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Reposted by Lee Katz

Joshua Weitz @joshuasweitz.bsky.social · 13h

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...

Trump Administration Will Rehire Scores of Experts Fired in Error

www.nytimes.com

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Tim Onion @bencollins.bsky.social · 2d

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

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Lee Katz @lskatz.github.io · 3d

Oh damn I was just talking about doing this for bioinformatics in government on my podcast but I stopped because I don't think I have the pull. @carlzimmer.com 's is going to be incredible.

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Lee Katz @lskatz.github.io · 9d

Are you studying leptospirosis in your free time?

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Lee Katz @lskatz.github.io · 14d

@benchapmanncsu.bsky.social happy birthday 🎂

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Jonathan M. Katz @katz.theracket.news · 19d

Shanah Tovah to everyone, even the haters and losers

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The Onion @theonion.com · Sep 11

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

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Lee Katz @lskatz.github.io · Sep 11

🎙️ 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...

144 - micro binfie Pathoplexus part 1

pca.st

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Lee Katz @lskatz.github.io · Sep 10

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

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Reposted by Lee Katz

Zamin Iqbal @zaminiqbal.bsky.social · Sep 10

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...

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

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Lee Katz @lskatz.github.io · Sep 7

The workflow is triggered once a week but eventually be deactivated if no activity is found in the github repo, even if there is activity on the website. Therefore, I have it triggering if I push new code to the repo or if someone even adds a github issue.

Lee Katz @lskatz.github.io · Sep 7

This works by using github actions in this workflow: github.com/lskatz/mirro...

The dataset is downloaded and then placed into a directory. That directory finds its way into a website. The website has a table that links to it.

github.com

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Lee Katz @lskatz.github.io · Sep 7

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/

Mirrors

This is an attempt to make a mirror for some commonly used bioinformatics datasets.

lskatz.github.io

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Reposted by Lee Katz

Aaron Rupar @atrupar.com · Sep 4

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"

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Lee Katz @lskatz.github.io · Aug 30

I love your feedback for the podcast but maybe this one is one of the best

#microbinfie

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Senator Patty Murray @murray.senate.gov · Aug 28

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.

New C.D.C. Director Resists Ouster as Other Officials Resign

www.nytimes.com

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Lee Katz @lskatz.github.io · Aug 28

@drdemetre.bsky.social will you repost your resignation letter? I was so sad when I read it but it was really thoughtful and eloquent.

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Theo Sanderson @theo.io · Aug 27

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 👇

Pathoplexus @pathoplexus.org · Aug 27

🗓 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...

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Reposted by Lee Katz

Dr Emma Hodcroft @firefoxx66.bsky.social · Aug 26

Keep and eye 👁️ (and an ear! 👂) out for a new Binfie podcast all about Pathoplexus 1 year in!

Lee Katz @lskatz.github.io · Aug 25

@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

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Lee Katz @lskatz.github.io · Aug 25

@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

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Reposted by Lee Katz

Angie Rasmussen @angierasmussen.bsky.social · Aug 12

The shooting at CDC was domestic terrorism. It was instigated by the HHS Secretary's years-long campaign against an agency he oversees.
open.substack.com/pub/rasmusse...

When Dissent Becomes Domestic Terrorism

The call is coming from inside HHS

open.substack.com

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Reposted by Lee Katz

Alt CDC (they/them) @altcdc.altgov.info · Aug 8

There's an active shooter situation that started near the front entrance to CDC's roybal campus. The exteriors of buildings 21 and 24 and reportedly 18 were struck by bullets on the public-facing side. Emory just reissued a shelter in place warning.

Stay sheltering in place. Stay away from windows

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Reposted by Lee Katz

Joshua Weitz @joshuasweitz.bsky.social · Jul 27

Sunday reminder from #SCIMaP:

The White House FY26 budget includes $18B in cuts to NIH that will lead to >$46B in economic losses in communities nationwide + long-term impacts on our biomedical + health discovery pipeline. It's well past time to rethink & reset.

scienceimpacts.org/fy26

SCIMaP - Impacts of Federal Cuts to Science and Medical Research

View Projected Impact of the FY2026 Budget Cuts to the NIH

scienceimpacts.org

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Lee Katz @lskatz.github.io · Jul 25

Just finished another recording with @andrewjpage.bsky.social and @happykhan.mstdn.science.ap.brid.gy ! Trying to get back into the #microbinfie habit. Search for Micro Binfie wherever you get podcasts.

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Lee Katz @lskatz.github.io · Jul 23

I don’t think I’ve ever advertised this, but I built pdtk - a CLI toolkit for parsing NCBI Pathogens.
It downloads from the NCBI Pathogens FTP, builds a local database, and lets you query the results.

🛠️ Useful for outbreak surveillance
📍 github.com/lskatz/pdtk
#Bioinformatics #GenomicEpidemiology

GitHub - lskatz/pdtk: NCBI Pathogen Detection Portal toolkit

NCBI Pathogen Detection Portal toolkit. Contribute to lskatz/pdtk development by creating an account on GitHub.

github.com

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