news: Evolution of antifungal resistance in the environment www.nature.com/articles/s41... This started out as a little thought way back in early 2024 between @normanvanrhijn.bsky.social and I, and turned into a full on review! We hope it proves useful to the community.

nature.com

Evolution of antifungal resistance in the environment - Nature Microbiology

This Review discusses the evolution, emergence and expansion of environmental fungicide and antifungal drug resistance.

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Colin Carlson @colincarlson.bsky.social · 25/07/2025

New workshop paper out today with 60 of our closest friends, providing guidance on how to design a study attributing health impacts to climate change. Hopefully this helps expand the field and start closing the representation gaps we discuss in our forthcoming work link.springer.com/article/10.1...

link.springer.com

The attribution of human health outcomes to climate change: transdisciplinary practical guidance - Climatic Change

For over 30 years, detection and attribution (D&A) studies have informed key conclusions in international and national assessments of climate science, providing compelling evidence for the reality and...

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Te Pūnaha Matatini @tepunahamatatini.bsky.social · 17/07/2025

A new paper in The Lancet Microbe lays the groundwork for a global science-policy body to tackle pandemic threats — modeled after the IPCC for climate change 🧪🧵

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Colin Carlson @colincarlson.bsky.social · 22/07/2025

We're launching a Global Burden of Climate Change Study with support from @yalesph.bsky.social! It's been 20 years since the last one, and at least 4 million people have died. Stay tuned for preliminary results and a more formal announcement in a month or so. #CountEveryClimateDeath

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 22/07/2025

A big announcement today! A huge round of thanks to @yalesph.bsky.social for the support to launch a Global Burden of Climate Change Study. There's nowhere in the world that's better positioned to do this kind of cross-cutting work than @yaleemd.bsky.social and YCCCH. ysph.yale.edu/news-article...

ysph.yale.edu

New YSPH Pilot Grants Support Innovative Interdisciplinary Research

The Yale School of Public Health recently launched its inaugural Transformational Pilot Funding grants, providing internal seed money to empower faculty to

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The Carlson Lab @ Yale @carlsonlab.bsky.social · 21/07/2025

In a few weeks, we'll be publishing the finding that [redacted] people die every year because of climate change, equivalent to a loss of $[redacted]T USD, every year. Here's what it costs us to open that publication to you. We have no federal grants for that work, and can't apply for them.

$12,690 OA fees for Nature Climate Change

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Erin Sauer @sauerscientist.bsky.social · 21/07/2025

New paper out modelling how the nutritional content of wild bird foods could affect disease transmission - a nice follow-up application of our Molecular Ecology study showing that food quality can affect immune function and disease tolerance. doi.org/10.1093/icb/... @durantlab.bsky.social

doi.org

The nutritional content of anthropogenic resources affects wildlife disease dynamics

Synopsis. Wildlife have become increasingly reliant on human-supplemented food, affecting interactions between individuals and subsequently pathogen transm

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

3️⃣ An "IPCC for pandemics" would let scientists develop consensus on key issues where the evidence is complex and sometimes contradictory - think airborne transmission, social distancing, herd immunity, school closures, pathogen origins, and most importantly, future risks - BEFORE the next pandemic.

Two women social distancing on a park bench, wearing masks

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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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Dave Larsen @dalarsen.bsky.social · 16/07/2025

Estimating the reproductive number from wastewater. It is much easier than some would suggest, and can be done without high-powered computing. A review and comparison of different methods from our team over here. 🧪 #EpiSky www.sciencedirect.com/science/arti...

sciencedirect.com

Estimating the effective reproduction number from wastewater (Rt): A methods comparison

The effective reproduction number (Rt) is a dynamic indicator of current disease spread risk. Wastewater measurements of viral concentrations are know…

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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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The Carlson Lab @ Yale @carlsonlab.bsky.social · 16/07/2025

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...

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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