Will Fondrie
@willfondrie.com
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
I also blog sometimes: https://willfondrie.com/post
Pinned
Will Fondrie
@willfondrie.com
· Apr 17
Targeting Transcription Factors with AI, featuring Will Fondrie from Talus Bio
Data in Biotech · Episode
open.spotify.com
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...
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...
Reposted by Will Fondrie
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
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 24, 2025 at 7:23 PM
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
Reposted by Will Fondrie
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...
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...
November 20, 2025 at 2:02 PM
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...
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.
Highly recommended if you're sick of paying Adobe $. Maybe Canva can buy NPG too and get rid of the OA fees.
Why we made Affinity free, and how we’ll keep it that way
We’ve made Affinity completely free, empowering professional designers with studio-grade creative software, supported by Canva’s sustainable ecosystem.
www.canva.com
November 19, 2025 at 2:49 AM
Affinity has been my favorite design software for awhile now. Now that its free is even better!
Reposted by Will Fondrie
Getting started with everyone's favourite framework just got easier ✨
A basic FastAPI app in one command 🚀
Install uv: docs.astral.sh/uv/getting-s...
Run:
uvx fastapi-new awesomeapp
✨ Done! ✨
Thanks @savannah.dev ! 🙌
github.com/fastapi/fast...
Install uv: docs.astral.sh/uv/getting-s...
Run:
uvx fastapi-new awesomeapp
✨ Done! ✨
Thanks @savannah.dev ! 🙌
github.com/fastapi/fast...
GitHub - fastapi/fastapi-new: Create a new FastAPI project in one command
Create a new FastAPI project in one command. Contribute to fastapi/fastapi-new development by creating an account on GitHub.
github.com
November 10, 2025 at 11:09 PM
Getting started with everyone's favourite framework just got easier ✨
Reposted by Will Fondrie
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.
November 10, 2025 at 6:25 AM
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.
November 7, 2025 at 9:39 PM
Reposted by Will Fondrie
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 ☺️!
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...
umd.wd1.myworkdayjobs.com
October 31, 2025 at 3:14 AM
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 ☺️!
Reposted by Will Fondrie
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.
a spongebob squarepants scene with a mailbox and a flower
ALT: a spongebob squarepants scene with a mailbox and a flower
media.tenor.com
October 28, 2025 at 4:39 PM
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.
Reposted by Will Fondrie
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
Join us Nov. 3–4 for the #ASMSFallWorkshop on Fundamentals of Instrumentation. This 2-day program offers an in-depth look at the essential technologies that drive modern mass spectrometry from ion sources to analyzers and detectors.
This is an IN-PERSON event. Register here: https://bit.ly/4okbr41
This is an IN-PERSON event. Register here: https://bit.ly/4okbr41
Fall Workshop Homepage
Help us promote the workshop:
www.asms.org
October 21, 2025 at 6:46 PM
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
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
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
October 16, 2025 at 9:49 AM
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!
Reposted by Will Fondrie
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/2025/10/its-...
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...
proteomicsnews.blogspot.com
October 14, 2025 at 10:51 PM
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/2025/10/its-...
I’ve done a lot of math in my day…
But none quite as confusing as early elementary Common Core.
But none quite as confusing as early elementary Common Core.
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
media.tenor.com
October 15, 2025 at 3:31 AM
I’ve done a lot of math in my day…
But none quite as confusing as early elementary Common Core.
But none quite as confusing as early elementary Common Core.
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.
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.
October 14, 2025 at 10:10 PM
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.
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
L: Kill a gram? That sounds dangerous
October 12, 2025 at 5:14 AM
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
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!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 11, 2025 at 1:10 PM
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!
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/...
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
October 10, 2025 at 5:53 PM
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/...
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. 🐍
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
October 1, 2025 at 9:19 PM
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...
@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
September 17, 2025 at 6:29 PM
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
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
September 15, 2025 at 4:35 PM
@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!
September 15, 2025 at 3:40 PM
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
September 15, 2025 at 4:43 PM
@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
I just saw this manuscript from @lindsaykpino.com @willfondrie.com @jspaezp.bsky.social Native, Spatiotemporal Profiling of the Global Human Regulome www.biorxiv.org/content/10.1... using #quantms. It just made my day!!! So glad hours of coding are used by others. Thanks guys
Native, Spatiotemporal Profiling of the Global Human Regulome
The regulome, comprising transcription factors, cofactors, chromatin remodelers, and other regulatory proteins, forms the core machinery by which cells interpret signals and execute gene expression pr...
www.biorxiv.org
September 10, 2025 at 2:13 PM
I just saw this manuscript from @lindsaykpino.com @willfondrie.com @jspaezp.bsky.social Native, Spatiotemporal Profiling of the Global Human Regulome www.biorxiv.org/content/10.1... using #quantms. It just made my day!!! So glad hours of coding are used by others. Thanks guys
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.
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
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
September 4, 2025 at 9:25 AM
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.
Worth tuning in if you’re curious about leveraging your expertise into something other than (or in addition to) papers and grants.
It was nice to get away to Mt Rainier 🏔️ for a long weekend camping trip.
We even got to see some marmots!
We even got to see some marmots!
August 27, 2025 at 3:21 AM
It was nice to get away to Mt Rainier 🏔️ for a long weekend camping trip.
We even got to see some marmots!
We even got to see some marmots!