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...
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 😊
So many smiles and laughs have been shared in our epic battles for the basement today 😊
December 25, 2025 at 10:38 PM
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 😊
So many smiles and laughs have been shared in our epic battles for the basement today 😊
Reposted by Will Fondrie
Perspectives in computational mass spectrometry: recent developments and key challenges #BioinformAdv academic.oup.com/bioinformati...
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
academic.oup.com
December 22, 2025 at 9:24 PM
Perspectives in computational mass spectrometry: recent developments and key challenges #BioinformAdv academic.oup.com/bioinformati...
Looking for an internship next summer? Join my team @talusbio.bsky.social!
Apply 👇 by Jan 31 🤖🧬💻
www.applicantpro.com/openings/tal...
Apply 👇 by Jan 31 🤖🧬💻
www.applicantpro.com/openings/tal...
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 ...
www.applicantpro.com
December 21, 2025 at 3:49 AM
Looking for an internship next summer? Join my team @talusbio.bsky.social!
Apply 👇 by Jan 31 🤖🧬💻
www.applicantpro.com/openings/tal...
Apply 👇 by Jan 31 🤖🧬💻
www.applicantpro.com/openings/tal...
December 18, 2025 at 12:02 AM
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...
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...
Progress Update: Sep-Nov 2025
Regulome profiling, new paths to the androgen receptor, and oncogenic fusion proteins
blog.talus.bio
December 10, 2025 at 3:54 PM
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...
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/...
December 5, 2025 at 12:04 AM
😳 ... 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?
December 3, 2025 at 4:57 PM
Who in the training data used so many emojis in their code?
Reposted by Will Fondrie
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.
November 30, 2025 at 12:06 AM
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.
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/...