Lee Katz
@lskatz.github.io
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!
Reposted by Lee Katz
Weaponization of the premier public health agency in the country for personal clout and gain. The CDC website should not be trusted given the fact that it is controlled by people who will profit from spurious and false attempts to link vaccines to autism.
www.cdc.gov/vaccine-safe...
www.cdc.gov/vaccine-safe...
Autism and Vaccines
Answers to common questions about vaccine safety and autism.
www.cdc.gov
November 20, 2025 at 3:32 AM
Weaponization of the premier public health agency in the country for personal clout and gain. The CDC website should not be trusted given the fact that it is controlled by people who will profit from spurious and false attempts to link vaccines to autism.
www.cdc.gov/vaccine-safe...
www.cdc.gov/vaccine-safe...
The last episode of the three part debate is out today! Check it out on the platform of your choice
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
🍏 We just finished a three part debate on @nextflow.io! Please don't hate me for volunteering on the cons side of the debate! Subscribe to #microbinfie on the podcast app of your choice or go here m.soundcloud.com/microbinfie/...
146 - NextFlow debate 1
Play 146 - NextFlow debate 1 by Micro Binfie Podcast on desktop and mobile. Play over 320 million tracks for free on SoundCloud.
m.soundcloud.com
November 13, 2025 at 5:17 PM
The last episode of the three part debate is out today! Check it out on the platform of your choice
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
🤩 Don't forget to give us stars and reviews to help spread the podcast to new listeners!
On #foodsafetytalk, the podcast co-hosts said that the food safety world needs something like a federated and possibly industry-led system for regulators. I wonder if this extends to genomic epidemiology? Let me take you on a tangent.
November 13, 2025 at 2:21 AM
On #foodsafetytalk, the podcast co-hosts said that the food safety world needs something like a federated and possibly industry-led system for regulators. I wonder if this extends to genomic epidemiology? Let me take you on a tangent.
Reposted by Lee Katz
We hope you'll join us tomorrow night at 7 for our first episode!
Decaturish launches new streaming show and podcast
Starting Nov. 13, Decaturish will launch the Decaturish Download, a new streaming show that will feature the latest news and interviews with local newsmakers.
www.decaturish.com
November 13, 2025 at 1:32 AM
We hope you'll join us tomorrow night at 7 for our first episode!
Reposted by Lee Katz
We are a two fed family, so no income for 40 days. I am incandescent with rage about the Dems caving.
November 10, 2025 at 1:45 AM
We are a two fed family, so no income for 40 days. I am incandescent with rage about the Dems caving.
Reposted by Lee Katz
pre-writing a devastating obituary for your enemy is god-tier hating of a kind you don’t often see anymore. renaissance haterism. beautiful stuff.
A Sharon Begley byline, almost 5 years after her death.
Upon hearing the news James Watson had died, a STAT reporter said in our Slack, "I wish I could read what Sharon would have written."
Incredible news: Sharon in fact did pre-write a Watson obit. And it is masterful and excoriating.
🧪🧬🧫
Upon hearing the news James Watson had died, a STAT reporter said in our Slack, "I wish I could read what Sharon would have written."
Incredible news: Sharon in fact did pre-write a Watson obit. And it is masterful and excoriating.
🧪🧬🧫
James Watson, dead at 97, was a scientific legend and a pariah among his peers
James Watson, the co-discoverer of the structure of DNA who died Thursday at 97, was a scientific legend and a pariah among his peers.
www.statnews.com
November 9, 2025 at 12:55 AM
pre-writing a devastating obituary for your enemy is god-tier hating of a kind you don’t often see anymore. renaissance haterism. beautiful stuff.
Reposted by Lee Katz
That would have been big news a few years ago, unfortunately the great science that gives important understanding in coronaviruses is now back to the small circle of scientists. Anyway: A fully functional furin cleavage site in a bat betacorarnavirus! Congrats to the authors!
We’ve identified a highly divergent betacoronavirus from South American bat that encodes a functional furin cleavage site.
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
Another fascinating reminder of how diverse coronavirus evolution is in wildlife reservoirs.
#Virology #VirusEvolution #Bats #Coronavirus
www.biorxiv.org/content/10.1...
A divergent betacoronavirus with a functional furin cleavage site in South American bats
Bats are natural reservoirs for a wide range of RNA viruses. Members of the genus Betacoronavirus, including Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome...
www.biorxiv.org
October 29, 2025 at 9:56 PM
That would have been big news a few years ago, unfortunately the great science that gives important understanding in coronaviruses is now back to the small circle of scientists. Anyway: A fully functional furin cleavage site in a bat betacorarnavirus! Congrats to the authors!
Reposted by Lee Katz
My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...
Remembering Hamilton O. Smith
Hamilton O. Smith
August 31, 1931 – October 25, 2025
It is with profound sorrow that we announce the loss of Hamilton O. Smith, M.D., a...
www.jcvi.org
October 29, 2025 at 11:26 PM
My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...
Reposted by Lee Katz
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:33 PM
Proud of the latest edition of my free intro biostats book.
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
gitrepo: github.com/ybrandvain/b...
book: ybrandvain.github.io/biostats/
Not complete but at a good point to take a break, and I think its quite usable
dm me with comments , ideas etc
Reposted by Lee Katz
Just another normal HHS week: CDC researchers cannot present work at an annual Infectious Disease conference in (checks notes) Atlanta. As a CDC researcher put it:
“It appears to me that HHS’s goal is to prevent the dissemination of scientific information. It’s insane.”
apnews.com/article/infe...
“It appears to me that HHS’s goal is to prevent the dissemination of scientific information. It’s insane.”
apnews.com/article/infe...
Government shutdown means many CDC experts are skipping a pivotal meeting on infectious disease
An annual conference about infectious diseases is seeing a dramatic attendance decline, in part because Centers for Disease Control and Prevention experts can’t participate.
apnews.com
October 21, 2025 at 2:46 AM
Just another normal HHS week: CDC researchers cannot present work at an annual Infectious Disease conference in (checks notes) Atlanta. As a CDC researcher put it:
“It appears to me that HHS’s goal is to prevent the dissemination of scientific information. It’s insane.”
apnews.com/article/infe...
“It appears to me that HHS’s goal is to prevent the dissemination of scientific information. It’s insane.”
apnews.com/article/infe...
🚀 New in Fasten: fasten_head
Unix head, but FASTQ-aware 🧬
✅ Get first N reads (not just lines!)
✅ Works with paired-end reads
✅ Can limit by bases OR reads
✅ Blazingly fast (it's Rust 🦀)
cat huge.fq | fasten_head -r 1000
Stop doing math with -n. Let the tool understand your data.
Unix head, but FASTQ-aware 🧬
✅ Get first N reads (not just lines!)
✅ Works with paired-end reads
✅ Can limit by bases OR reads
✅ Blazingly fast (it's Rust 🦀)
cat huge.fq | fasten_head -r 1000
Stop doing math with -n. Let the tool understand your data.
October 21, 2025 at 12:13 AM
🚀 New in Fasten: fasten_head
Unix head, but FASTQ-aware 🧬
✅ Get first N reads (not just lines!)
✅ Works with paired-end reads
✅ Can limit by bases OR reads
✅ Blazingly fast (it's Rust 🦀)
cat huge.fq | fasten_head -r 1000
Stop doing math with -n. Let the tool understand your data.
Unix head, but FASTQ-aware 🧬
✅ Get first N reads (not just lines!)
✅ Works with paired-end reads
✅ Can limit by bases OR reads
✅ Blazingly fast (it's Rust 🦀)
cat huge.fq | fasten_head -r 1000
Stop doing math with -n. Let the tool understand your data.