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
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.