Lee Katz
@lskatz.github.io
Co host of the Micro Binfie podcast
Just added a measles genome (subtype D8) to Kalamari.
Useful for screening + as a reference genome - and a reminder that we still maintain a living list of public health reference genomes.
Measles is relevant again. Infrastructure matters. 🦑
Useful for screening + as a reference genome - and a reminder that we still maintain a living list of public health reference genomes.
Measles is relevant again. Infrastructure matters. 🦑
February 6, 2026 at 11:33 PM
Just added a measles genome (subtype D8) to Kalamari.
Useful for screening + as a reference genome - and a reminder that we still maintain a living list of public health reference genomes.
Measles is relevant again. Infrastructure matters. 🦑
Useful for screening + as a reference genome - and a reminder that we still maintain a living list of public health reference genomes.
Measles is relevant again. Infrastructure matters. 🦑
Reposted by Lee Katz
More than a week after his death, I’m still reflecting on the life and legacy of Bill Foege—the Babe Ruth of public health—whose work with others saved the lives of literally hundreds of millions of people. His accomplishments are in a league of their own.
February 6, 2026 at 1:01 AM
More than a week after his death, I’m still reflecting on the life and legacy of Bill Foege—the Babe Ruth of public health—whose work with others saved the lives of literally hundreds of millions of people. His accomplishments are in a league of their own.
Happy Groundhog Day to all those who enjoy orderly shutdowns
February 2, 2026 at 1:21 PM
Happy Groundhog Day to all those who enjoy orderly shutdowns
@planetmoney.bsky.social have you seen Wonder Man yet?
January 31, 2026 at 3:04 AM
@planetmoney.bsky.social have you seen Wonder Man yet?
Reposted by Lee Katz
(1/2) MMWR: Measles Outbreak Linked to Air Travel — Colorado, 2025
An unvaccinated traveler exposed others during an international flight and at Denver International Airport, leading to:
• 9 secondary & 1 tertiary case in Colorado
• 7 more cases in other states
• 4 hospitalizations, mostly unvaxxed
An unvaccinated traveler exposed others during an international flight and at Denver International Airport, leading to:
• 9 secondary & 1 tertiary case in Colorado
• 7 more cases in other states
• 4 hospitalizations, mostly unvaxxed
January 30, 2026 at 1:50 AM
(1/2) MMWR: Measles Outbreak Linked to Air Travel — Colorado, 2025
An unvaccinated traveler exposed others during an international flight and at Denver International Airport, leading to:
• 9 secondary & 1 tertiary case in Colorado
• 7 more cases in other states
• 4 hospitalizations, mostly unvaxxed
An unvaccinated traveler exposed others during an international flight and at Denver International Airport, leading to:
• 9 secondary & 1 tertiary case in Colorado
• 7 more cases in other states
• 4 hospitalizations, mostly unvaxxed
Reposted by Lee Katz
I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...
January 29, 2026 at 10:37 AM
I've just released #rust-htslib 1.0. After a long time with a pretty stable API usage of rust-htslib in production, it feels like the right time to finally move to 1.0. Most important change is probably a switch to thread-safe pointers in BAM record handling. github.com/rust-bio/rus...
Reposted by Lee Katz
After being held in two of them as a boy, I fought for decades urging America to never again build concentration camps and put human beings in them. It breaks my heart to watch this happen twice now in my own lifetime.
January 27, 2026 at 9:30 PM
After being held in two of them as a boy, I fought for decades urging America to never again build concentration camps and put human beings in them. It breaks my heart to watch this happen twice now in my own lifetime.
RFK Jr. Is Practically Running a Tuskegee Syphilis Study and Almost No One Is Talking About It
pca.st
January 20, 2026 at 1:11 AM
Reposted by Lee Katz
> An alternative to GISAID has been gaining ground. In 2024, Chen, Stadler, and others launched Pathoplexus, a platform that also seeks to protect the interests of those uploading sequences but aims to allow data to be shared more freely.
And if you love podcasts:
open.spotify.com/episode/0wrp...
And if you love podcasts:
open.spotify.com/episode/0wrp...
January 7, 2026 at 5:08 PM
> An alternative to GISAID has been gaining ground. In 2024, Chen, Stadler, and others launched Pathoplexus, a platform that also seeks to protect the interests of those uploading sequences but aims to allow data to be shared more freely.
And if you love podcasts:
open.spotify.com/episode/0wrp...
And if you love podcasts:
open.spotify.com/episode/0wrp...
Reposted by Lee Katz
Just a couple shots protect you from having to bury your child.
THIS ISN’T HARD. VACCINATE!
THIS ISN’T HARD. VACCINATE!
High school student suddenly dies from bacterial meningitis: School district
YouTube video by ABC News
youtu.be
January 5, 2026 at 8:42 PM
Just a couple shots protect you from having to bury your child.
THIS ISN’T HARD. VACCINATE!
THIS ISN’T HARD. VACCINATE!
Happy anniversary of Jesus's bris to those who celebrate
January 1, 2026 at 3:44 PM
Happy anniversary of Jesus's bris to those who celebrate
Happy new years for those who celebrate
January 1, 2026 at 3:34 AM
Happy new years for those who celebrate
Literal LOL from me when the Jewish chief comes into the church breaking out her Yiddish
re: Wake Up Dead Man. IMO the line from Chief Geraldine, “So, what, facts schmacts, you believe in God and all this mishigas is real” is an answer key to the movie
December 31, 2025 at 5:01 AM
Literal LOL from me when the Jewish chief comes into the church breaking out her Yiddish
I just completed "Secret Entrance" - Day 1 - Advent of Code 2025 #AdventOfCode adventofcode.com/2025/day/1
I did it in scratch!
scratch.mit.edu/projects/126...
I did it in scratch!
scratch.mit.edu/projects/126...
Day 1 - Advent of Code 2025
adventofcode.com
December 30, 2025 at 6:14 PM
I just completed "Secret Entrance" - Day 1 - Advent of Code 2025 #AdventOfCode adventofcode.com/2025/day/1
I did it in scratch!
scratch.mit.edu/projects/126...
I did it in scratch!
scratch.mit.edu/projects/126...
'Denmark explicitly declined to add rotavirus vaccination. Their health authority concluded that rotavirus infection “hardly ever results in death or long-term harm” in a country with universal health care access.'
Tens of thousands of annual cases of chickenpox, rotavirus, and other vaccine preventable diseases a year - in a country of six million people.
Not only will Denmark’s vaccine schedule not work for the US, it already isn’t working for Denmark.
Not only will Denmark’s vaccine schedule not work for the US, it already isn’t working for Denmark.
Should the US adopt Denmark's vaccine schedule for children? @jakescottmd.bsky.social argues no in a piece that points out the risks such a move would pose for American kids. www.statnews.com/2025/12/19/d...
December 20, 2025 at 1:29 PM
'Denmark explicitly declined to add rotavirus vaccination. Their health authority concluded that rotavirus infection “hardly ever results in death or long-term harm” in a country with universal health care access.'
Reposted by Lee Katz
The media needs to stop writing headlines like “The CDC changes course on vaccines and autism” and “The CDC defends measles response”.
NONE of this is coming from legitimate scientists at the CDC.
ALL of it is coming from RFK Jr.
Every such headline is causing further harm to public health.
NONE of this is coming from legitimate scientists at the CDC.
ALL of it is coming from RFK Jr.
Every such headline is causing further harm to public health.
December 17, 2025 at 1:49 AM
The media needs to stop writing headlines like “The CDC changes course on vaccines and autism” and “The CDC defends measles response”.
NONE of this is coming from legitimate scientists at the CDC.
ALL of it is coming from RFK Jr.
Every such headline is causing further harm to public health.
NONE of this is coming from legitimate scientists at the CDC.
ALL of it is coming from RFK Jr.
Every such headline is causing further harm to public health.
Reposted by Lee Katz
Honestly, as a micro binfie, I couldn't feel more honored than to be entrusted with this! 😃
Prokka has served so many so well, and deeply inspired me how to write Bakta.
I'm thankful to be part of this open science com, and will do my best to meet these high quality standards.
Thanks Torsten! 🦠💻
Prokka has served so many so well, and deeply inspired me how to write Bakta.
I'm thankful to be part of this open science com, and will do my best to meet these high quality standards.
Thanks Torsten! 🦠💻
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Release Heading into the sunset · tseemann/prokka
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
December 16, 2025 at 11:50 AM
Honestly, as a micro binfie, I couldn't feel more honored than to be entrusted with this! 😃
Prokka has served so many so well, and deeply inspired me how to write Bakta.
I'm thankful to be part of this open science com, and will do my best to meet these high quality standards.
Thanks Torsten! 🦠💻
Prokka has served so many so well, and deeply inspired me how to write Bakta.
I'm thankful to be part of this open science com, and will do my best to meet these high quality standards.
Thanks Torsten! 🦠💻
Reposted by Lee Katz
💾 Shovill 1.4.1 has been released!
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
Releases · tseemann/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill
github.com
December 13, 2025 at 9:15 PM
💾 Shovill 1.4.1 has been released!
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
I just looked up my notes from 2014 when we were in the rhythm of it all, uploading thousands of genomes. It was like five one liners in perl, some curl commands, and a combination of bash and python scripts. Documented in NOTES.txt. Bioinformatics was wild.
December 9, 2025 at 2:20 PM
I just looked up my notes from 2014 when we were in the rhythm of it all, uploading thousands of genomes. It was like five one liners in perl, some curl commands, and a combination of bash and python scripts. Documented in NOTES.txt. Bioinformatics was wild.
Reposted by Lee Katz
WCHA disagrees with CDC’s Advisory Committee’s change to decades-long vaccine recommendation that has reduced pediatric hepatitis B infections by 99 percent.
doh.wa.gov/newsroom/wes...
doh.wa.gov/newsroom/wes...
West Coast Health Alliance, WA DOH, and Leading National Medical Organizations Continue to Recommend Hepatitis B Vaccination for Newborns
For immediate release: December 5, 2025 (25-145) Contact: DOH Communications
doh.wa.gov
December 6, 2025 at 12:52 AM
WCHA disagrees with CDC’s Advisory Committee’s change to decades-long vaccine recommendation that has reduced pediatric hepatitis B infections by 99 percent.
doh.wa.gov/newsroom/wes...
doh.wa.gov/newsroom/wes...
Reposted by Lee Katz
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
I can't help but notice that #pizzintwatch doesn't track pizza places close to CDC.
December 2, 2025 at 8:02 PM
I can't help but notice that #pizzintwatch doesn't track pizza places close to CDC.
Did you hear about the fight between the fork and the turkey? It was tine-y and short lived.
Happy Thanksgiving!
Happy Thanksgiving!
November 27, 2025 at 6:06 PM
Did you hear about the fight between the fork and the turkey? It was tine-y and short lived.
Happy Thanksgiving!
Happy Thanksgiving!