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Nathan Grubaugh

@nathangrubaugh.bsky.social
1.2K followers 203 following 86 posts

Professor of Epidemiology at the Yale School of Public Health. Studies 🦟🦠 🧬transmission, evolution, and emergence. PI of dengue-lineages.org. Will sequence for 🍺. Lab website: grubaughlab.com

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Reposted by Nathan Grubaugh
Colin Carlson @colincarlson.bsky.social · 01/10/2026
Very cool new preprint I was very excited to be a VERY small part of, from @viralverity.bsky.social and @nathangrubaugh.bsky.social: "Phylodynamic analysis reveals asymmetric and accelerating global spread of dengue virus" www.biorxiv.org/content/10.6...
Figure 1Figure 4
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Nature Microbiology @natmicrobiol.nature.com · 30/09/2026
Out Now! A generalized lineage nomenclature for viral genomic epidemiology #MicroSky
go.nature.com
A generalized lineage nomenclature for viral genomic epidemiology
Nature Microbiology, Published online: 30 September 2026; doi:10.1038/s41564-026-02468-3This study extends the Pango lineage nomenclature system beyond SARS-CoV-2, introducing a dynamic framework for tracking and communicating viral diversity, demonstrated through its application to CHIKV.
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Carl T. Bergstrom @carlbergstrom.com · 29/09/2026
"I believe that science derives its authority from something more than mastering the pipeline from data generation to publication. Rather, it comes from interactions within a community of people trained to interrogate evidence and answer for the conclusions they draw from it."
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C. Brandon Ogbunu @cbo.bsky.social · 27/09/2026
In my latest for @undark.org, I compare AI adoption in science to the Ship of Theseus: "If you swap out every wooden plank on a ship over time, is it still the same vessel?" I argue that science derives authority from something more than data generation + publication. undark.org/2026/09/25/o...
undark.org
AI Presents Science with a ‘Ship of Theseus’ Problem
Opinion | AI can replace each part of the scientific process, leaving the enterprise recognizable but devoid of human judgment.
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Colin Carlson @colincarlson.bsky.social · 25/09/2026
David Quammen's essay in The New York Times today closes with this paragraph. It's both a scientific falsehood, and an incredibly dangerous narrative. If you're willing to give me five minutes of your time, I'd like to explain why.
The Ebola virus doesn’t need to spill back. It abides in its reservoir host, and awaits its next opportunity. A virus can’t climb out of a bat or a monkey and fly off in search of human prey. It can only spill over. If humans left the reservoir host alone — not hunting it, not capturing it, not eating it, not exporting it live, not disturbing its forest habitat — the virus wouldn’t re-emerge in humans. It would remain where it is, harming no one. But of course that’s not what happens. And when viruses spill, they often spill into us, because the human population is such a big, busy target.
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Pathogen Dynamics Unit @pducambridge.bsky.social · 25/09/2026
We have an open Assistant/Associate Professor position in Pathogen Genetics - come and join our department! 🦠 🧫 🧬https://www.cam.ac.uk/jobs/assistantassociate-professor-in-pathogen-genetics-pc51175
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Colin Carlson @colincarlson.bsky.social · 23/09/2026
What's behind this tidal wave of epidemics? In the largest study ever conducted on emerging infectious diseases, we show that the popular explanation - "our relationship with nature is out of balance" - doesn't hold up. Out now in Nature, after half a decade of work: www.nature.com/articles/s41...
nature.com
The anthropogenic fingerprint on emerging infectious diseases - Nature
Emerging infectious disease outbreak risks are ubiquitous worldwide, and highest in landscapes where people, livestock and fragmented natural ecosystems coexist, but detection and data ...
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Gytis Dudas @evogytis.bsky.social · 23/09/2026
And here is the preprint, available online on Baltic Unity Day (Sep 22). Happy citing! www.biorxiv.org/content/10.6... Thanks again to @barney-potter.bsky.social, @gkarthik.com, @sidneymbell.bsky.social, and @mftorresj.bsky.social
biorxiv.org
baltic: the Backronymed Adaptable Lightweight Tree vIsualisation Code
For ten years, baltic (Backronymed Adaptable Lightweight Tree vIsualization Code) has been used to make annotated phylogeny figures in molecular epidemiology, including during the West African Ebola e...
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Gytis Dudas @evogytis.bsky.social · 22/09/2026
baltic v1.0.0 is live! Get it via pip or clone from Github repo. Now with documentation (baltic.readthedocs.io) & a gallery of tutorials & examples (phylo-baltic.github.io/baltic-gallery, still WIP). Huge thanks to @barney-potter.bsky.social for all the initiative & help along the way. #ViroSky
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Raphaëlle K @raph-klitting.bsky.social · 17/09/2026
Happy to share the final version of our latest study on the 2024-2025 chikungunya virus epidemic on Réunion island published today in @pnas.org 🎉 www.pnas.org/doi/10.1073/...
pnas.org
Unraveling the epidemiological and dispersal dynamics of the 2024–2025 chikungunya virus epidemic on Réunion Island | PNAS
Réunion Island experienced a massive chikungunya virus epidemic in 2024–2025, with >54,000 confirmed cases. This is the second major chikungunya ep...
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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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Kristian G. Andersen @kgandersen.bsky.social · 10/09/2026
Inspired by recent website shenanigans from USG - and prompted by one of my talented graduate students - I present to you a new subdomain of our website... Play along: arcade.andersen-lab.com
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Drummond Lab @drummondlab.bsky.social · 08/09/2026
We are hiring! 🌟 Dept of Biochemistry and Molecular Biology at the University of Chicago is searching for a tenure-track assistant professor. It's a broad search: we want great colleagues doing serious biological work at the molecular scale. Join us! apply.interfolio.com/191981 bcmb.uchicago.edu
A picture of the University of Chicago campus, with downtown Chicago in the distance and Lake Michigan on the horizon. The campus's central quad is pictured, a classical collegiate quad with paths and old trees and stone architecture. It's really pretty and I love it.
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Carolina Lucas @carolilucas.bsky.social · 04/09/2026
Dengue vaccines face a uniquely difficult challenge: protecting against four distinct viral serotypes at once. 🦟 Our new study in JEM: rupress.org/jem/article/... A 🧵 on why tetravalent vaccine design does not necessarily mean tetravalent immunity.
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Simon W Davis @woodforbrains.bsky.social · 03/09/2026
Ho-LEE fuck democrats-appropriations.house.gov/news/press-r...
democrats-appropriations.house.gov
Defense Officials Attempt to Raid NIH Funds to Cover Department of Defense Activities
House Appropriations Committee Ranking Member Rosa DeLauro (D-CT-03) has learned that officials at the Department of Defense (DoD) are working to divert billions of dollars from the National Institute...
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Greg Folkers @gregfolkers.bsky.social · 03/09/2026
Defense Officials Attempt to Raid NIH Funds to Cover Department of Defense Activities bit.ly/3UziCvO
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Michael Cappello @cappmic.bsky.social · 04/09/2026
"The Democrat said the agreement would pull from the NIH’s National Institute of Allergy and Infectious Diseases (NIAID), its leading institute for infectious-disease research."
thehill.com
Pentagon sought to divert NIH funds for defense use, top House Appropriations Democrat says
The Pentagon is attempting to divert billions of dollars from the National Institutes of Health (NIH) to bolster the agency’s budget, according to the top Democrat on the House Appropria…
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Nels Elde @elearlybird.bsky.social · 28/08/2026
Open your lab here at Utah! utah.peopleadmin.com/postings/208...
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Gytis Dudas @evogytis.bsky.social · 28/08/2026
Attention, baltic (github.com/evogytis/bal...) users! Barney Potter & I have been working on a major update to baltic with a new API & docs (& a paper later). The pip version will be updated on Sep 22 (Baltic Unity Day). Please share with any baltic users who might be affected! 1/2 #evosky #virosky
github.com
GitHub - evogytis/baltic: baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branc...
baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here). - evogyt...
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Yale University @yale.edu · 21/08/2026
Climate change is reshaping the spread of one of the world's deadliest infectious diseases. A Yale-led study found that climate change is shifting childhood malaria risk across Africa by changing the environmental conditions that influence mosquito-borne disease.
bit.ly
Climate change is likely worsening childhood malaria, study finds
In a new study, Yale researchers found that hot temperatures and extreme precipitation are probably increasing the prevalence of malaria in parts of Africa.
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C. Brandon Ogbunu @cbo.bsky.social · 20/08/2026
1/8: 🚨New Paper🚨 "Structural causal influence captures the forces of social inequality in models of infectious disease." Published in 'Biology Letters' (@royalsocietypublishing.org) Coverage here: www.santafe.edu/news-center/... Paper link here: royalsocietypublishing.org/rsbl/article...
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Ana Bento @anaisabelbento.bsky.social · 18/08/2026
The committee reviewing US measles elimination status met this month. PAHO decides in November. Our new paper in @NatureMedicine shows this wasn’t sudden. It was visible years ago, in data nobody was looking at. 🧵
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Prof Ian Hall @ianhall.bsky.social · 15/08/2026
The fact that nobody alive today has seen an event of this magnitude should really make us stop and think. And yes, I know El Niño is a natural cycle. But that doesn’t make records like this any less remarkable…or any less concerning.
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Collin Schwantes @collin-schwantes.bsky.social · 12/08/2026
Do you enjoy implementing data standards and creating well designed APIs? Verena is looking for a full stack developer for the Pathogen Harmonized Observatory (PHAROS)! See the Verena website for more details and to apply: 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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Ran Blekhman @blekhman.bsky.social · 09/08/2026
Huge faculty recruitment effort at the University of Chicago -- a division-wide, open-rank search looking to hire about 20 faculty across 5 research areas in biology. Come be our colleague! Full announcement: uchicago.app.box.com/s/ckih9zv3rj...
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The Global Vector Hub @globalvectorhub.bsky.social · 07/08/2026
📢 #Internship opportunity at @who.int's Emerging Zoonosis and High Impact Epidemics Unit, focusing on #arboviruses and an early warning system for #chikungunya and other #arboviral threats.🦟 Closing date: 21 August 2026. More info ⬇️ careers.who.int/careersectio...
careers.who.int
Internship – Emerging Zoonosis and High Impact Epidemics
Click the link provided to see the complete job description.
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Noah Whiteman @nkwhiteman.bsky.social · 06/08/2026
I’m thrilled to share that our search for a tenure-track colleague in my *truly wonderful and collegial* Genetics, Genomics, Evolution and Development Division in the MCB Department at Berkeley @berkeleymcb.bsky.social is live! Please share this broad search widely: aprecruit.berkeley.edu/JPF05481
aprecruit.berkeley.edu
Assistant Professor -Genetics, Genomics, Evolution, and Development - Molecular and Cell Biology
University of California, Berkeley is hiring. Apply now!
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C. Brandon Ogbunu @cbo.bsky.social · 04/08/2026
🚨NEW PAPER 🚨 "Deconstructing empirical fitness seascapes across scales of granularity" published in #G3 (@genetics-gsa.bsky.social) 1/2 The fitness landscape has been among the most influential instruments in evolutionary theory for nearly a century. But we often treat them as fixed and static.
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Amy Maxmen, PhD @amymaxmen.bsky.social · 30/07/2026
The US owes the Pan-American Health Organization $135 million in past dues. Trump's budget proposal cuts funding for PAHO entirely, even though our contribution is 0.001% of federal spending. The result will be even weaker defenses agst measles, dengue & more. www.nytimes.com/2026/07/30/h...
nytimes.com
Former Officials Protest U.S. Plan to Defund Pan American Health Organization
The group of former health and national security officials warned that Americans will be more vulnerable to infectious disease threats.
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Stephen Kissler @skissler.bsky.social · 29/07/2026
I'm excited to share a preprint that's been years in the making: the idea took shape during the COVID pandemic. Anecdotally, people would sometimes spread COVID at work but not at home, and vice versa. Why? One explanation would be if infectiousness is fleeting...
medrxiv.org
How bursty infectiousness shapes epidemic dynamics
An epidemic’s expected course is determined by the magnitude and timing of a typical person’s infectiousness — captured, in turn, by the basic reproduction number and the generation-time distribution....
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Colin Carlson @colincarlson.bsky.social · 29/07/2026
🚨 New today in Nature 🦟 After decades of debate, we show that climate change has probably made malaria worse in sub-Saharan Africa, causing about 1 extra case per 1,000 children. But: malaria eradication efforts have pulled the other direction 200 times harder. 🔓 www.nature.com/articles/s41...
Graphical abstract for "The past and future impact of climate change on childhood malaria in Africa"
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Spyros Lytras @spyroslytras.bsky.social · 23/07/2026
Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!
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Andrew Rambaut (🐏🎀) @arambaut.bsky.social · 23/07/2026
This is so important - allowing individual uses of data to be tracked as citations will be so useful for demonstrating impact and reach of genome data. When you use data from Pathoplexus, create a SetSet & DOI for the sequences used and cite it in your paper.
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Ellie Bourgikos @ebourgikos.bsky.social · 07/07/2026
"Jamestown Canyon virus may not be an emerging pathogen in the usual sense. It has been here for centuries. The emergence is in our awareness of it." Such a great summary of our JCV work by John Drake!! Would highly encourage giving it a read! 🦟 www.forbes.com/sites/johndr...
forbes.com
A Virus That Predates The Republic Has Been Hiding In American Mosquitoes. Scientists Just Decoded Its History
A mosquito-borne virus circulating since the 1700s went unnoticed until genomic sequencing revealed its centuries-long history and unique two-cycle transmission.
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Helen Branswell 🇨🇦 @helenbranswell.bsky.social · 06/07/2026
C.J. Peters, one of the legendary virus hunters of decades past, has died. In 2018, I traveled to his home in Galveston, Tex., where he told me jaw-dropping story after jaw-dropping story. He had an extraordinary brain and was hugely curious. Such a loss. www.statnews.com/2018/02/20/v...
statnews.com
The virus hunter: In a bygone era, C.J. Peters learned how to bend the rules
A legendary scientist reflects on why he became so successful: He got out of the office — and away from bosses.
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Gregg Gonsalves @gregggonsalves.bsky.social · 30/06/2026
We've hit the 3,000 mark in letters to Congress on the mad power-grab by Russell Vought at OMB to take over all federal grant making with a team of political commissars reporting to him. Let's get to 4,000 letters this week. Share. Share. Share. actionnetwork.org/letters/oppo...
actionnetwork.org
Oppose OMB Proposal to Put ALL Federal Government Funding Decisions in the Hands of Political Appointees
On May 29, 2026, the Office of Management and Budget issued a Notice of Proposed Rulemaking (NPRM), OMB-2026-0034, Regulation for Federal Financial Assistance. The scope of this proposed regulation is...
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Climate.us @climate.us · 26/06/2026
We got a big bump in traffic yesterday when people learned about us on NPR. Thank you to @npr.org for covering our launch and bringing our story to people's attention! And thank you to all our new followers. We can do this together! 🌍️🧪💪 #ClimateAction #ClimateForUs #ProtectScience
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Gregg Gonsalves @gregggonsalves.bsky.social · 27/06/2026
Stand Up for Yale, a group representing thousands of #Yale alums condemns the Trump administration investigation and warns against settlement, calls on the university to defend its students, its independence, its lawful commitment to an inclusive academic community. More at www.standupforyale.org
standupforyale.org
STAND UP FOR YALE
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Gregg Gonsalves @gregggonsalves.bsky.social · 26/06/2026
@yale.edu bows down to fascism. President MacInnis and the trustees show what it means to obey in advance. A sad day for my alma mater. What cowards. #VichyYale www.nytimes.com/2026/06/26/u...
nytimes.com
Yale Seeks Trump Administration Deal as It Faces Sprawling Investigation
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Colin Carlson @colincarlson.bsky.social · 22/06/2026
Our lab website is updated with a new postdoc opening! This is a 2-year, in-person position looking at the relationships between climate change, pandemic risk, and policy choices over the 21st century. Please reach out (not on here)! www.carlsonlab.bio/join
carlsonlab.bio
Opportunities — The Carlson Lab
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James Hay @jameshay.bsky.social · 22/06/2026
Are you a computational immunologist or bioinformatician interested in impactful vaccine research? We're hiring a postdoc to join @psioxford.bsky.social work in vaccine immunology and evaluation, working on the ChAdOx1 Nipah vaccine. Please get in touch! my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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The Sickos CBB Committee @sickoscbb.bsky.social · 11/06/2026
It seems like it was a mistake to let Jon Scheyer coach the Spurs last night.
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The Sickos CBB Committee @sickoscbb.bsky.social · 04/06/2026
kind of appropriate for Duke to play in a baseball stadium given the number of blown saves they've had recently
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Colin Carlson @colincarlson.bsky.social · 01/06/2026
Happy pride 🦇🦠🦟🏳️‍🌈
notice of award for my grant
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Dan Garisto @dangaristo.bsky.social · 27/05/2026
Scoop: NSF has been quietly blocking new funds and grants to four top universities: Duke, Harvard, Princeton, and Yale. Dozens of proposals from PIs at these universities—and their collaborators—have been stuck at the Office of Award Management awaiting finalization for months.
nature.com
Exclusive: NSF puts new research grants to top universities on hold
US science funder once again restricts awards to Harvard University and other research institutions.
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Josh Quick @scalene.bsky.social · 22/05/2026
New preprint from us! 🦠 Clinical metagenomics is great for sequencing pathogens directly from patient samples but for some protocols sensitivity for RNA viruses lags behind bacteria & fungi. We have shown why, and how to fix it. www.medrxiv.org/content/10.6...
medrxiv.org
Library preparation strategy critically impacts RNA virus sensitivity in clinical metagenomics
Clinical metagenomics uses sequencing for culture-independent identification of pathogens directly from clinical specimens. While a number of protocols claim to be pathogen agnostic, sensitivity for R...
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Joaquín Baldwin @joabaldwin.com · 17/05/2026
I have found the source of all mosquitoes
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Andrew Roger @andrewjroger.bsky.social · 06/05/2026
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
academic.oup.com
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
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