Travis Wheeler

My department (UMD Computer Science) is hiring! If you're on the market, you should apply. LMK if you have any questions not answered in the ad. umd.wd1.myworkdayjobs.com/en-US/UMCP/d...

The other BioEmu: wildroseemuranch.com/nutritional-...

astronomical

I guess maybe that's a problem ... but on the bright side, they're sloppily written (yes, slop)

It's cool that @anthropic.com is making free/cheap licenses available to academic labs. I was an early adopter, and paid for annual licenses for several people in my group. Anthropic won't reimburse those charge. It stinks to pay a cost for being an early adopter, and doesn't engender loyalty.

This is the most important piece of software that has ever been created.

There's a less-stressful way to deal with that: sell your house.

Usually I do that, then copy one checked box and paste it in to replace each unchecked box I want to change. But if you make your own document and you want it to work correctly: Word → Preferences → Ribbon & Toolbar, then tick Developer. Then in the Developer toolbar, you'll see the option! ☒

AF2 gets much of its signal from the MSA. AF3 has deprioritized the MSA. Meanwhile, ESM2 predicts from just sequence (though it allows for "optional MSA input for enhanced accuracy on challenging targets".) Worth asking @gallseeker.bsky.social : have you tried w/ AF3 or ESM2 (w/o MSA)?

We are recruiting an experienced research programmer to drive the next steps of several exciting generative modeling and biotechy projects! (You will see this ad again soon accompanying preprints of said projects, but here's a chance to apply early 🤓) recruiting2.ultipro.com/SCR1003TSRI/...

ToLWeb was my very first project tied to bioinformatics, only possible because @bembidion.bsky.social let me work on it despite clearly insufficient experience. It's awesome to see the site working again. Those trees were a labor of love for a newbie to the field.

Recruitment for the EMBL International PhD Programme is officially open! 📣 At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us! 🔎 Read more and apply here: bit.ly/4x9Edss

Anthropic let the academics in, and everything fell apart within a week

PLAS-20k (www.nature.com/articles/s41597-023-02872-y) introduced nearly 100,000 simulatons over close to 20,000 protein-ligand systems, intended for training AI binding inference models. We've worked with the PLAS-20k creators to make them available in mdrepo.org.

MDRepo is has exceeded 500K individual open access #MolecularDynamics trajectories and is rapidly approaching 80,000 entries. We've received submissions containing ~20k entries and others with just a few - all contributions are welcome!

This job ad is now live! Please share or apply here: jobs.montana.edu/postings/52780 Screening of applicants begins Sept 15, 2026 #MicroSky #PhageSky #ScienceJobs

(Without saying your age, what was your favourite film that came out when you were 20 years old.) At the time, I'd have said #1 (still great, see photo on my lab website); now I'm partial to #2

I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...

@prsecor.bsky.social is amazing - jump at the chance to do a postdoc with him!

100% - for me, it's Do molecular fingerprints identify diverse active drugs in large-scale virtual screening? (no) It's a fine paper, I guess, but not something that would cause me to be invited to submit to "Journal of Nanotechnology and Nanomaterials" or "Current Research in Psychiatry"

Try for your protein at py2dmol.solab.org (Style → Cartoon)

Do the physics of this planet allow an individual to be in many locations at the same time?

lol

Dynamic PDB (arxiv.org/abs/2408.12413) ran 1-µs all-atom MD on ~12,600 PDB structures, and has released ~3,300 so far, downsampled to 1 ns frame spacing. Those are now available in mdrepo.org. We'll expand coverage as the remainder are released, with links out to the full-resolution trajectories.

My lab at Stanford University School of Medicine is recruiting! We are looking for a postdoc at the interface of quantitative proteomics, structural biology and G protein-coupled receptor (GPCR) biology: postdocs.stanford.edu/prospective/...

mdrepo.org is also designed to support user-contributed data. We currently host a few thousand user-contributed entries, with a lot more in flight. Add yours to the growing list, so others can see and use your data! mdrepo.org/faq

See below. And if you're super nervous about contacting Jason, you can reach out to me. I promise not to tell him.

Status update for mdrepo.org We've ingested the mdCATH dataset: 26,990 replicate sets (5,398 CATH domains, each at 5 temps). A couple examples: mdrepo.org/explore/MDR0... mdrepo.org/explore/MDR0... We now provide easy access to data from mdCATH, MISATO, ATLAS, and GPCRmd; more coming soon.

It's the moment the whole world has been waiting for! the MDRepo bluesky account is here. We'll give occasional updates about the status of MDRepo - what notable new data have made their way into the system, what new features are available, etc. For starters: we now have >50,000 replicate sets

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

Orthology is central to comparative genomics. Join us at the tail end of eccb2026.org in Geneva (3 Sep) for a full day of orthology: bit.ly/ECCB_ortho Intro to major tools, hands-on tutorials, and an "orthology clinic" for your own data. Extend your ECCB trip, or come just for the tutorial.

Come be our colleague. I have been in this Division for 27 years (4 as a postdoc and 23 as a PI). It is an amazing place to work, collaborate, and be inspired. If you are applying to be an Assistant or Associate Professor this Fall, don't miss this deadline.

Thanks for the advert, @martinsteinegger.bsky.social. If you're reading this and you're sitting on a pile of molecular dynamics simulations, please consider contributing them to MDRepo. This is the path to AI for dynamics (And if you're wondering: yes, there was only 1 person in the audience! 🤥)

See @rberrens.bsky.social's post below. Also, there's an archive of the TransposonsWorldwide slack history, at: tehub.org/slack_archive

We're recruiting! An open functional genomics postdoc position at @scilifelab-ngi.bsky.social / my lab / Robert Månsson lab. Top notch environment for technology and applications development in lovely Stockholm. Please spread the word or apply if interested: www.kth.se/lediga-jobb/...

Senior Bioinformatics Software Developer opening in my team in ONT's Applications department! Hybrid with a few days a week in our Oxford headquarters. We can sponsor visas! www.linkedin.com/jobs/view/44...

🚨 MANUSCRIPT ALERT 🚨 The VGP Phase I manuscript pre-print is now live on bioRxiv! 🧬 doi.org/10.64898/202... Over 8 years, the VGP generated reference genomes for more than 800 vertebrate species, spanning ~95% of vertebrate orders and delivering some of the highest-quality genomes ever produced.

New! R-scape version v2.6.11 github.com/EddyRivasLab... with drawings of R-scape annotated RNA consensus structures with many fewer overlaps!! Using RFview github.com/dincarnato/R... Shout out to @incarnatolab.bsky.social for displaying R-scape's covariation outputs + CaCoFold-R3D structures.

Not Claude advertising their new model to me using a left-handed helix

Pls share: U of Washington has an opening for a tenure-track faculty position at the rank of Assistant Professor. This position is expected to specialize in molecular virology or bacteriology. Here is a link: microbiology.washington.edu/index.php/ne...

An exciting day for TE research and open science. #tesky

Yes, that's a coyote and a bobcat. I understand what the bobcat is thinking, but what's going through that coyote's tiny little brain?

What happened: my camera decided to stop recording. It was like "oh well, nothing interesting happening here..."

Please caption this interaction in my driveway

ICML is happening in Seoul this year, and I’ve been getting several messages about lab visits. Who else will be in town and would like to meet? @milot.bsky.social lab and mine are planning a dinner on July 7th, after the reception. Let me know if you’re interested!

You're asking about biology? You're a terrorist: This query was flagged and refused :) "can I rely on k-mers to recognize sequences that are 75% identical or better?"

NIH T32 proposal with @joannamasel.bsky.social and @wheelerlab.org to renew the Computational and Mathematical Modeling in Biological Systems program for PhD students is funded, starting July 1! I look forward to supporting the next generation of quantitative biology researchers! cmmbs.arizona.edu

21 !

(1) Close to perfect scaling. We routinely run it with 96 threads (2) Yes, we can. The gap is from two things: - the prefilter fails on some seqs that should get a good score; we're building a better filter - see section "HMMER-only multi-domain hits [get] score from weak, fragmentary matches"