@benchapmanncsu.bsky.social happy birthday 🎂

Shanah Tovah to everyone, even the haters and losers

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...

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...

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...

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/

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"

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

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.

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

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 👇

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

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...

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

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

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.

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

I think it's worth bringing up this site again for those who are job hunting in bioinformatics. github.com/lskatz/aweso...

Btw, zoom in by district and local impacts are already viewable for the WH's NIH FY26 budget proposal scienceimpacts.org/fy26

Kinda undermines the whole MAHA healthy food agenda, right?

🚨 New paper alert! How do you pick the right genomes for public health surveillance—when you’ve got 10,000+ E. coli to choose from? We built an MLST framework to do just that. 🧵👇 🔗 www.mdpi.com/2076-2607/13...

Y'all it's my fault (and a whole host of other factors I won't get into) that we haven't had #microbinfie episodes but I finally pushed out some episodes we had in the queue! Starting tomorrow, we'll start releasing the three "lost episodes" - the ones we recorded before 2025.

Subject matter experts (SMEs) and the Advisory Committee for Immunization Practices (ACIP): Why do SMEs matter? RFKJoker claims vaccine SMEs are corrupt because they're vaccine experts in bed with Big Pharma (most aren't) But the truth is, we need SMEs on ACIP And we need SMEs presenting to ACIP

1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.

Support the Bethesda Declaration! Sign the open letter supporting the statement from NIH employees. www.standupforscience.net/bethesda-dec...

Welp, there it is. RFK Jr. has removed all 17 members that comprise CDC’s vaccine advisory committee and will make new appointments. I said on PBS News Hour in February that this was a red line for me. www.hhs.gov/press-room/h...

One amazing and funny outcome of The Rehearsal should be improv groups coming government contractors for the FAA.

In the mid 90s, as a resident in South India, I never saw a case It boggles my mind that we've allowed infections like whooping cough to return and play havoc www.nytimes.com/2025/06/06/w...

One major plot hole is that midnight begins at the first bell. Yet, Cinderella transforms at 12:00:12am.

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

Autocycler: long-read consensus assembly for bacterial genomes www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/rrwick/Autoc...

The May 2025 supplemental issue of Emerging Infectious Diseases journal is now live: “Advances in Pathogen Genomics for Infectious Disease Surveillance, Control, and Prevention.” wwwnc.cdc.gov/eid/articles...

So proud of the work we did www.linkedin.com/posts/heathe...

🚨 Teaching bioinformatics? Or learning it solo? Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required. 🔬🧬👩‍💻 📚 github.com/lskatz/funda... ⭐️ Star it, share it, and level up! #bioinformatics #opensource #STEMeducation

I have my own frustrations with nextflow sometimes. However, no one can deny that it's stood up by some amazing people.

Someone is voluntarily leaving the meningococcus workplace for another job and I don't know her too well. I wanted to say that she is very competent and inflames my brain, but my wife wisely told me that was going to come off wrong. So, here you are, Internet.

I, too, sometimes have zero fuculose kinases

🚀 New proof-of-principle: An interactive, searchable MLST hash database... all in your browser! 🔥 Live demo ➡️ lskatz.github.io/mlst-hash-te... A natural extension of the hash database spec I developed last year: lskatz.github.io/mlst-hash-te... 🧵

We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue doi.org/10.1093/nar/... Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI: bakta.computational.bio (1/5)

Reminder for later, "I was just following orders" is not an acceptable defense

Spoiler for today's NYT Strands below

🚨 Tomorrow! 🧬NCBI Pathogen Detection is hosting a public seminar showcasing how their open data resource is being used by researchers and public health professionals. 📅 April 11 | 🕒 12:00 p.m.–1:00p.m. ET datascience.nih.gov/news/april-2... #PathogenSurveillance #DataSharing #RadicalTransparency

Today is going to be a long and difficult day.

One of my favorite artifacts from my years at CDC is also the least remarkable - a brick from the old Building 1 at Royal Campus.

I'd like to tell you a story about a scientist you may not have heard of, but who shaped a lot of modern health research... 🧵

This is so destructive and idiotic. mRNA vaccines are one of the most exciting opportunities to tackle diseases - from infectious disease to cancer and beyond - and these morons want to shut it down.