>1,000 human genomes sequenced with PacBio HiFi, offering many new insights into human structural variation and its associations with disease. www.medrxiv.org/content/10.1...

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

I am grieving the barbarism that is going to unfurl from all this. People are going to die. Livelihoods gone. All to feed a corrupt kleptocracy. I see every day up close how different it is from the first time around. There are no guardrails. A disaster. I’m sorry we have to live through this.

The efficiency of the market

What the actual fuck is this

And now officially out in Oxford Bioinformatics :) academic.oup.com/bioinformati...

For those using WDL for their bioinformatic workflows: I wrote an extension for the @zed.dev code editor enabling syntax highlighting and integration with wdl-lsp. It also supports bash highlighting in command blocks. Installable through the Zed extensions pane! github.com/broadinstitu...

A printed thesis! Did not expect it would feel so good to have the final version physically in your hands 🙌

Diversity and consequences of structural variation in the human genome go.nature.com/4awEtaY #Review by Ryan L. Collins & Michael E. Talkowski @broadinstitute.org @harvard.edu @harvardmed.bsky.social

COMPUTER SCIENTISTS: "k" means one thousand and twenty-four STORAGE MANUFACTURERS: "k" means one thousand DISPLAY MANUFACTURERS [thinking hard]: "K" means nine hundred and sixty

Still in beta, so possible minor API changes ... but our Suffix Array library (in Rust) is ready for business. Builds on lovely ideas in CaPS-SA from @robp.bsky.social. Low mem construction. Spaced seeds. Optional crazy-low-mem search. More info on the horizon.

5/ In my experience, most of the time, you don’t need deep learning. Often, simple methods like linear regression or random forests work well — especially for moderate-sized datasets. Deep learning excels in image analysis & protein structure prediction.

Anyone insight how I can configure pylsp such that it finds and autocompletes packages installed with uv?

Found ChatGPT in Fallout New Vegas: "Are you some kind of AI?" "Regrettably not, sir. All modules in this habitat are synthetic personalities atop a mundane operating system. There is no intelligence here, sir." www.youtube.com/watch?v=4XJw...

💡 Tip: You can set your website as your username on Bluesky! This is one form of self-verification, and we especially encourage official organizations and brands to do this! Examples include @npr.org @react.dev @duolingobrasil.com.br. Here's our guide for how to do this:

I want to hear some bioinformatics war stories! What was the most weird bug or sequencing artifact you had to debug? I'll start: Did you know that changing the number of threads used by bwa-mem can influence your BAM output?

[looking at Bluesky over the past 2 days] So this is what the Cambrian explosion must have felt like

I think Philip Eng deserves a statue in the Boston common

Working through Prince's excellent "Understanding Deep Learning" book. Full of great insights like these: by optimizing using SGD we implicitly regularize the weights towards values where the gradients are similar across batches 🤯

The protein emoji was rejected in 2022. With the #alphafold #proteindesign #chemnobel, it's the perfect time for a revival ! go go @lindorfflarsen.bsky.social and col. !!!!!

Excited to share a new preprint! We developed a new algorithm for POA, POASTA (pronounce it with your best Bo-ah-ston accent). It is based on the A* framework and inspired by other recent alignment algorithms such as the WFA and Astarix. www.biorxiv.org/content/10.1...

"To Kahn, democracy is a partisan issue and he’s not taking sides." Think about that for a moment. Dan Froomkin says the old guard at the New York Times has reasserted control "over the rabble," and Joe Kahn's interview with Ben Smith demonstrates it. presswatchers.org/2024/05/new-...

Advocates Win Concessions As State Starts Value-Engineering Allston I-90 Megaproject

an earthquake three days before a total eclipse of the sun would absolutely have taken out a whole ass dynasty back in the day

(Did I never post this tip here?) Do you like bibtex? Do you do doi? Do you want bibtex refs from doi on the command line? Yes you do, you wonderful monster. Try this line (adjust doi as needed, and see alt text for source too): curl -LH "Accept: application/x-bibtex" doi.org/10.1002/evan...

Currently pondering novelty requirements by glamour methods / technology journals, both as an author and reviewer. There's an expectation to show that with the method you can do something that couldn't be done before. I understand the logic, but it strikes me, as an analogy, as ...

Live from NPR News, we’re now on Bluesky 👋🎙️

Good to see people still take the T

I guess the Netherlands definitely counts as a tech hub these days: someone dedicated to the advent of code at 830am in the train, programming in Rust

Pretty crazy how effective modern hardware is at processing contiguous blocks of memory (e.g., a DP matrix) compared to for example graph traversal algorithms that have much more irregular computations.

this is a bloody great name for a climate report www.unep.org/resources/em...

Hard to believe he pleaded not guilty in the first place 🥲

I believe the field has landed on "Computeral Bioinfologist" @mikelove.bsky.social @robp.bsky.social