I'll be recruiting PhD students this cycle! If you're interested in working on program synthesis, type systems, program analysis, and in general ways to make programming better, please reach out. Here some things we are working on: ku-progsys.github.io RTs appreciated 🙏

I want to try something new at #ASHG24 this year: I'm going to block some time on Friday afternoon to meet with any trainees who would be interested to chat on any topic.

This new paper is a follow up of the WABI'24 paper featuring the mod-minimizer: it introduces the "open-closed" mod-minimizer scheme. Fantastic collaboration with Ragnar {Groot Koerkamp} 🦋 and Daniel Liu! (A bioRxiv preprint is forthcoming.) jermp.github.io/assets/pdf/pap… 1/16

The open-closed mod-minimizer is officially out, with Daniel Liu and Giulio Ermanno Pibiri :D A single simple & practical & efficient scheme that is best in class for k>w (closing ~half the remaining gap to optimal), and close to the best there currently is for k<w. 1/5

A k-mer index for the entire SRA, finally.

DuckDB has SQL-pilled me. There's a strong case that with DuckDB and various extensions, more higher level genomic data analytics could and should happen in SQL. Having a declarative language upstream of intermediate data and results is a huge win.

Exciting news! I've left Prescient to co-found Guide Labs an interpretability startup with Julius Adebayo. We're building interpretable foundational models to address key AI challenges. While I loved my time at Prescient, I'm thrilled to build something I'm very passionate about!

If you're a scientist that serves on an NSF panel that got cancelled today, I'd love to talk to you about it for an NPR story. DM, email or reach out on signal.

stopping PEPFAR is genuinely cruel and evil with no upside. a very cheap program that saves tens of millions of lives. it is a brainworm to see everything in the language of exploitation and the exploited and does not bring out the best in a culture

Despicable. As families grieve, Trump should be leading, not lying. We put safety first, drove down close calls, grew Air Traffic Control, and had zero commercial airline crash fatalities out of millions of flights on our watch. President Trump now oversees the military and the

Tom Sherwood And yet it is still being (illegally) implemented at NSF, DOE, EPA and CDC.

David Van Horn Tom Sherwood And NIH as far as I know.

If you have an NIH award pending, I'd encourage you to check the ERA commons portal. For our pending award, *all* of the relevant information is now missing (the reviews are not accessible, the dates have all been changed, all of the history of the process isn't accessible)!

It is unambiguously illegal to deport U.S. citizens, even if they’ve committed a crime

vcfexpress applies simple user expressions variants in a VCF. it can replace one-off python scripts to manipulate VCFs, likely with better performance. we'd like to collect use-cases here: github.com/brentp/vcfexpr… if you have a use-case and want some pointers, open an issue

We are hosting free bioinformatics office hours on Feb 19th at 10am-noon PST. Bring your bioinformatics career or technical questions, and Robert Aboukhalil and I will try to answer them. Sign up here: tally.so/r/mOb6dM Please share especially with early career scientists!

What a killer program for DSB '25 in Pisa! Can't wait to meet you there next week! dsb-meeting.github.io/DSB2025/

Katerina Siniakova doesn't have a partner because Jannik Sinner was forced to withdraw from the US Open Mixed Doubles event. Instead of repairing her with a different partner, they replaced her entirely. She skipped Cleveland to play this event. Her resume: - 11 Grand Slam

Thrilled to finally share Open-dCoder, a project led by Fred Zhangzhi Peng & Shuibai Zhang. We saw a gap in diffusion LLMs for code, lots of closed APIs or partial releases. So we built the first truly open stack. Not just weights. We're releasing the entire pipeline.👇

Thrilled to announce I'm starting as a Principal Investigator at #Aithyra in Vienna! We'll be developing generative models to understand cell biology and design proteins. I'm hiring PhDs, Postdocs, & Visiting Researchers! PhD applications by Sept 10: apply.cemm.at