Curtis Kapsak
@curtiskapsak.bsky.social
Bioinformatics Scientist @theiagen.bsky.social
Likely swimming in a sea of pathogen genomes 🏊🧬 or riding my bike 🚴
Public Health | Infectious Diseases | Bioinformatics | Software Dev
Likely swimming in a sea of pathogen genomes 🏊🧬 or riding my bike 🚴
Public Health | Infectious Diseases | Bioinformatics | Software Dev
Reposted by Curtis Kapsak
1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN).
👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...
#EVD68 #Enterovirus #OpenData
👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...
#EVD68 #Enterovirus #OpenData
November 20, 2025 at 12:49 PM
1/ 🚀 Exciting news: we’ve just released the first Nextclade dataset for Enterovirus D68 (EV-D68), developed in collaboration with the European Non-Polio Enterovirus Network (ENPEN).
👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...
#EVD68 #Enterovirus #OpenData
👉🏻 Check out the dataset on Nextclade! clades.nextstrain.org?dataset-name...
#EVD68 #Enterovirus #OpenData
Reposted by Curtis Kapsak
Please join us for the @who.int EPI-WIN webinar introducing WHO’s report on Attributes and Principles of Pathogen Genomic Data-Sharing Platforms. 24 November 2025, 1-2pm CET.
🔗 Register: who.zoom.us/webinar/regi...
👉 Webinar info: www.who.int/news-room/ev...
📄 Report: iris.who.int/bitstreams/f...
🔗 Register: who.zoom.us/webinar/regi...
👉 Webinar info: www.who.int/news-room/ev...
📄 Report: iris.who.int/bitstreams/f...
November 18, 2025 at 12:15 PM
Please join us for the @who.int EPI-WIN webinar introducing WHO’s report on Attributes and Principles of Pathogen Genomic Data-Sharing Platforms. 24 November 2025, 1-2pm CET.
🔗 Register: who.zoom.us/webinar/regi...
👉 Webinar info: www.who.int/news-room/ev...
📄 Report: iris.who.int/bitstreams/f...
🔗 Register: who.zoom.us/webinar/regi...
👉 Webinar info: www.who.int/news-room/ev...
📄 Report: iris.who.int/bitstreams/f...
Reposted by Curtis Kapsak
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 Curtis Kapsak
RFK Jr. Promotes Natural Immunity With Invitation To Touch His Festering Sore https://theonion.com/rfk-jr-promotes-natural-immunity-with-invitation-to-touch-his-festering-sore/
September 24, 2025 at 3:08 PM
RFK Jr. Promotes Natural Immunity With Invitation To Touch His Festering Sore https://theonion.com/rfk-jr-promotes-natural-immunity-with-invitation-to-touch-his-festering-sore/
Reposted by Curtis Kapsak
Rocky start for new #CDC director Susan Monarez, whose first week was punctuated by Friday's attack. Her first all-hands meeting lasted ~13 minutes, with technical challenges with dead air for a time & some staff unable to join the call. "This is a mess," one said. www.statnews.com/2025/08/12/c...
CDC leaders attempt to reassure staff after shooting, but meeting is brief
An all-hands meeting at the CDC to discuss the attack on the agency on Friday was brief and chaotic, staffers say.
www.statnews.com
August 12, 2025 at 4:22 PM
Rocky start for new #CDC director Susan Monarez, whose first week was punctuated by Friday's attack. Her first all-hands meeting lasted ~13 minutes, with technical challenges with dead air for a time & some staff unable to join the call. "This is a mess," one said. www.statnews.com/2025/08/12/c...
Reposted by Curtis Kapsak
@kevinlibuit.bsky.social & @curtiskapsak.bsky.social were two of the co-authors on a new paper on Freyja 2 — a bioinformatics tool for real-time, multi-pathogen wastewater surveillance.
Read about it here: www.medrxiv.org/content/10.1...
Read about it here: www.medrxiv.org/content/10.1...
Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2
Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...
www.medrxiv.org
August 4, 2025 at 3:12 PM
@kevinlibuit.bsky.social & @curtiskapsak.bsky.social were two of the co-authors on a new paper on Freyja 2 — a bioinformatics tool for real-time, multi-pathogen wastewater surveillance.
Read about it here: www.medrxiv.org/content/10.1...
Read about it here: www.medrxiv.org/content/10.1...
Reposted by Curtis Kapsak
A few days ago we preprinted our Freyja 2 paper, describing the expansion of our original Freyja method to a real-time, multi-pathogen surveillance tool to track pathogen lineage prevalence and dynamics from sequencing of wastewater and other complex samples (like milk). 🧵
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2
Case-based infectious disease surveillance is fundamental to public health, but is resource-intensive, logistically complex, and prone to sampling bias. Wastewater testing and sequencing have increasi...
doi.org
July 31, 2025 at 7:18 PM
A few days ago we preprinted our Freyja 2 paper, describing the expansion of our original Freyja method to a real-time, multi-pathogen surveillance tool to track pathogen lineage prevalence and dynamics from sequencing of wastewater and other complex samples (like milk). 🧵
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Reposted by Curtis Kapsak
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
July 30, 2025 at 2:11 AM
Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Curtis Kapsak
Schrier to RFK Jr: You gave Cassidy the answer he needed to hear in order to get his confirmation vote, then as soon as you were secretary you turned around & fired all 17 members. You lied. I also want to be clear that I will lay all responsibility for every vaccine-preventable death at your feet.
June 24, 2025 at 3:54 PM
Schrier to RFK Jr: You gave Cassidy the answer he needed to hear in order to get his confirmation vote, then as soon as you were secretary you turned around & fired all 17 members. You lied. I also want to be clear that I will lay all responsibility for every vaccine-preventable death at your feet.
Reposted by Curtis Kapsak
RUIZ: Did you read the report & fact-check its sources prior to publication?
RFK JR: I did not fact check
RUIZ: It included citations to sources that don't exist. How does that happen?
RFK JR: All of the foundational assertions are accurate
RUIZ: They did not exist. How can they be accurate?
RFK JR: I did not fact check
RUIZ: It included citations to sources that don't exist. How does that happen?
RFK JR: All of the foundational assertions are accurate
RUIZ: They did not exist. How can they be accurate?
June 24, 2025 at 3:26 PM
RUIZ: Did you read the report & fact-check its sources prior to publication?
RFK JR: I did not fact check
RUIZ: It included citations to sources that don't exist. How does that happen?
RFK JR: All of the foundational assertions are accurate
RUIZ: They did not exist. How can they be accurate?
RFK JR: I did not fact check
RUIZ: It included citations to sources that don't exist. How does that happen?
RFK JR: All of the foundational assertions are accurate
RUIZ: They did not exist. How can they be accurate?
Reposted by Curtis Kapsak
Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance wwwnc.cdc.gov/eid/article/... 🧬🖥️🧪
May 20, 2025 at 12:06 PM
Advantages of Software Containerization in Public Health Infectious Disease Genomic Surveillance wwwnc.cdc.gov/eid/article/... 🧬🖥️🧪
Reposted by Curtis Kapsak
You might be wondering why we haven't updated outbreak.info for months.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
May 28, 2025 at 11:02 PM
You might be wondering why we haven't updated outbreak.info for months.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.
Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.
After a ♾️ back and forth, that is now permanent.
More on that soon - and why GISAID should not be trusted with critical data.