Nathan Grubaugh
@nathangrubaugh.bsky.social
Associate Professor YaleEMD / YaleSPH. Studies 🦟🦠 🧬transmission, evolution, and emergence. PI of http://dengue-lineages.org. Will sequence for 🍺.
Lab website: https://grubaughlab.com/
Lab website: https://grubaughlab.com/
Pinned
If you do dengue virus sequencing +/- phylogenetic analysis, check out our new system for classifying lineages.
Led by Verity Hill, this was a large collaborative effort by dengue researchers from 14 countries.
Paper -> journals.plos.org/plosbiology/...
Website-> dengue-lineages.org
Led by Verity Hill, this was a large collaborative effort by dengue researchers from 14 countries.
Paper -> journals.plos.org/plosbiology/...
Website-> dengue-lineages.org
Reposted by Nathan Grubaugh
Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...
Ecology and spread of the North American H5N1 epizootic - Nature
The panzootic of highly pathogenic H5N1 since 2021 was driven by around nine introductions into the Atlantic and Pacific flyways, followed by rapid dissemination through wild migratory birds, primaril...
www.nature.com
November 12, 2025 at 7:33 PM
Our lab's paper describing the North American H5N1 epizootic is out now in Nature! So thrilled to have this out, and congratulations to @lambod50.bsky.social for all the fantastic work on this: www.nature.com/articles/s41...
Reposted by Nathan Grubaugh
Check out our new study entitled "Navigating sampling bias in discrete phylogeographic analysis: assessing the performance of an adjusted Bayes factor" and now published in Molecular Biology & Evolution: academic.oup.com/mbe/article/... (1/9)
November 12, 2025 at 6:35 PM
Check out our new study entitled "Navigating sampling bias in discrete phylogeographic analysis: assessing the performance of an adjusted Bayes factor" and now published in Molecular Biology & Evolution: academic.oup.com/mbe/article/... (1/9)
Reposted by Nathan Grubaugh
PSA for people with NIH grant periods starting January 1st (including most NIGMS MIRAs): your RPPR is due Saturday, but they haven’t sent out the usual automated reminders, presumably due to the shutdown
November 11, 2025 at 1:20 AM
PSA for people with NIH grant periods starting January 1st (including most NIGMS MIRAs): your RPPR is due Saturday, but they haven’t sent out the usual automated reminders, presumably due to the shutdown
Reposted by Nathan Grubaugh
It's been more than a decade (😱) since opening the lab here in La Jolla, so it was time for a website refresh!
Want to see what kind of trouble we have been up to lately? Give our tools and data a spin? Maybe even provide some tips and feedback?
Head on over to: andersen-lab.com
Want to see what kind of trouble we have been up to lately? Give our tools and data a spin? Maybe even provide some tips and feedback?
Head on over to: andersen-lab.com
November 11, 2025 at 12:30 AM
It's been more than a decade (😱) since opening the lab here in La Jolla, so it was time for a website refresh!
Want to see what kind of trouble we have been up to lately? Give our tools and data a spin? Maybe even provide some tips and feedback?
Head on over to: andersen-lab.com
Want to see what kind of trouble we have been up to lately? Give our tools and data a spin? Maybe even provide some tips and feedback?
Head on over to: andersen-lab.com
Reposted by Nathan Grubaugh
The new US official: in exchange for restarting foreign aid, the US gets other countries’ genomic data on diseases.
No promise to share the benefits of that IP, though - in contrast to WHO agreements that are under negotiation.
www.reuters.com/business/hea... 🛟🧪🩺
No promise to share the benefits of that IP, though - in contrast to WHO agreements that are under negotiation.
www.reuters.com/business/hea... 🛟🧪🩺
www.reuters.com
November 8, 2025 at 2:58 PM
The new US official: in exchange for restarting foreign aid, the US gets other countries’ genomic data on diseases.
No promise to share the benefits of that IP, though - in contrast to WHO agreements that are under negotiation.
www.reuters.com/business/hea... 🛟🧪🩺
No promise to share the benefits of that IP, though - in contrast to WHO agreements that are under negotiation.
www.reuters.com/business/hea... 🛟🧪🩺
Reposted by Nathan Grubaugh
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 7, 2025 at 2:41 PM
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
Reposted by Nathan Grubaugh
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 6, 2025 at 9:46 PM
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
Reposted by Nathan Grubaugh
Twenty-nine sailors drowned when the Edmund Fitzgerald went down in the Great Lakes' icy waters on Nov. 10, 1975. The ship was immortalized in a surprise hit 1976 folk ballad by Gordon Lightfoot. n.pr/3JKj19D
50 years ago, the Edmund Fitzgerald, a 'rock star' ship, sank in Lake Superior
Twenty-nine sailors drowned when the Edmund Fitzgerald went down in the Great Lakes' icy waters on Nov. 10, 1975. The ship was immortalized in a surprise hit 1976 folk ballad by Gordon Lightfoot.
n.pr
November 6, 2025 at 7:43 PM
Twenty-nine sailors drowned when the Edmund Fitzgerald went down in the Great Lakes' icy waters on Nov. 10, 1975. The ship was immortalized in a surprise hit 1976 folk ballad by Gordon Lightfoot. n.pr/3JKj19D
Reposted by Nathan Grubaugh
🚨 NEW: The majority holder of the world's genetic sequence data is a bad actor who can cut off access to critics and competing services. We've tolerated this for years, and now it threatens the pandemic treaty. Time for WHO to step in. With @ctrlalttim.com: www.thinkglobalhealth.org/article/to-f...
To Finish the Pandemic Agreement, WHO Needs a Trustworthy Viral Database | Think Global Health
Online platforms for sharing virus sequences are in disarray. The World Health Organization has a chance to build something new
www.thinkglobalhealth.org
November 5, 2025 at 3:31 PM
🚨 NEW: The majority holder of the world's genetic sequence data is a bad actor who can cut off access to critics and competing services. We've tolerated this for years, and now it threatens the pandemic treaty. Time for WHO to step in. With @ctrlalttim.com: www.thinkglobalhealth.org/article/to-f...
Reposted by Nathan Grubaugh
CIDRAP joins global partners in the DeZi Network — uniting 15+ countries to strengthen dengue & Zika surveillance and response across Africa and Asia.
🔗 www.imperial.ac.uk/news/269973/...
#GlobalHealth #Dengue #Zika
🔗 www.imperial.ac.uk/news/269973/...
#GlobalHealth #Dengue #Zika
International collaborative effort to understand dengue and Zika | Imperial News | Imperial College London
An international team launched the DeZi network to understand how the viruses spread, interact, and cause disease across Africa and Asia.
www.imperial.ac.uk
November 4, 2025 at 6:56 PM
CIDRAP joins global partners in the DeZi Network — uniting 15+ countries to strengthen dengue & Zika surveillance and response across Africa and Asia.
🔗 www.imperial.ac.uk/news/269973/...
#GlobalHealth #Dengue #Zika
🔗 www.imperial.ac.uk/news/269973/...
#GlobalHealth #Dengue #Zika
Reposted by Nathan Grubaugh
Between grants getting politically targeted and my lab’s building getting literally fucking bombed, 2025 is going great thanks
A device exploded inside the Goldenson Building in Harvard’s Longwood medical campus early Saturday morning, according to a message from the Harvard University Police Department to University affiliates.
Matan H. Josephy and Laurel M. Shugart report.
www.thecrimson.com/article/2025...
Matan H. Josephy and Laurel M. Shugart report.
www.thecrimson.com/article/2025...
Authorities Investigating Explosion on Harvard’s Medical Campus, Believed To Be Intentional | News | The Harvard Crimson
A device exploded inside the Goldenson Building in Harvard’s Longwood medical campus early Saturday morning, according to a message from the Harvard University Police Department to University…
www.thecrimson.com
November 1, 2025 at 10:41 PM
Between grants getting politically targeted and my lab’s building getting literally fucking bombed, 2025 is going great thanks
Reposted by Nathan Grubaugh
New in ‘Virus Evolution’ from #QVEU! PhD student Jack Dorman used deep mutational scanning to measure evolutionary constraints on the Envelope protein of West Nile Virus in human, mosquito, and bird cell lines, doing a lot of work to put it into a structural context #VirEvol
Constraint in West Nile Virus Envelope Protein across Mosquito, Human, and Avian Host Cell Environments
Abstract. Arthropod-borne viruses are a major cause of global viral infections, displaying evolutionary dynamics that differ significantly from vertebrate-
academic.oup.com
November 1, 2025 at 6:44 PM
Reposted by Nathan Grubaugh
q: why did the outfielders raise their arms during this play?
a: according to the ancient scrolls in which the rules of baseball were found, if a ball lands and doesn't bounce that ball is declared god. the players were worshipping god. i doubt there will be a game 7 or any further baseball seasons
a: according to the ancient scrolls in which the rules of baseball were found, if a ball lands and doesn't bounce that ball is declared god. the players were worshipping god. i doubt there will be a game 7 or any further baseball seasons
November 1, 2025 at 3:19 AM
q: why did the outfielders raise their arms during this play?
a: according to the ancient scrolls in which the rules of baseball were found, if a ball lands and doesn't bounce that ball is declared god. the players were worshipping god. i doubt there will be a game 7 or any further baseball seasons
a: according to the ancient scrolls in which the rules of baseball were found, if a ball lands and doesn't bounce that ball is declared god. the players were worshipping god. i doubt there will be a game 7 or any further baseball seasons
Reposted by Nathan Grubaugh
1/5: Interested in basketball? Disease ecology? Epidemics?
5 years ago, the NBA embarked on a great experiment in infection control: "The NBA Bubble." In a new preprint led by Dr. Yun Tao + Dr. Nita Bharti, we examine it's underlying disease ecology principles.
www.medrxiv.org/content/10.1...
5 years ago, the NBA embarked on a great experiment in infection control: "The NBA Bubble." In a new preprint led by Dr. Yun Tao + Dr. Nita Bharti, we examine it's underlying disease ecology principles.
www.medrxiv.org/content/10.1...
Pandemic-era sports league operations as a new paradigm for local epidemic resilience
Strategic, coordinated, and rapid responses are essential when pathogens emerge, yet these responses are often mishandled during epidemics due to myriad factors, including entrenched socioeconomic and...
www.medrxiv.org
October 31, 2025 at 11:56 AM
1/5: Interested in basketball? Disease ecology? Epidemics?
5 years ago, the NBA embarked on a great experiment in infection control: "The NBA Bubble." In a new preprint led by Dr. Yun Tao + Dr. Nita Bharti, we examine it's underlying disease ecology principles.
www.medrxiv.org/content/10.1...
5 years ago, the NBA embarked on a great experiment in infection control: "The NBA Bubble." In a new preprint led by Dr. Yun Tao + Dr. Nita Bharti, we examine it's underlying disease ecology principles.
www.medrxiv.org/content/10.1...
Reposted by Nathan Grubaugh
Virological.org is up and running, yes - and should remain so (I foot the monthly $25 bill for @arambaut.bsky.social 😆)! But as Duncan says, not for data sharing.
@pathoplexus.org is the best alternative, although IMO we need data producer-driven focus first, not just data-consumers.
@pathoplexus.org is the best alternative, although IMO we need data producer-driven focus first, not just data-consumers.
Virological
A discussion forum for analysis and interpretation of virus molecular evolution and epidemiology.
Virological.org
October 31, 2025 at 2:13 AM
Virological.org is up and running, yes - and should remain so (I foot the monthly $25 bill for @arambaut.bsky.social 😆)! But as Duncan says, not for data sharing.
@pathoplexus.org is the best alternative, although IMO we need data producer-driven focus first, not just data-consumers.
@pathoplexus.org is the best alternative, although IMO we need data producer-driven focus first, not just data-consumers.
Reposted by Nathan Grubaugh
As expected, unfortunately.
If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further.
Time to move on to more trusted and transparent solutions.
If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further.
Time to move on to more trusted and transparent solutions.
October 31, 2025 at 1:41 AM
As expected, unfortunately.
If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further.
Time to move on to more trusted and transparent solutions.
If ever you needed a reason for never using GISAID ever again (as a data producer or data user - we're both), look no further.
Time to move on to more trusted and transparent solutions.
@andersonfbrito.bsky.social and I are seeking input from the community on hosting/sharing arbovirus sequencing data (DENV, CHIKV, OROV, ZIKV, & YFV) on @pathoplexus.org.
Please consider filling out this VERY SHORT survey about your interest and/or concerns.
docs.google.com/forms/d/e/1F...
Please consider filling out this VERY SHORT survey about your interest and/or concerns.
docs.google.com/forms/d/e/1F...
Community survey on the addition of Dengue, Chikungunya, Oropouche, Zika and Yellow fever virus to Pathoplexus
Pathoplexus is a new platform for sharing pathogen sequence data, launched in August 2024 [1], with the primary aim of making sharing and accessing pathogen genomic data easier, faster, and more effic...
docs.google.com
October 30, 2025 at 8:11 PM
@andersonfbrito.bsky.social and I are seeking input from the community on hosting/sharing arbovirus sequencing data (DENV, CHIKV, OROV, ZIKV, & YFV) on @pathoplexus.org.
Please consider filling out this VERY SHORT survey about your interest and/or concerns.
docs.google.com/forms/d/e/1F...
Please consider filling out this VERY SHORT survey about your interest and/or concerns.
docs.google.com/forms/d/e/1F...
Reposted by Nathan Grubaugh
Now out in @nejm.org :
Between 2023–2024: Sixteen human infections with A/H5N1 in Cambodia. Six deaths. Most in children. All exposed to sick or dead poultry.
www.nejm.org/doi/full/10....
Between 2023–2024: Sixteen human infections with A/H5N1 in Cambodia. Six deaths. Most in children. All exposed to sick or dead poultry.
www.nejm.org/doi/full/10....
Resurgence of Zoonotic Highly Pathogenic Avian Influenza A(H5N1) Virus in Cambodia | NEJM
In this report from Cambodia, 16 human cases of highly pathogenic avian influenza
A(H5N1) virus infection that occurred from February 2023 through August 2024 are described.
www.nejm.org
October 23, 2025 at 5:04 AM
Now out in @nejm.org :
Between 2023–2024: Sixteen human infections with A/H5N1 in Cambodia. Six deaths. Most in children. All exposed to sick or dead poultry.
www.nejm.org/doi/full/10....
Between 2023–2024: Sixteen human infections with A/H5N1 in Cambodia. Six deaths. Most in children. All exposed to sick or dead poultry.
www.nejm.org/doi/full/10....
Reposted by Nathan Grubaugh
UChicago Microbiology is searching for tenured or tenure-track faculty working in host-pathogens interactions, viral and bacterial pathogenesis, and emerging infectious diseases. Come join our vibrant Department! microbiology.uchicago.edu
Apply here apply.interfolio.com/174404
Apply here apply.interfolio.com/174404
Department of Microbiology | The University of Chicago
microbiology.uchicago.edu
October 6, 2025 at 5:32 PM
UChicago Microbiology is searching for tenured or tenure-track faculty working in host-pathogens interactions, viral and bacterial pathogenesis, and emerging infectious diseases. Come join our vibrant Department! microbiology.uchicago.edu
Apply here apply.interfolio.com/174404
Apply here apply.interfolio.com/174404
Reposted by Nathan Grubaugh
Our paper on the phenomenon of persistence and latency in Ebola virus in an unobserved reservoir is finally out in preprint: www.biorxiv.org/content/10.1...
Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics
Ebola virus (EBOV) has caused severe outbreaks of haemorrhagic fever in Central and West Africa since the first observed zoonotic epidemic in the late 1970s. While recent outbreaks have revealed much ...
www.biorxiv.org
October 19, 2025 at 11:36 AM
Our paper on the phenomenon of persistence and latency in Ebola virus in an unobserved reservoir is finally out in preprint: www.biorxiv.org/content/10.1...
Reposted by Nathan Grubaugh
There have been 12 players to hit 3+ HR in a Postseason game.
There have been 16 pitchers to have a Postseason game with 6+ IP, 2 hits or fewer, 10+ K, and 0 runs allowed.
Only one did both on the same night.
There have been 16 pitchers to have a Postseason game with 6+ IP, 2 hits or fewer, 10+ K, and 0 runs allowed.
Only one did both on the same night.
October 18, 2025 at 1:34 PM
There have been 12 players to hit 3+ HR in a Postseason game.
There have been 16 pitchers to have a Postseason game with 6+ IP, 2 hits or fewer, 10+ K, and 0 runs allowed.
Only one did both on the same night.
There have been 16 pitchers to have a Postseason game with 6+ IP, 2 hits or fewer, 10+ K, and 0 runs allowed.
Only one did both on the same night.
Reposted by Nathan Grubaugh
Top EV
Top distance
Top pitch velo
Most whiffs
SHOHEI IS SO SPECIAL
Top distance
Top pitch velo
Most whiffs
SHOHEI IS SO SPECIAL
October 18, 2025 at 1:55 AM
Top EV
Top distance
Top pitch velo
Most whiffs
SHOHEI IS SO SPECIAL
Top distance
Top pitch velo
Most whiffs
SHOHEI IS SO SPECIAL
Reposted by Nathan Grubaugh
Interesting that there has been absolutely no communication with submitters/users of the system, and no statements from the scientific governance or compliance boards on what would seem to be a fairly significant change to GISAID data access policy and platform operations. gisaid.org/about-us/gov...
October 17, 2025 at 7:07 PM
Interesting that there has been absolutely no communication with submitters/users of the system, and no statements from the scientific governance or compliance boards on what would seem to be a fairly significant change to GISAID data access policy and platform operations. gisaid.org/about-us/gov...
Reposted by Nathan Grubaugh
Wahl is also expanding interdisciplinary research at Yale, linking public health, architecture, and language studies to strengthen impact.
👉 Read more: macmillan.yale.edu/southasia/st...
#GlobalHealth #PublicHealth #CommunityEngagement
@yalesph.bsky.social @brianwahl.bsky.social
👉 Read more: macmillan.yale.edu/southasia/st...
#GlobalHealth #PublicHealth #CommunityEngagement
@yalesph.bsky.social @brianwahl.bsky.social
In Service of Healthier Communities: Brian Wahl drives change through partnership in Uttar Pradesh, India
Wahl's SEWARTH initiative brings the Yale School of Public Health into partnership with the Department of Medical Health and Family Welfare, Government of Uttar Pradesh, and the All India Institute of...
macmillan.yale.edu
October 17, 2025 at 2:29 AM
Wahl is also expanding interdisciplinary research at Yale, linking public health, architecture, and language studies to strengthen impact.
👉 Read more: macmillan.yale.edu/southasia/st...
#GlobalHealth #PublicHealth #CommunityEngagement
@yalesph.bsky.social @brianwahl.bsky.social
👉 Read more: macmillan.yale.edu/southasia/st...
#GlobalHealth #PublicHealth #CommunityEngagement
@yalesph.bsky.social @brianwahl.bsky.social
Reposted by Nathan Grubaugh
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
October 16, 2025 at 7:48 PM
And now NextStrain as well.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.
Next up, will GISAID start charging open-source community tools to have access?
That would completely shaft users who contributed to GISAID, where we never agreed to that and assumed GISAID would be good custodians of the data we contributed. They're not.