Lee Katz
@lskatz.github.io
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.
Reposted by Lee Katz
The loss of an IRB at CDC would be catastrophic. CDC does quite a lot of research, and protecting people and their data is important.
October 19, 2025 at 8:22 PM
The loss of an IRB at CDC would be catastrophic. CDC does quite a lot of research, and protecting people and their data is important.
🍏 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
October 17, 2025 at 5:11 PM
🍏 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/...
Reposted by Lee Katz
~1300 fired on a Friday, about half unfired the next day, due to an apparent “coding error”. But sure, your data will be secure.
They’re all in a competition for who can be the most maliciously incompetent. So much winning. Participation trophies for eveyone. Nobel Prizes in Nonsense.
They’re all in a competition for who can be the most maliciously incompetent. So much winning. Participation trophies for eveyone. Nobel Prizes in Nonsense.
CDC purge hits 600 workers in key offices despite reversals
The casualties include employees working on health statistics, injury and violence prevention, congressional outreach and human resources.
www.axios.com
October 13, 2025 at 9:57 PM
~1300 fired on a Friday, about half unfired the next day, due to an apparent “coding error”. But sure, your data will be secure.
They’re all in a competition for who can be the most maliciously incompetent. So much winning. Participation trophies for eveyone. Nobel Prizes in Nonsense.
They’re all in a competition for who can be the most maliciously incompetent. So much winning. Participation trophies for eveyone. Nobel Prizes in Nonsense.
Reposted by Lee Katz
New reporting: many apparently fired at CDC in 'error'. This is a failure by design given that the admin does not care about fulfilling agency missions. This is the kind of error that should have political consequences.
Unserious people cause real-world harm.
🎁
www.nytimes.com/2025/10/11/h...
Unserious people cause real-world harm.
🎁
www.nytimes.com/2025/10/11/h...
Trump Administration Will Rehire Scores of Experts Fired in Error
www.nytimes.com
October 11, 2025 at 10:35 PM
New reporting: many apparently fired at CDC in 'error'. This is a failure by design given that the admin does not care about fulfilling agency missions. This is the kind of error that should have political consequences.
Unserious people cause real-world harm.
🎁
www.nytimes.com/2025/10/11/h...
Unserious people cause real-world harm.
🎁
www.nytimes.com/2025/10/11/h...
Reposted by Lee Katz
Welp, here it is: maybe the funniest thing we've ever done, in its entirety.
The Onion Investigates: Jeffrey Epstein
YouTube video by The Onion
www.youtube.com
October 9, 2025 at 11:35 PM
Welp, here it is: maybe the funniest thing we've ever done, in its entirety.
@benchapmanncsu.bsky.social happy birthday 🎂
September 27, 2025 at 7:23 PM
@benchapmanncsu.bsky.social happy birthday 🎂
Reposted by Lee Katz
Shanah Tovah to everyone, even the haters and losers
September 23, 2025 at 12:36 AM
Shanah Tovah to everyone, even the haters and losers
Reposted by Lee Katz
Witnesses Assumed Charlie Kirk Shooter Was Just Ordinary Gunman On School Campus
Witnesses Assumed Charlie Kirk Shooter Was Just Ordinary Gunman On School Campus
OREM, UT—As law enforcement officials search for a person of interest in the assassination of 31-year-old Turning Point USA co-founder Charlie Kirk, witnesses on the scene at Utah Valley University ad...
theonion.com
September 11, 2025 at 7:41 PM
Witnesses Assumed Charlie Kirk Shooter Was Just Ordinary Gunman On School Campus
🎙️ Just dropped: #MicroBinfie Pathoplexus Part 1!
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
144 - micro binfie Pathoplexus part 1
pca.st
September 11, 2025 at 12:05 PM
🎙️ Just dropped: #MicroBinfie Pathoplexus Part 1!
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
Join @happykhan.mstdn.science.ap.brid.gy, Lee & guest Clint as they deep-dive with @firefoxx66.bsky.social, Theo Sanderson & Arthur Shem Kasambula into Pathoplexus.
Ready for a journey? 🚀 Listen now: pca.st/episode/c1f8...
Reflecting back on the time when the podcast Risky or Not answered my question with a qualifier of (paraphrasing) "This isn't stupid or not; it's risky or not!" www.riskyornot.co/episodes/279...
279. Letting a 20 Month Old Try Kombucha — Risky or Not?
Dr. Don and Professor Ben talk about the risks letting a 20 month old try kombucha. Dr. Don - not risky 👍🏼 Professor Ben - not risky 👍🏼
www.riskyornot.co
September 10, 2025 at 4:23 PM
Reflecting back on the time when the podcast Risky or Not answered my question with a qualifier of (paraphrasing) "This isn't stupid or not; it's risky or not!" www.riskyornot.co/episodes/279...
Reposted by Lee Katz
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Mirrors! 🪞
I created a site to download and host small datasets in mirrors in the github pages space. Therefore, any region that github has better connectivity to would be able to download more quickly.
I started with NCBI taxonomy. What else? lskatz.github.io/mirror/
I created a site to download and host small datasets in mirrors in the github pages space. Therefore, any region that github has better connectivity to would be able to download more quickly.
I started with NCBI taxonomy. What else? lskatz.github.io/mirror/
Mirrors
This is an attempt to make a mirror for some commonly used bioinformatics datasets.
lskatz.github.io
September 7, 2025 at 2:33 AM
Mirrors! 🪞
I created a site to download and host small datasets in mirrors in the github pages space. Therefore, any region that github has better connectivity to would be able to download more quickly.
I started with NCBI taxonomy. What else? lskatz.github.io/mirror/
I created a site to download and host small datasets in mirrors in the github pages space. Therefore, any region that github has better connectivity to would be able to download more quickly.
I started with NCBI taxonomy. What else? lskatz.github.io/mirror/
Reposted by Lee Katz
Ossoff on RFK Jr: "Absolutely he should resign. And he never should've been confirmed to begin with... in any normal Senate, he never would've gotten so much as a hearing. This is someone who throughout his public life has embraced just about every piece of quackery & pseudoscience he's come across"
September 4, 2025 at 1:55 AM
Ossoff on RFK Jr: "Absolutely he should resign. And he never should've been confirmed to begin with... in any normal Senate, he never would've gotten so much as a hearing. This is someone who throughout his public life has embraced just about every piece of quackery & pseudoscience he's come across"
August 30, 2025 at 2:40 PM
Reposted by Lee Katz
I had serious doubts about CDC Director Monarez’s willingness to stand up against RFK Jr.’s personal mission to destroy public health in America—I’m glad that I was wrong.
If there are any adults left in the White House: we cannot let RFK Jr. burn what's left of CDC. FIRE HIM.
If there are any adults left in the White House: we cannot let RFK Jr. burn what's left of CDC. FIRE HIM.
New C.D.C. Director Resists Ouster as Other Officials Resign
www.nytimes.com
August 28, 2025 at 12:52 AM
I had serious doubts about CDC Director Monarez’s willingness to stand up against RFK Jr.’s personal mission to destroy public health in America—I’m glad that I was wrong.
If there are any adults left in the White House: we cannot let RFK Jr. burn what's left of CDC. FIRE HIM.
If there are any adults left in the White House: we cannot let RFK Jr. burn what's left of CDC. FIRE HIM.
@drdemetre.bsky.social will you repost your resignation letter? I was so sad when I read it but it was really thoughtful and eloquent.
August 28, 2025 at 12:05 AM
@drdemetre.bsky.social will you repost your resignation letter? I was so sad when I read it but it was really thoughtful and eloquent.
Reposted by Lee Katz
It's our birthday! Super proud of what this little database has become in the past year.
Today we launched support for measles and a bunch of new features 👇
Today we launched support for measles and a bunch of new features 👇
🗓 Pathoplexus turns ONE! 🎂🎉
In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...
1/10
In the past year we’ve grown from 4 pathogens to a truly global, community-driven platform for transparent, equitable & impactful pathogen sequence sharing.
📰 Read the full update: pathoplexus.org/news/2025-08...
1/10
August 27, 2025 at 4:01 PM
It's our birthday! Super proud of what this little database has become in the past year.
Today we launched support for measles and a bunch of new features 👇
Today we launched support for measles and a bunch of new features 👇
Reposted by Lee Katz
Keep and eye 👁️ (and an ear! 👂) out for a new Binfie podcast all about Pathoplexus 1 year in!
@happykhan.mstdn.science.ap.brid.gy and I had a great time recording last week with @firefoxx66.bsky.social @theo.io and Arthur Shem, with the help of Clint. Episodes set to be released starting September 11.
#microbinfie
#microbinfie
August 26, 2025 at 8:37 AM
Keep and eye 👁️ (and an ear! 👂) out for a new Binfie podcast all about Pathoplexus 1 year in!