Congratulations and welcome back to Baltimore! JHU genomics is lucky to have you!

i think if you tweet "a whole civilization will die tonight" you shouldn't go to the hague, the hague should get to come to you

Here are 5 reasons why I would wear a respirator, if I lived somewhere with a Meningitis B outbreak.

Reposting the image with alt text. So EVERYONE can see which of the thirteen airports will have ICE agents on site

What is happening in the US right now is nothing short of disastrous. It is a human rights issue, a reproductive rights issue, a scientific issue, an issue of conscience. Marginalized communities are in pain right now and anyone privileged enough to help your neighbors should absolutely be doing so.

White text on black background reading: "ICE OUT! NATIONWIDE SHUTDOWN! NO WORK. NO SCHOOL. NO SHOPPING. JAN 30, 2026 Sign on to join us: nationalshutdown.org "

I am taking tomorrow off to stand in solidarity with the people of the Twin Cities (nationalshutdown.org). It has been a very difficult few weeks for Minnesota and I urge you to contribute to local rapid response networks or those of the Twin Cities: www.standwithminnesota.com.

Something important to understand about ICE thugs in the Twin Cities is that they're harassing innocent kids and parents at bus stops and schools every single day. Even after the Pretti shooting. It's terrorism.

If they are doing this to white people in broad daylight imagine what they are doing to non-white people in detention facilities.

Congratulations!!! 🎉🎉

I know people on Bsky know this but I hope it filters out: The feds are OCCUPYING the Twin Cities. This is a blockade, a siege. They are shutting down economic and civic activity. They are conducting "papers please" stops. They are criminalizing being a bystander/witness.

You could be next.

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

My kitchen table issue is “don’t shoot people at their kitchen tables”

A wrong Grok post making up a white guy who stopped the Australian mass shooting.

BBC 'Hero' who wrestled gun from Bondi shooter named as Ahmed al Ahmed Emily Atkinson Sun, December 14, 2025 at 1:06 p.m. CST 2 min read A "hero" bystander who was filmed wrestling a gun from one of the Bondi Beach attackers has been named as 43-year-old Ahmed al Ahmed. Video verified by the BBC showed Mr Ahmed run at the gunman and seize his weapon, before turning the gun round on him, forcing his retreat. Mr Ahmed, a fruit shop owner and father of two, remains in hospital, where he has undergone surgery for bullet wounds to his arm and hand, his family told 7News Australia.

This is fucking grim. Somebody invented a white guy, an "IT professional" named Edward Crabtree, who stopped the Bondi shooting and spread it all over the internet, which was picked up by AI agents and slop aggregation sites.

The real hero is a fruit stand owner named Ahmed el Ahmed.

A bad thing is unfolding at NIH this week: It looks like the Trump administration is trying to replace key civil servant scientific leaders, the Institute Directors, with political hires. These directors control the NIH budget, tens of billions.

A bit of a video explainer here: 1/ 🧪

Congratulations!!

Just published an interactive article about a magical algorithm known as the Burrows-Wheeler Transform, which powers sequence alignment tools like bowtie and bwa: sandbox.bio/concepts/bwt

It's also notoriously unintuitive so I'm hoping this article helps you build that intuition.

Burrows-Wheeler Indexing - YouTube Videos on : (a) the Burrows-Wheeler Transform (BWT), (b) the FM Index, which uses the BWT to construct a full-text index, (c) Wheeler graphs, (d) r-index, an...

I've added 7 videos to my Burrows-Wheeler indexing playlist (www.youtube.com/playlist?lis...), rounding out the r-index series and adding a 5-part series on the move structure. Now 27 videos in that playlist. I aim to add videos on prefix-free parsing, PBWT, Wheeler languages/automata in the future.

🦒Long read giraffe is out!🦒
Mapping long reads to pangenome graphs is ~10x faster than with GraphAligner, with veeery slightly better mapping accuracy, short variant calling, and SV genotyping than GraphAligner or Minimap2

This is mostly true, but I do quote "somehow, Palpatine returned" all the time

Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.

The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP

jasonjwilliamsny.github.io/grfp2025/

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

Make no mistake, this remains catastrophic.

It makes it near impossible for people to stay and work in the US, no matter how qualified they are, unless they work for a handful of extremely wealthy companies.

For so many of us, it’s time to make other plans.

The protests yesterday reminded me of this movement. Seeing the recent corruption feels like a repeat of history.

If you are in the Philippines, know that I am thinking of you. If you're taking part in the protests, know I am proud of you and wish for you and your loved ones to be safe. Ingat ka.

The protests took place yesterday, which was also the anniversary of declaration of martial law by Ferdinand Marcos, who is the father of the current president. He was known to also take tax payers money to fund his family's lifestyle. He was forced out in 1986 by the People Power Revolution.

Over the last day I've seen many videos of Filipinos protesting against corruption (within flooding projects) in the Philippines.

Every time I see these videos, I feel emotional. I am so proud to see Filipinos participating. But also sad because of seeing years of corruption and injustice.

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

7/ If you’re under 65 and not high risk, the window to get a Covid-19 vaccine is right now—before the FDA label changes. Once it happens, access will be limited immediately (if it isn’t already). CVS is no longer booking appointments. As far as we know, Walgreens and local pharmacies still are.

Congratulations @benlangmead.bsky.social! 🎉

Your footnote of "if you're a woman, you have XX chromosomes, and if you're a man, you have XY chromosomes" is inaccurate. Things are not so clear-cut and representing them as such perpetuates misinformation and does a disservice to our trans colleagues and trans people in general.