Will Fondrie
@willfondrie.com
1.4K followers 850 following 170 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: https://willfondrie.com/post
Posts Media Videos Starter Packs
Pinned
Listen to Ross Katz and I chat about @talusbio.bsky.social on the Data in Biotech podcast! 🎧 🧬

We talk about a lot of things, including my background, our platform, and lessons I’ve learned along the way.

Did I mention it’s my first time ever on a podcast?
open.spotify.com/episode/2r0U...
Targeting Transcription Factors with AI, featuring Will Fondrie from Talus Bio
Data in Biotech · Episode
open.spotify.com
Reposted by Will Fondrie
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!
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
Reposted by Will Fondrie
Meet the PIs powering ProtAIomics. Explore the labs & projects and apply for our 16 fully funded PhD positions: www.protaiomics.eu

#ResearchCareers #Proteomics #ArtificialIntelligence #MSCA #PhDOpportunities #FullyFundedPhD
Reposted by Will Fondrie
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.
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
Reposted by Will Fondrie
For the weekend crowd. I'm hiring a postdoc! If you're interested in algorithms, data structures and high-dimensional inference, and if you want to invent new methods for genomics and implement them in high-performance, robust and easy-to-use software, do I have a lab for you; ours!
Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....

If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
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/...
mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format
Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amplifies these challenges in proteomics, metabolomics, and lipidomics. Current open formats such as mzML and imzML struggle to keep pace due to large file sizes, slow data access, and limited metadata support. Vendor-specific formats offer faster access but lack interoperability and long-term archival guarantees. We here lay the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multidimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human- and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will support complex workflows and regulatory compliance through faster access, improved metadata, and interoperability. For vendors, it offers a streamlined, open alternative to proprietary formats. mzPeak aims to become a cornerstone of MS data management, enabling sustainable, high-performance solutions for future data types and fostering collaboration across the mass spectrometry community.
pubs.acs.org
Oh and it plays nicely with uv, which I use for all the things 📦
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. 🐍
marimo | a next-generation Python notebook
Explore data and build apps seamlessly with marimo, a next-generation Python notebook.
marimo.io
Reposted by Will Fondrie
New 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...
Faculty Recruitment
chemh.stanford.edu
Reposted by Will Fondrie
@lindsaykpino.com talking about the power of using proteomics to measure the regulome of live cells using our platform here at Talus Bio, and how far we have been able to scale this platform up to further cancer drug discovery and more. #regulomesummit
Reposted by Will Fondrie
Regulome Summit kicks off in 20 minutes! We have food, coffee, marmots, posters, and lots of great content coming up. Stop by Dempsey Hall on UW campus to learn about gene regulation, nuclear proteomics, and AI-driven drug discovery!
Reposted by Will Fondrie
@willfondrie.com discussing how we use AI and ML to further drug discovery here at Talus Bio. Come check it out to learn more! #regulomesummit
Reposted by Will Fondrie
PhD-based positions (beyond post-doc) are becoming scarce but these four presenters have made their own paths.

Worth tuning in if you’re curious about leveraging your expertise into something other than (or in addition to) papers and grants.
Join us for our 19th YPIC Webinar – “Transition from Academia to Start-Up”

Ever wondered what it takes to turn your research into a company?! 🧪

Information in comments!
1/3

#YPIC #Proteomics #ScienceToStartup #ScienceCareers #Entrepreneurship #Biotech #AcademicTransition #Webinar #StartUpScience
It was nice to get away to Mt Rainier 🏔️ for a long weekend camping trip.

We even got to see some marmots!
I get this is likely due to tokenization, but come one - you can’t claim PhD level reasoning and not solve these kinds of problems.
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 🙃
Reposted by Will Fondrie
If you're working on cool chromatin biology, gene regulation, or nuclear regulome science, I want to work with you!! Our "Early Access Program" is officially open. Everything we generate together will be open-sourced with the community.

--> Apply here: forms.gle/cJqtTkRRZU5m... <--

11/?
Talus Bio Technology Early Program Application
This is our exclusive sandbox for scientists who want to peer into the regulome before anyone else. Participants have the option to send samples directly to the Talus Bio lab for regulome profiling o...
forms.gle
Check out just a piece of the cool stuff we’ve been up to! 🧬