Will Fondrie
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
- Reposted by Will FondrieYep, 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.
- I love that @obsidian.md requires you to type the key sequence to exit vim before enabling vim key bindings 😆
- This one is good read!
- How do you deal with missing values and "unique" proteins that were only identified in one condition in proteomics data? Mengchun Li, an amazing PhD student in my lab, developed this great Bayesian approach. Please try it and give feedback! www.biorxiv.org/content/10.6...
- Reposted by Will FondrieI 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...
- 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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- Looking for an internship next summer? Join my team @talusbio.bsky.social! Apply 👇 by Jan 31 🤖🧬💻 www.applicantpro.com/openings/tal...
- Ha. Good to know I still get to code a bit 😀 git-wrapped.com
- 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...
- 😳 ... it was me. I'm part of the problem. Forgot about this PR github.com/lazear/sage/...
- Who in the training data used so many emojis in their code?
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- Reposted by Will FondrieOpen 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
- Reposted by Will FondrieMy 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...
- Affinity has been my favorite design software for awhile now. Now that its free is even better!
- I'm a longtime fan of Affinity Designer as an affordable Illustrator-killer for figures, and... it's now free?! www.canva.com/newsroom/new... Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
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- I couldn't help it. Now for polars in #python 🐍🐻❄️ github.com/wfondrie/gen...
- Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp.... genzplyr is dplyr, but bussin fr fr no cap.
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- Reposted by Will FondrieThese 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!
- Registration is now open for the EuBIC-MS Winter School 2026! Join us in Harrachov, Czechia for a week of keynotes, workshops, and networking on computational MS. Info and registration: eubic-ms.org/events/2026-... #EuBIC2026 #MassSpectrometry #MassSpec #Bioinformatics #Proteomics #Metabolomics
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- I’ve done a lot of math in my day… But none quite as confusing as early elementary Common Core.
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- 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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- I'm a huge fan of this proposal! If we can get vendor buy-in to an open, common format, it could bring more computational folks into the field. How can these folks be excited about #proteomics when its hard to even read the already complicated data? pubs.acs.org/doi/10.1021/...
- I finally gave Marimo a try and it's pretty cool. I definitely recommend giving it a shot if you find yourself coding #Python in Jupyter notebooks with any frequency. marimo.io Clean UI, stored as a git-friendly plain python script, with reactivity for reproducibility. 🐍
- Reposted by Will FondrieNew faculty position opening at @stanford-chemh.bsky.social . Especially interested in candidates with deep expertise and vision for the future of AI/ML/computational models of biomolecules. Please RT
- Please apply to our tenure-track faculty position at @stanford-chemh.bsky.social! We are searching for a new colleague working at the interface between computation and molecular sciences. See post below and pls forward widely! chemh.stanford.edu/opportunitie...
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- It was nice to get away to Mt Rainier 🏔️ for a long weekend camping trip. We even got to see some marmots!
- Definitely PhD level. No question 👏 But seriously, I thought other folks were joking 🙃
- Just had an #AI agent (Gemini CLI) write data models to validate outputs of a pipeline and unit tests for the workflow. They need some work, but were pretty good. However, the best part is this was all while I was eating dinner and reading physical books with the kids. Pretty cool 😎
- Even with everything going on, happy Indepenence Day to my friend in the US. Here is a version of “Battle Hymn of the Republic” that I’ve been working on. 🪕 I’ll eventually learn to sing, but today is not that day 🙃
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- Check out just a piece of the cool stuff we’ve been up to! 🧬
- Here we go, my first skeet-torial(?) on Bluesky for my first paper from @talusbio.bsky.social ! www.biorxiv.org/content/10.1... This preprint describes our scalable, mass spec-based method for measuring which (and how many of them) proteins are interacting with DNA. 1/?
- Reposted by Will FondrieHere we go, my first skeet-torial(?) on Bluesky for my first paper from @talusbio.bsky.social ! www.biorxiv.org/content/10.1... This preprint describes our scalable, mass spec-based method for measuring which (and how many of them) proteins are interacting with DNA. 1/?
- A nap and grilling fajitas on Father’s Day. What could be better than this? 🎵 Queue the Moana 2 soundtrack 🙃
- Our website @talusbio.bsky.social has a new look! 👀 talus.bio
- Nothing deflates a mood faster than a flat tire with no tube or patch 😔 🚲
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- Reposted by Will FondrieWe recently released a tool to help you with this. 🚀 Say hello to pridepy — your Python for grabbing data from the @pride-ebi.bsky.social! To search metadata or download files via FTP, Aspera, Globus, or S3, and is perfect for bioinfo workflows. Check it out 👉 github.com/PRIDE-Archiv...
- Stop by poster ThP 289 to… calmly discuss… metadata collection and management with Anastasiya 👏 #ASMS2025
- Reposted by Will FondrieNew in DeepLC! Ability to deal with wild, weird, and wobbly LC setups or peptide modifications. This ability is possible with transfer learning; where only a minimal amount of training peptides are needed for accurate retention time predictions. www.biorxiv.org/content/10.1...
- It was a lot of fun participating in the Biomarker workshop panel at #ASMS2025. Thank you to all of you who were there! Also, they got some pictures:
- Cred to @lindsaykpino.com for the meme inspiration here 😆
- Come out - it’s going to be awesome! 👏 #ASMS2025
- I’m at poster 510 today. Stop by and say hi! 👋
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- That’s a wrap on our #ML for #MassSpec short course at #ASMS2025 🎉 Thanks to all of the participants who made it a joy to teach 👏
- Fueling up with a cortado at Ceremony again this morning Come see my poster #ASMS2025 on Tuesday about our recommender system method for predicting the retention times od undetected peptides… called Cortado 😉 #ASMSBmoreEats
- ☕️ ✅ #ASMS2025 #ASMSBmoreEats
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- ☕️ ✅ #ASMS2025 #ASMSBmoreEats
- Going to #ASMS2025 and curious about what we've been up to @talusbio.bsky.social? Check out our posters, talk, and workshops! Check out all of our events here 👇 talusbio.github.io/talusbio-at-... Here are the events I'll be presenting at or helping with so far. Come by and say hi! 👋 🧵 (1/6)
- What, not brunch time at #ASMS2015?!? If you do find yourself needing a break, treat yourself to Spoons in Fed Hill. It’s tiny, quaint, and delicious 😋 www.spoonsbaltimore.com #ASMSBmoreEats
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- Need another great coffee shop while at #ASMS2015? Try ceremonycoffee.com Ceremony is both delicious and has two nice locations: one that is an easy walk from the convention center and the other in Harbor East has a great view! #ASMSBmoreEats
