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Travis Wheeler

@wheelerlab.org
434 followers 230 following 324 posts

Professor, University of Arizona Algorithms, Machine Learning, Data Resources Computational Genomics, Drug Discovery, etc. wheelerlab.org

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Travis Wheeler @wheelerlab.org · 29/09/2026
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! ☒
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Travis Wheeler @wheelerlab.org · 24/09/2026
Super useful info. Not surprised that MSA is needed, but good that you confirmed it (careful, as always)
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Travis Wheeler @wheelerlab.org · 23/09/2026
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)?
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Ann Kennedy @antihebbiann.bsky.social · 23/09/2026
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/...
recruiting2.ultipro.com
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Travis Wheeler @wheelerlab.org · 08/09/2026
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.
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EMBL @embl.org · 01/09/2026
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
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Travis Wheeler @wheelerlab.org · 03/09/2026
Anthropic let the academics in, and everything fell apart within a week
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MDRepo @mdrepo.bsky.social · 03/09/2026
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.
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MDRepo @mdrepo.bsky.social · 03/09/2026
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!
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Patrick R. Secor @prsecor.bsky.social · 02/09/2026
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
jobs.montana.edu
Postdoctoral Researcher - Lyme Disease Bacteriophage Biology
The Secor Lab seeks a postdoctoral researcher to investigate bacteriophage biology in the Lyme disease spirochete Borrelia burgdorferi. The successful candidate will help define how phiBB-1 controls h...
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Travis Wheeler @wheelerlab.org · 01/09/2026
(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
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Brian J. Enquist @bjenquist.bsky.social · 31/08/2026
Thrilled to announce that my department - Ecology and Evolutionary Biology - at the U of Arizona will likely be hiring for a tenure-track position in "Population and Community Ecology" this fall. Watch this space for more details and official announcements coming soon ... #Ecology #EcologyJobs 🌐🌾🧪
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Travis Wheeler @wheelerlab.org · 29/08/2026
Quit your navel-gazing. I've sent you 2 e-mails and 4 slack messages in the last hour, each on a separate topic. I need an answer within the next 30 minutes on all of the slack messages and the first e-mail. The second e-mail can wait until Monday, so you have some time to relax.
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026
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...
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Travis Wheeler @wheelerlab.org · 21/08/2026
@prsecor.bsky.social is amazing - jump at the chance to do a postdoc with him!
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Travis Wheeler @wheelerlab.org · 20/08/2026
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"
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Sergey Ovchinnikov @sokrypton.org · 15/08/2026
Try for your protein at py2dmol.solab.org (Style → Cartoon)
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Travis Wheeler @wheelerlab.org · 16/08/2026
Do the physics of this planet allow an individual to be in many locations at the same time?
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Travis Wheeler @wheelerlab.org · 16/08/2026
I'm already thinking about manuscripts while I'm in the shower, so it's not much of a jump.
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Travis Wheeler @wheelerlab.org · 16/08/2026
lol
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MDRepo @mdrepo.bsky.social · 14/08/2026
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.
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Ruth Huttenhain @rhuttenhain.bsky.social · 13/08/2026
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/...
postdocs.stanford.edu
Open Postdoctoral position, faculty mentor Ruth Huttenhain | Office of Postdoctoral Affairs
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MDRepo @mdrepo.bsky.social · 12/08/2026
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
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Travis Wheeler @wheelerlab.org · 13/08/2026
See below. And if you're super nervous about contacting Jason, you can reach out to me. I promise not to tell him.
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MDRepo @mdrepo.bsky.social · 12/08/2026
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.
mdrepo.org
MDRepo
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MDRepo @mdrepo.bsky.social · 12/08/2026
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
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026
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
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Travis Wheeler @wheelerlab.org · 07/08/2026
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.
bit.ly
Tutorials and workshops
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Harmit Singh Malik @harmitmalik.bsky.social · 06/08/2026
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.
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Travis Wheeler @wheelerlab.org · 01/08/2026
Have you reached out to the author, either via e-mail or as followup to the issue? (I checked, so I know the answer to the later is "no") If you've reached out and not received a response, then it seems like fair game to me.
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Travis Wheeler @wheelerlab.org · 17/07/2026
Storage is generously provided by CyVerse, with backup at TACC. No cost to uploader. Think if it like PDB or Uniprot. The only burden on the uploader is to prepare data for upload (with appropriate metadata). I was co-author on that paper. We don't solve all the needs yet, but provide a good start.
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Travis Wheeler @wheelerlab.org · 17/07/2026
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! 🤥)
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Travis Wheeler @wheelerlab.org · 15/07/2026
FWIW, I'm not seeing the same problems.
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Travis Wheeler @wheelerlab.org · 10/07/2026
See @rberrens.bsky.social's post below. Also, there's an archive of the TransposonsWorldwide slack history, at: tehub.org/slack_archive
tehub.org
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Tuuli Lappalainen @tuuliel.bsky.social · 10/07/2026
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/...
kth.se
KTH | Postdoc in genomics
KTH jobs is where you search for jobs at www.kth.se.
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Travis Wheeler @wheelerlab.org · 10/07/2026
grrr
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Sergey Nurk @sergeynurk.bsky.social · 07/07/2026
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...
linkedin.com
Oxford Nanopore Technologies hiring Senior Bioinformatics Software Engineer, Applications in Oxfordshire, England, United Kingdom | LinkedIn
Posted 3:04:10 PM. Job DescriptionOur goal is to bring the widest benefits to society through enabling the analysis of…See this and similar jobs on LinkedIn.
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Vertebrate Genomes Project @vertebrategenomes.bsky.social · 06/07/2026
🚨 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.
A graphic announcing the release of the Vertebrate Genomes Project Phase 1 manuscript on bioRxiv with drawings of various vertebrate creatures.The title and author list of the VGP manuscript, "The Vertebrate Genomes Project Phase I: A global reference genome resource"A QR code linking to the pre-print of the VGP manuscript
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Elena Rivas @rivaselenarivas.bsky.social · 05/07/2026
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.
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Indigo V. L. Rose @ivlrose.bsky.social · 02/07/2026
Not Claude advertising their new model to me using a left-handed helix
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George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 30/06/2026
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...
microbiology.washington.edu
Micro is Hiring! | UW Microbiology
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Travis Wheeler @wheelerlab.org · 26/06/2026
An exciting day for TE research and open science. #tesky
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Travis Wheeler @wheelerlab.org · 21/06/2026
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?
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Travis Wheeler @wheelerlab.org · 19/06/2026
What happened: my camera decided to stop recording. It was like "oh well, nothing interesting happening here..."
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Travis Wheeler @wheelerlab.org · 19/06/2026
Please caption this interaction in my driveway
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 19/06/2026
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!
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Travis Wheeler @wheelerlab.org · 10/06/2026
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?"
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Ryan Gutenkunst @ryangutenkunst.bsky.social · 09/06/2026
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
cmmbs.arizona.edu
Home | Computational and Mathematical Modeling of Biomedical Systems
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Travis Wheeler @wheelerlab.org · 05/06/2026
21 !
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Travis Wheeler @wheelerlab.org · 31/05/2026
(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"
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