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
My department at Washington State University is recruiting an Assistant or Associate Professor in vector-borne disease 🕷️🦟🦠
Full job description is linked below.
Come join us on the Palouse!
Full job description is linked below.
Come join us on the Palouse!
February 2, 2026 at 9:02 PM
My department at Washington State University is recruiting an Assistant or Associate Professor in vector-borne disease 🕷️🦟🦠
Full job description is linked below.
Come join us on the Palouse!
Full job description is linked below.
Come join us on the Palouse!
Reposted by Nathan Grubaugh
This is finally out.
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections
Snell et al. develop sequencing methodology to identify full-length spike haplotypes
and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence,
accelerating viral evolution an...
www.cell.com
February 2, 2026 at 4:09 PM
This is finally out.
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Very short take home. All the variation in spike that produced the immune escape characteristics of Omicron can occur in one single persistently infected individual over the period of a year.
This is why persistent infections matter
www.cell.com/cell-reports...
Reposted by Nathan Grubaugh
PacBio folds its short-read sequencing hand.
-Sad for us because Omniome's tech (the current Onso instrument) was promising for its Q40 reads that help those interested in calling rare variants accurately (like me).
-Sad for them too because $$$
aseq.substack.com/p/pacbio-sel...
-Sad for us because Omniome's tech (the current Onso instrument) was promising for its Q40 reads that help those interested in calling rare variants accurately (like me).
-Sad for them too because $$$
aseq.substack.com/p/pacbio-sel...
PacBio Sells Short Read Tech To Illumina
PacBio has finally sold their short read sequencing assets to Illumina for ~$50M.
aseq.substack.com
February 2, 2026 at 5:23 PM
PacBio folds its short-read sequencing hand.
-Sad for us because Omniome's tech (the current Onso instrument) was promising for its Q40 reads that help those interested in calling rare variants accurately (like me).
-Sad for them too because $$$
aseq.substack.com/p/pacbio-sel...
-Sad for us because Omniome's tech (the current Onso instrument) was promising for its Q40 reads that help those interested in calling rare variants accurately (like me).
-Sad for them too because $$$
aseq.substack.com/p/pacbio-sel...
Reposted by Nathan Grubaugh
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...
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
medicine.yale.edu
February 2, 2026 at 5:30 PM
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...
Reposted by Nathan Grubaugh
Reposted by Nathan Grubaugh
Our paper on the Genomic Epidemiology of DENV2/3 in Colombia and the Americas is finally out @cp-cellreports.bsky.social, check it out: www.sciencedirect.com/science/arti...
Big thanks to my collaborators @lambod50.bsky.social, @viralverity.bsky.social, @nathangrubaugh.bsky.social, and many others!
Big thanks to my collaborators @lambod50.bsky.social, @viralverity.bsky.social, @nathangrubaugh.bsky.social, and many others!
January 16, 2026 at 6:28 PM
Our paper on the Genomic Epidemiology of DENV2/3 in Colombia and the Americas is finally out @cp-cellreports.bsky.social, check it out: www.sciencedirect.com/science/arti...
Big thanks to my collaborators @lambod50.bsky.social, @viralverity.bsky.social, @nathangrubaugh.bsky.social, and many others!
Big thanks to my collaborators @lambod50.bsky.social, @viralverity.bsky.social, @nathangrubaugh.bsky.social, and many others!
Check out our new print that combines dense sequencing and phylodynamics to uncover a bunch of 😎 things about an understudied virus.
- Doesn't evolve for 10 months a year ✅
- Uses some mossies for maintenance, others for spread ✅
- Established in Northeast for ~300 years ✅
- Doesn't evolve for 10 months a year ✅
- Uses some mossies for maintenance, others for spread ✅
- Established in Northeast for ~300 years ✅
January 12, 2026 at 5:49 PM
Check out our new print that combines dense sequencing and phylodynamics to uncover a bunch of 😎 things about an understudied virus.
- Doesn't evolve for 10 months a year ✅
- Uses some mossies for maintenance, others for spread ✅
- Established in Northeast for ~300 years ✅
- Doesn't evolve for 10 months a year ✅
- Uses some mossies for maintenance, others for spread ✅
- Established in Northeast for ~300 years ✅
Reposted by Nathan Grubaugh
Our latest study dedicated to the massive 2024-2025 chikungunya virus outbreak on Réunion island is now available as a preprint on medRxiv: doi.org/10.64898/202.... With more than 54,000 confirmed cases this is the second major chikungunya outbreak on the island, following the 1° one 20 yrs ago. 1/9
Unravelling the epidemiological and dispersal dynamics of the 2024-2025 chikungunya virus outbreak on Reunion island
Reunion island just experienced a massive chikungunya virus outbreak in 2024-2025, with more than 54,000 confirmed cases. This is the second major chikungunya outbreak on the island, following the fir...
doi.org
January 12, 2026 at 7:30 AM
Our latest study dedicated to the massive 2024-2025 chikungunya virus outbreak on Réunion island is now available as a preprint on medRxiv: doi.org/10.64898/202.... With more than 54,000 confirmed cases this is the second major chikungunya outbreak on the island, following the 1° one 20 yrs ago. 1/9
Reposted by Nathan Grubaugh
I am very glad to share the preprint for our latest study on the 2024-2025 chikungunya virus outbreak on Réunion island, with primary data produced thanks to the massive efforts performed by Marie-C Jaffar and Etienne Frumence and analyses led by Simon Dellicour. www.medrxiv.org/content/10.6...
Unravelling the epidemiological and dispersal dynamics of the 2024-2025 chikungunya virus outbreak on Reunion island
Reunion island just experienced a massive chikungunya virus outbreak in 2024-2025, with more than 54,000 confirmed cases. This is the second major chikungunya outbreak on the island, following the fir...
www.medrxiv.org
January 12, 2026 at 9:54 AM
I am very glad to share the preprint for our latest study on the 2024-2025 chikungunya virus outbreak on Réunion island, with primary data produced thanks to the massive efforts performed by Marie-C Jaffar and Etienne Frumence and analyses led by Simon Dellicour. www.medrxiv.org/content/10.6...
Reposted by Nathan Grubaugh
🦟📄 New preprint! Our first large-scale phylodynamic study of Jamestown Canyon virus (JCV) reveals how mosquito ecology shapes the evolution, persistence, and spread of this understudied arbovirus in North America.
Read it here! www.biorxiv.org/content/10.6...
Read it here! www.biorxiv.org/content/10.6...
Evolutionary history of Jamestown Canyon virus disentangles complex multi-vector ecology
Jamestown Canyon virus (JCV) is a re-emerging mosquito-borne virus of increasing concern in North America. It has been historically understudied, leading to significant gaps in our understanding of it...
www.biorxiv.org
January 12, 2026 at 10:58 AM
🦟📄 New preprint! Our first large-scale phylodynamic study of Jamestown Canyon virus (JCV) reveals how mosquito ecology shapes the evolution, persistence, and spread of this understudied arbovirus in North America.
Read it here! www.biorxiv.org/content/10.6...
Read it here! www.biorxiv.org/content/10.6...
noice. Is that The Rob + mushrooms? looks like some sort of choose your own adventure.
My favs are Garbage, Sweetballs, and when I'm in the mood, The King.
My favs are Garbage, Sweetballs, and when I'm in the mood, The King.
January 12, 2026 at 2:48 AM
noice. Is that The Rob + mushrooms? looks like some sort of choose your own adventure.
My favs are Garbage, Sweetballs, and when I'm in the mood, The King.
My favs are Garbage, Sweetballs, and when I'm in the mood, The King.
It used to be Next Door but they closed
January 11, 2026 at 9:52 PM
It used to be Next Door but they closed
Reposted by Nathan Grubaugh
🚨Call for papers🚨
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health
Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me
This will be great, please submit and share!
academic.oup.com/emph/pages/m...
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health
Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me
This will be great, please submit and share!
academic.oup.com/emph/pages/m...
January 9, 2026 at 4:49 PM
🚨Call for papers🚨
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health
Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me
This will be great, please submit and share!
academic.oup.com/emph/pages/m...
Microbial Evolution: Impacts on Human Health
in the society journal Evolution, Medicine, and Public Health
Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa
EIC: me
This will be great, please submit and share!
academic.oup.com/emph/pages/m...
Reposted by Nathan Grubaugh
👀There will be a Keystone Symposium with a focus on Vector-Pathogen Interactions to be held in Geneva, Switzerland in February 2027. It should be a great meeting and hope to see you there! www.keystonesymposia.org/conferences/...
Vector-Pathogen Interactions: From Vector Biology to Innovative Control Strategies | Keystone Symposia
Join us at the Keystone Symposia on Vector-Pathogen Interactions: From Vector Biology to Innovative Control Strategies, February 2027, in Geneva, with field leaders!
www.keystonesymposia.org
January 7, 2026 at 3:32 PM
👀There will be a Keystone Symposium with a focus on Vector-Pathogen Interactions to be held in Geneva, Switzerland in February 2027. It should be a great meeting and hope to see you there! www.keystonesymposia.org/conferences/...
Reposted by Nathan Grubaugh
Children will die with RFK Jr.'s new vaccine recommendations. We're NOT doing the "experts disagree" game. The US vaccine schedule was painstakingly constructed through a deep & thorough process by experts with unquestionable expertise. This is policy by fiat. It is pre-meditated murder. 1/
January 5, 2026 at 10:39 PM
Children will die with RFK Jr.'s new vaccine recommendations. We're NOT doing the "experts disagree" game. The US vaccine schedule was painstakingly constructed through a deep & thorough process by experts with unquestionable expertise. This is policy by fiat. It is pre-meditated murder. 1/
Reposted by Nathan Grubaugh
I cannot emphasize this enough, if you're cold-emailing me applying to my lab I would so much rather get the bulleted broken list of genuine interests than whatever letter ChatGPT spits out in its stead
If you're training with me, I'm working with you not an LLM. I want to see who you are!
If you're training with me, I'm working with you not an LLM. I want to see who you are!
January 5, 2026 at 4:25 PM
I cannot emphasize this enough, if you're cold-emailing me applying to my lab I would so much rather get the bulleted broken list of genuine interests than whatever letter ChatGPT spits out in its stead
If you're training with me, I'm working with you not an LLM. I want to see who you are!
If you're training with me, I'm working with you not an LLM. I want to see who you are!
Reposted by Nathan Grubaugh
December 25th. The day the Fellowship departs Rivendell to destroy the One Ring.
Whatever you celebrate, may you have the courage to take the first steps to defy and endure against the dark, and rekindle light into the world.
Whatever you celebrate, may you have the courage to take the first steps to defy and endure against the dark, and rekindle light into the world.
December 25, 2025 at 3:52 PM
December 25th. The day the Fellowship departs Rivendell to destroy the One Ring.
Whatever you celebrate, may you have the courage to take the first steps to defy and endure against the dark, and rekindle light into the world.
Whatever you celebrate, may you have the courage to take the first steps to defy and endure against the dark, and rekindle light into the world.
Reposted by Nathan Grubaugh
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...
Last one of the year (unless...?) 👉 www.medrxiv.org/content/10.6...
December 23, 2025 at 2:32 PM
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...
Last one of the year (unless...?) 👉 www.medrxiv.org/content/10.6...
Reposted by Nathan Grubaugh
Variations in annual dengue intensities are explained by temperature anomalies
Our new work led by Abbey Porzucek, @rafalpx.bsky.social, @colincarlson.bsky.social, Dan Weinberger to develop a method to compare relative dengue intensity between years and countries.
www.medrxiv.org/content/10.6...
Our new work led by Abbey Porzucek, @rafalpx.bsky.social, @colincarlson.bsky.social, Dan Weinberger to develop a method to compare relative dengue intensity between years and countries.
www.medrxiv.org/content/10.6...
December 22, 2025 at 11:37 PM
Variations in annual dengue intensities are explained by temperature anomalies
Our new work led by Abbey Porzucek, @rafalpx.bsky.social, @colincarlson.bsky.social, Dan Weinberger to develop a method to compare relative dengue intensity between years and countries.
www.medrxiv.org/content/10.6...
Our new work led by Abbey Porzucek, @rafalpx.bsky.social, @colincarlson.bsky.social, Dan Weinberger to develop a method to compare relative dengue intensity between years and countries.
www.medrxiv.org/content/10.6...
Reposted by Nathan Grubaugh
We are recruiting two postdoc roles to work with #DeZiNetwork on dengue, Zika, and other emerging arboviruses:
🔬 Viral Computational Genomics
🔗 Apply here: lnkd.in/eq-dqCJb
🧪 Viral Genomics and Immunology
🔗 Apply here: lnkd.in/eMEKWb9b
More on DeZi here: lnkd.in/edwBg-qX
Deadline: 15 Jan 2026
🔬 Viral Computational Genomics
🔗 Apply here: lnkd.in/eq-dqCJb
🧪 Viral Genomics and Immunology
🔗 Apply here: lnkd.in/eMEKWb9b
More on DeZi here: lnkd.in/edwBg-qX
Deadline: 15 Jan 2026
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
December 23, 2025 at 9:50 AM
We are recruiting two postdoc roles to work with #DeZiNetwork on dengue, Zika, and other emerging arboviruses:
🔬 Viral Computational Genomics
🔗 Apply here: lnkd.in/eq-dqCJb
🧪 Viral Genomics and Immunology
🔗 Apply here: lnkd.in/eMEKWb9b
More on DeZi here: lnkd.in/edwBg-qX
Deadline: 15 Jan 2026
🔬 Viral Computational Genomics
🔗 Apply here: lnkd.in/eq-dqCJb
🧪 Viral Genomics and Immunology
🔗 Apply here: lnkd.in/eMEKWb9b
More on DeZi here: lnkd.in/edwBg-qX
Deadline: 15 Jan 2026
Finally, we identified that temperature anomalies are most strongly associated with elevated RISc.
This study provides the first standardized global analysis of dengue intensity, and provides a window into how spatial and temporal trends of dengue intensity may continue to evolve into the future.
This study provides the first standardized global analysis of dengue intensity, and provides a window into how spatial and temporal trends of dengue intensity may continue to evolve into the future.
December 22, 2025 at 11:37 PM
Finally, we identified that temperature anomalies are most strongly associated with elevated RISc.
This study provides the first standardized global analysis of dengue intensity, and provides a window into how spatial and temporal trends of dengue intensity may continue to evolve into the future.
This study provides the first standardized global analysis of dengue intensity, and provides a window into how spatial and temporal trends of dengue intensity may continue to evolve into the future.
We found that globally, 1995, 1998, 2019, and 2023 represented the highest RISc years and that high RISc tends to follow multi-year cycles.
*Note that we used an annual time frame from July to June for the Southern Hemisphere (so the 2023-24 transmission season is listed as 2023).
*Note that we used an annual time frame from July to June for the Southern Hemisphere (so the 2023-24 transmission season is listed as 2023).
December 22, 2025 at 11:37 PM
We found that globally, 1995, 1998, 2019, and 2023 represented the highest RISc years and that high RISc tends to follow multi-year cycles.
*Note that we used an annual time frame from July to June for the Southern Hemisphere (so the 2023-24 transmission season is listed as 2023).
*Note that we used an annual time frame from July to June for the Southern Hemisphere (so the 2023-24 transmission season is listed as 2023).
We created three categories of RISc, with the highest akin to outbreak conditions.
This provides a standardized measure of incidence intensity that adjusts for location- and time-specific contexts, thereby allowing intensities to be compared across geographies and timeframes.
This provides a standardized measure of incidence intensity that adjusts for location- and time-specific contexts, thereby allowing intensities to be compared across geographies and timeframes.
December 22, 2025 at 11:37 PM
We created three categories of RISc, with the highest akin to outbreak conditions.
This provides a standardized measure of incidence intensity that adjusts for location- and time-specific contexts, thereby allowing intensities to be compared across geographies and timeframes.
This provides a standardized measure of incidence intensity that adjusts for location- and time-specific contexts, thereby allowing intensities to be compared across geographies and timeframes.