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Will Fondrie

@willfondrie.com
1.4K followers 864 following 213 posts

Head of Data Science & Engineering at Talus Bio. I post about data science, BioML, AI drug discovery, Python, mass spec, proteomics, and silly things my kids do. I also blog sometimes: willfondrie.com/post

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Reposted by Will Fondrie
Maitreya Dunham @maitreya.bsky.social · 24/09/2026
Exciting news: @uwgenome.bsky.social will be hiring for two tenure-track faculty positions this year, one open rank and one assistant professor. Both are “Genome Sciences” interpreted broadly so we welcome applicants working in a variety of fields and methods. Ad will be out shortly.
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Will Fondrie @willfondrie.com · 07/09/2026
Don't mind me... just bought a 3rd pair of the exact same shoe, because I like them and they're on (final) sale. Been wearing one pair for awhile and now I have two backups so I don't have to find something to replace it for the 10+ years. Is that weird?
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Will Fondrie @willfondrie.com · 24/08/2026
If you are (still) using Opus 5, change the output style to “Concise” now. You’ll thank me later 😉 code.claude.com/docs/en/outp...
code.claude.com
Output styles - Claude Code Docs
Adapt Claude Code for uses beyond software engineering
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Reposted by Will Fondrie
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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Will Fondrie @willfondrie.com · 30/07/2026
New @talusbio.bsky.social #AI preprint just dropped 🚀 Meet Ptarmigan-1. It predicts which small molecules bind a protein, and which residues they hit, from sequence and 2D chemistry alone. No structures, no docking, no poses. www.biorxiv.org/content/10.6... Time for a 🧵 (1/13)
biorxiv.org
Structure-free, site-resolved contrastive learning extends small-molecule discovery beyond the reach of structure-based modeling
Virtual screening asks which molecules, among an enormous space of drug-like chemistry, are worth synthesizing and testing against a protein target. Most modern methods answer by building and scoring ...
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Michael Lazear @michaellazear.bsky.social · 15/07/2026
Do you want to work at the frontier of structural and chemical #proteomics? Interested in induced proximity and building a feedback loop for machine learning models to explore biology? I'm hiring! Apply below ⬇️ jobs.ashbyhq.com/proxima/6e39...
jobs.ashbyhq.com
Proteomics Scientist
Proteomics Scientist
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Will Fondrie @willfondrie.com · 02/07/2026
Celebrating 250 years of America the right way tonight… Watching National Treasure of course.
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Will Fondrie @willfondrie.com · 03/06/2026
#ASMS2026 coffee pilgrimage day 4: Torque Coffee. I had a nice cortado with their lighter espresso, Yellow Diamond (yes, they have two options!) This one is a bit further out in North Park, but a nice trek for some good coffee. Thanks for the rec @michaellazear.bsky.social!
A nice cortado on a green plate with a bubbly water beside.
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Will Fondrie @willfondrie.com · 02/06/2026
#ASMS2026 coffee pilgrimage day 3: Goldchild coffee. It's a bit of a hike downtown, but 100% worth it. This one is the best I've tried so far. www.goldchildcoffee.com
A beautiful cortado on a wood tray.
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SCIEX @sciex.bsky.social · 01/06/2026
Discussing #chemoproteomics at #ASMS2026 with @lindsaykpino.com of @talusbio.bsky.social
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Will Fondrie @willfondrie.com · 01/06/2026
Come out this morning and see my AI talk in the chemoproteomics section at #ASMS2026! If nothing else, you’ll learn what a ptarmigan is 😉
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Will Fondrie @willfondrie.com · 01/06/2026
#ASMS2026 coffee pilgrimage day 2: Achilles Coffe Roasters. Coffee was pretty good - they have a nice single origin selection. Bonus is that it’s close to the convention center! achillescoffeeroasters.com
achillescoffeeroasters.com
Buy Single Origin Coffee | Achilles Coffee Roasters San Diego
Buy Single Origin Coffee Online at Achilles Coffee Roasters. A Specialty Coffee Roaster Located in San Diego With 5 San Diego County Cafes Serving Great Coffee and Killer Breakfast.
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Lindsay K Pino @lindsaykpino.com · 31/05/2026
Hello, #ASMS2026!! The @talusbio.bsky.social team is on-site and ready to nerd out! We've got everything from drug discovery to metadata records, from chemoproteomics to file format converters. 1/n
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Will Fondrie @willfondrie.com · 30/05/2026
#ASMS2026 coffee pilgrimage day 1: Bird Rock Coffee Roasters. I quite enjoyed my cortado 😉 www.birdrockcoffee.com
birdrockcoffee.com
Bird Rock Coffee Roasters
Bird Rock Coffee Roasters, San Diego California Roasting Direct Trade and Ethically Sourced Coffee Daily. Third Wave coffee roaster putting fresh award winning coffee out daily.
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Will Fondrie @willfondrie.com · 30/05/2026
Looking for a burrito at #ASMS2026? Definitely hit up The Taco Stand: maps.app.goo.gl/fSYTwvyUCs57...
maps.app.goo.gl
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Lindsay K Pino @lindsaykpino.com · 28/05/2026
Chemoproteomics is back at #ASMS2026 with a bang! After the oral session mysteriously vanished last year, now we're not only back on the schedule but kicking off the conference with Ben Cravatt?! 1/n
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Lindsay K Pino @lindsaykpino.com · 31/03/2026
Getting the ol' grad school gang back together with Carafe2 -- Bo Wen (@maccoss.bsky.social and Bill Noble) and @jspaezp.bsky.social (@willfondrie.com at @talusbio.bsky.social) teamed up for essentially some late night hackathons to build out Carafe for @brukercorporation.bsky.social timsTOF data.
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Will Fondrie @willfondrie.com · 23/03/2026
I 100% agree with this take. Plug: If you are working with #proteomics and/or #massspec data, check out our shortcourse at #ASMS2026 to get a jump start on many of these methods! (Course 04 here: www.asms.org/conferences/...)
asms.org
Short Courses
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Yasset Perez-Riverol @ypriverol.bsky.social · 15/03/2026
🚀 Introducing pyprideap — one unified Python API for #SomaScan & #Olink QC and analysis (finally!). Normalisation, LOD, DE, interactive HTML reports. Open source and community-oriented as part of the @pride-ebi.bsky.social Affinity Archive. github.com/PRIDE-Archiv... #Proteomics #OpenScience.
github.com
GitHub - PRIDE-Archive/pyprideap: pyprideap is a library to handle affinity proteomics files from PRIDE database; including reading; parsing validating and other algorithms
pyprideap is a library to handle affinity proteomics files from PRIDE database; including reading; parsing validating and other algorithms - PRIDE-Archive/pyprideap
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Will Fondrie @willfondrie.com · 22/02/2026
Saw a post about GPU depreciation and I could hardly believe what second-hand H100s were selling for. The GPU market is wild.
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Will Fondrie @willfondrie.com · 20/02/2026
Landed in St Louis for #USHUPO2026 and grabbed some BBQ 😋 2 things: 1. Salt + Smoke (www.saltandsmokebbq.com) is delicious. ⭐️ ⭐️ ⭐️ ⭐️ ⭐️ 2. I’m once again reminded that Seattle doesn’t know what to do with a smoker 😔
saltandsmokebbq.com
Best St. Louis BBQ - Salt + Smoke BBQ
St. Louis BBQ that will make your mouth water. We’re known for the good stuff. The meat stuff. The melt-in-your-mouth and fall-off-the-bone stuff. We’re Salt + Smoke and we know how to BBQ real good f...
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Reposted by Will Fondrie
Chris Ashwood @cashwood.proteaglyco.com · 18/02/2026
There's an art to representing MS-based bioinformatics, and these authors have done an amazing job.
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Will Fondrie @willfondrie.com · 19/02/2026
This is a work I’ve been following. Some cool ideas here - definitely check it out!
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Ben Neely @benneely.com · 30/01/2026
Yep, Ben @proteomicsnews.bsky.social and I finally got Bill Noble on #THEProteomicsShow. We had been wanting him on forever so he went and won an award to make it easier for us to meet. Enjoy the rambles (I hope), and mind the monkeys. Find it wherever you find fine podcasts.
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Will Fondrie @willfondrie.com · 20/01/2026
I love that @obsidian.md requires you to type the key sequence to exit vim before enabling vim key bindings 😆
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Will Fondrie @willfondrie.com · 15/01/2026
This one is good read!
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Reposted by Will Fondrie
Mitchell R. Vollger @mrvollger.bsky.social · 12/01/2026
I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt: employment.utah.edu/salt-lake-ci...
employment.utah.edu
Jobs | University of Utah
Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...
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Will Fondrie @willfondrie.com · 25/12/2025
Nerf guns + eye protection for the family (including us, the parents) were a huge hit. So many smiles and laughs have been shared in our epic battles for the basement today 😊
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Reposted by Will Fondrie
BioMassSpec @realbiomassspec.bsky.social · 22/12/2025
Perspectives in computational mass spectrometry: recent developments and key challenges #BioinformAdv academic.oup.com/bioinformati...
academic.oup.com
Perspectives in computational mass spectrometry: recent developments and key challenges
Abstract. Summary: Mass spectrometry (MS) is a cornerstone technology in modern molecular biology, powering diverse applications across proteomics, metabol
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Will Fondrie @willfondrie.com · 21/12/2025
Looking for an internship next summer? Join my team @talusbio.bsky.social! Apply 👇 by Jan 31 🤖🧬💻 www.applicantpro.com/openings/tal...
applicantpro.com
Data Science Intern - Seattle, WA
Talus Bioscience is seeking highly motivated summer interns to join our team! These paid summer internships provide opportunities to own and participate in challenging and impactful business-critical ...
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Will Fondrie @willfondrie.com · 18/12/2025
Ha. Good to know I still get to code a bit 😀 git-wrapped.com
Will's GitHub wrapped
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Will Fondrie @willfondrie.com · 10/12/2025
A nice write up of what we’ve been working on recently @talusbio.bsky.social by @afederation.bsky.social. Check it out to get a glimpse of our progress drugging AR and success from our lab-in-the-loop active learning cycles. And don’t forget to subscribe for more 👇 blog.talus.bio/p/progress-u...
blog.talus.bio
Progress Update: Sep-Nov 2025
Regulome profiling, new paths to the androgen receptor, and oncogenic fusion proteins
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Will Fondrie @willfondrie.com · 05/12/2025
😳 ... it was me. I'm part of the problem. Forgot about this PR github.com/lazear/sage/...
github.com
Specify some parameters from the CLI by wfondrie · Pull Request #19 · lazear/sage
This PR adds some parameters to the CLI, which overide the configuration provided in the param file. The included parameters are: mzml_paths database.fasta output_directory This makes it easier t...
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Will Fondrie @willfondrie.com · 03/12/2025
Who in the training data used so many emojis in their code?
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Lindsay K Pino @lindsaykpino.com · 30/11/2025
Fwiw chemistry is often called the bottleneck for platform biotech co's because the main affordable places to get chemistry done are WuXi and Enamine, and it takes 2-3 months to get compounds back from them. 2-3 month is a looong wait in startup time. Other places are more/too expensive.
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Maitreya Dunham @maitreya.bsky.social · 24/11/2025
Open faculty position (Assistant or Associate) in UW Medical Genetics. As you might expect, faculty often end up also interacting with Genome Sciences, so we're hoping for some great prospects! Note the clinical requirements for the position. apply.interfolio.com/176466
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Jacob Schreiber @jmschreiber91.bsky.social · 20/11/2025
My first @umasschan.bsky.social/@impvienna.bsky.social affiliated paper is up! tomtom-lite is a re-implementation of tomtom targeting the ML age of genomics. Fast annotations ("what is this motif?") and simple large-scale discovery of motifs. Check it out! academic.oup.com/bioinformati...
academic.oup.com
Tomtom-lite: accelerating Tomtom enables large-scale and real-time motif similarity scoring
AbstractSummary. Pairwise sequence similarity is a core operation in genomic analysis, yet most attention has been given to sequences made up of discrete c
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Will Fondrie @willfondrie.com · 19/11/2025
Affinity has been my favorite design software for awhile now. Now that its free is even better!
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Savannah Ostrowski @savannah.dev · 10/11/2025
Getting started with everyone's favourite framework just got easier ✨
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Lindsay K Pino @lindsaykpino.com · 10/11/2025
Upcoming talks at Human Proteome Organization! Come check out what Talus Bio has been working on over the last year, from mapping the regulome to manipulating it and modeling it, all using mass spectrometry proteomics as a driving force.
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Will Fondrie @willfondrie.com · 07/11/2025
I couldn't help it. Now for polars in #python 🐍🐻‍❄️ github.com/wfondrie/gen...
github.com
GitHub - wfondrie/genzolars: polars but make it bussin fr fr no cap
polars but make it bussin fr fr no cap. Contribute to wfondrie/genzolars development by creating an account on GitHub.
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Rob Patro @robp.bsky.social · 31/10/2025
Our department (Comp Sci) at UMD is hiring this cycle. We have an open-rank search (umd.wd1.myworkdayjobs.com/en-US/UMCP/j...). Consider applying to join our department; we’re a pretty cool group if I say so myself ☺️!
umd.wd1.myworkdayjobs.com
Assistant Professor, Associate Professor, Professor
Job Description Summary Organization's Summary Statement: The Department of Computer Science is top-ranked for research and teaching, with its undergraduate computer science program ranked 9th among p...
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John Yates @jyates.bsky.social · 28/10/2025
Hey @asms.org peeps. I’m running for VP for programs and I’d like your vote. Check out the asms web site for details and you will see an email with voting instructions in the near future. I approach this position with lots of experience organizing scientific conferences & I ❤️ asms. Please re-sky.
media.tenor.com
a spongebob squarepants scene with a mailbox and a flower
ALT: a spongebob squarepants scene with a mailbox and a flower
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Bush Lab @bushlab.bsky.social · 21/10/2025
Registration is still open for a couple more days. Will be an exciting and informative two days! Feel free to DM or email Matt Bush with any questions. #teammassspec
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Ralf Gabriels @ralf.gabriels.dev · 16/10/2025
These events have always been the highlight of my academic year. Want to connect to the computational mass spec community in Europe and beyond in a highly positive and welcoming environment? Join this conference!
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Ben Neely @benneely.com · 14/10/2025
Big news for you #HUPO2025 folks from @proteomicsnews.bsky.social, it seems there’s gonna be some #THEProteomicsShow action there. Our other shows at EuBIC and US HUPO were fun, so definitely mark your calendars for Monday after noon. proteomicsnews.blogspot.com/2025/10/its-...
proteomicsnews.blogspot.com
It's official! The Proteomics Show will be live at International HUPO!
Since no one asked for it (and ASMS ignored me)!  THE Proteomics Show will record live at International HUPO on Monday, November 10th. Mai...
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Will Fondrie @willfondrie.com · 15/10/2025
I’ve done a lot of math in my day… But none quite as confusing as early elementary Common Core.
media.tenor.com
a man in a suit and tie is sitting in a chair with his hands in the air
ALT: a man in a suit and tie is sitting in a chair with his hands in the air
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Nils Homer @nilshomer.com · 14/10/2025
Ever want a live code review of your #bioinformatics code? DM me if you’re at #ASHG25 and I’ll take look to give you suggestions on how to improve reproducibility, maintainability, and overall engineering quality.
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Will Fondrie @willfondrie.com · 12/10/2025
Me: Did you know that if something is a kilogram on earth, it’s still a kilogram on the moon? L: Kill a gram? That sounds dangerous
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