Just learned github exposes every user's public SSH keys at github.com/<username>.keys i removed one of mine, and a random throwaway account snatched it within seconds, killing the keypair for me.

It was an amazing meeting with very cool science!

Thrilled to share that my abstract was selected for a 15-minute talk at #bog26 @cshlmeetings.bsky.social! I'll present our prairie & meadow vole assemblies using CiFi long reads, we built the first chromosome-scale diploid assemblies that fully resolve the Avpr1a duplication linked to pair bonding 🐭

I had a blast working on this paper! This was the first mammalian assembly paper using the new CiFi tech, and we combined multiple lines of evidence to verify a prairie-vole-specific duplication of Avpr1a. All methods will be open source and reproducible, enabling the community to build on them.

Age verification? My first game was "↑ ↑ ↓ ↓ ← → ← → X O".

One of the most-viewed PNAS articles in the last week is “Tattoo ink induces inflammation in the draining lymph node and alters the immune response to vaccination.” Explore the article here: https://ow.ly/zhn450XGvmW For more trending articles, visit https://ow.ly/7BgF50XGvmV.

🎉🎉🎉

I watched a video titled “Why Smart People Struggle to Succeed” and the ideas were surprisingly accurate. Here is the breakdown:

Morning dew turned my windshield into a perfect pattern of glassy bubbles!

I did not expect to find a paper in a new graph genotyper (using colored de bruijn graphs) which quotes Maya Angelou on line 1! academic.oup.com/gigascience/...

A new paper from the lab! Work led by @drtamermansour.bsky.social and others not here on bsky. "We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem."

That is cool! webassembly.org/news/2025-09...

Can't say how much I love this type of education! phet.colorado.edu phet.colorado.edu/en/simulatio...

For decades, NIH funding has fueled breakthroughs in cancer, heart disease and more. But a new policy puts progress at risk. We need Congress to oppose this abrupt change. Join me in emailing lawmakers today! #SaveNIHresearch bit.ly/4hxmfsK

not paying indirect costs for research is like only paying the players in the Super Bowl. can't have a Super Bowl without coaches, referees, security, janitors, announcers, stadium staff, and a stadium - and you can't have research without supporting people and facilities

🚨 Keynotes at RECOMB-seq 2025! 🚨 🌟 Alicia Oshlack – computational transcriptomics @aliciao.bsky.social 🌟 Rayan Chikhi – sequencing data structures @rayanchikhi.bsky.social 🗓️ Dates: April 24–25, 2025 📍 Seoul, South Korea recomb-seq.github.io/speakers/

American science and medicine has been thrown into chaos and uncertainty over the past week. Here are some stories to get up to speed. 1/12

If you’re in the US and you’d like to know what projects and vital services federal grants currently fund in your state, you can search here: www.usaspending.gov And you can find the contact information for your elected representatives here: www.usa.gov/elected-offi... They need to hear from you.

Significant performance improvement in de-hashing sourmash signatures. Looking for 100k hash in 1.4B Reads using 32-cores took 2:30hrs and 95MB RAM.

Wow! I Am not sure they were waiting for permission, tho.

I couldn't be more thrilled to be part of this amazing lab!

I'm delighted to release the first half of my new textbook in human genetics: web.stanford.edu/group/pritch... "An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"

It was an extraordinary meeting full of exciting talks and interesting research!

ChatGPT has acquired a new procrastination skill.

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🎉🎉🎉

I am pleased to announce that I am joining the Dennis Lab as a postdoc. Very excited to be working with @mydennis.bsky.social!

New sourmash plugin to retrieve ACGT k-mers from sourmash signatures! github.com/mr-eyes/sour...

UC Davis students begin protest against genocide in Palestine www.sacbee.com/news/local/a... (good for them!) Admin emails saying they are actively working with protestors and "UC Davis cannot and will not discipline students for speech protected by the First Amendment." (good for them too!)

I cannot overstate how incredible this documentary series is.

Genotypic and phenotypic consequences of domestication in dogs https://www.biorxiv.org/content/10.1101/2024.05.01.592072v1

it's my duty to regularly remind everybody that the barreleye fish is real and exists on this planet with us. 🦑🧪https://www.discoverwildlife.com/animal-facts/fish/pacific-barreleye-fish-facts

Lovely!

A nice article on WebAssembly for scientific computing! Includes @luizirber.bsky.social work on sourmash ;)

First step in a community project to provide a uniformly assembled, annotated and searchable set of bacterial genomes, our preprint on our initial release of 1.9 million genome assemblies+taxonomic estimates. (figure compares with previous 661k dataset) www.biorxiv.org/content/10.1... #microsky

I refined the commonly used SRA Database Size Growth plot for my QE presentation and am sharing it as a cronjob with daily updates.

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The workshop, scheduled for January 22-23, 2024, is an exceptional opportunity for those interested in the genetic study of Golden Retrievers. The workshop is open for all, free of charge, but it requires prior registration. www.vetmed.ucdavis.edu/events/advan...

I love it when I make mistakes in the t-SNE plots; often, they end up looking visually appealing.

Nice blog post!

Trying to start a habit of blogging again. Not sure this qualifies as a microblog; I might need to go even shorter ... Anyway, here are some thoughts on licensing in open source (academic) projects!

It's been a long time since I did deep learning. Setting up everything with Cuda, Nvidia, ubuntu, TensorFlow, etc... is so quick now. Only 4 hours of fixing problems!

"my students left lab sessions with results, feeling their time had been well-spent. But I worried I was deceiving them about the actual experience of practicing science, which rarely produces data on the first try."

Distinguished leadership means more than guiding to flawless results right away. It's about creating a space where mistakes are part of learning, shaping individuals who are not just skilled in execution but also strong in critical analysis and thought.

Some tips for creating useful presentations. — "your slides are visual aids: you are the presentation."

I think this is interesting - for both faculty & research, as well as faculty/students/teaching: "The biggest driver of productivity at work today isn’t about the remote-versus-office tug-of-war, or generative AI. It’s trust."

It's kinda cool to find that 2023 is the MVP year with the highest active-coding time 🦖

This is good.

Reading: Cantaloupe recall: Salmonella outbreak leaves 8 dead, hundreds sickened in US and Canada www.usatoday.com/story/money/... via @usatoday