Lightnews — Scholar-powered news

Will Fondrie @willfondrie.com · 21h

a man in a blue shirt and tie is sitting down and saying `` alright , i 'm gonna go cry . ''

ALT: a man in a blue shirt and tie is sitting down and saying `` alright , i 'm gonna go cry . ''

media.tenor.com

2

Will Fondrie @willfondrie.com · 8d

Oh and it plays nicely with uv, which I use for all the things 📦

Will Fondrie @willfondrie.com · 8d

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

1 4

Reposted by Will Fondrie

Anshul Kundaje @anshulkundaje.bsky.social · 22d

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

Polly Fordyce @pollyfordyce.bsky.social · 22d

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

8 15

Reposted by Will Fondrie

Talus Bio @talusbio.bsky.social · 24d

@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

4 8

Reposted by Will Fondrie

Talus Bio @talusbio.bsky.social · 24d

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!

2 6

Reposted by Will Fondrie

Talus Bio @talusbio.bsky.social · 24d

@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

2 2

Reposted by Will Fondrie

Yasset Perez-Riverol @ypriverol.bsky.social · Sep 10

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

1 1 8

Reposted by Will Fondrie

Chris Ashwood @cashwood.proteaglyco.com · Sep 4

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.

ypic.bsky.social @ypic.bsky.social · Sep 4

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

2 1 9

Will Fondrie @willfondrie.com · Aug 27

It was nice to get away to Mt Rainier 🏔️ for a long weekend camping trip.

We even got to see some marmots!

Crossing a river on the trail at Mt Rainier

6

Will Fondrie @willfondrie.com · Aug 8

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.

1 2

Will Fondrie @willfondrie.com · Aug 8

Definitely PhD level. No question 👏

But seriously, I thought other folks were joking 🙃

1

Will Fondrie @willfondrie.com · Jul 19

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 😎

1 4

Will Fondrie @willfondrie.com · Jul 4

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 🙃

5

Reposted by Will Fondrie

Lindsay K Pino @lindsaykpino.com · Jul 2

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

1 3 8

Will Fondrie @willfondrie.com · Jul 2

Check out just a piece of the cool stuff we’ve been up to! 🧬

Lindsay K Pino @lindsaykpino.com · Jul 2

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/?

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

2

Reposted by Will Fondrie

Lindsay K Pino @lindsaykpino.com · Jul 2

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/?

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

4 20 60

Will Fondrie @willfondrie.com · Jun 29

💯 agree bsky.app/profile/will...

Will Fondrie @willfondrie.com · Jun 5

Stop by poster ThP 289 to… calmly discuss… metadata collection and management with Anastasiya 👏

#ASMS2025

Will Fondrie @willfondrie.com · Jun 28

Looks like it was fun!

I find folks tend to have very strong opinions about encoding metadata in filenames 🫠

1

Will Fondrie @willfondrie.com · Jun 16

A nap and grilling fajitas on Father’s Day. What could be better than this? 🎵

Queue the Moana 2 soundtrack 🙃

a woman is standing on a boat in the ocean with a bird standing on a barrel .

ALT: a woman is standing on a boat in the ocean with a bird standing on a barrel .

media.tenor.com

2

Will Fondrie @willfondrie.com · Jun 13

Our website @talusbio.bsky.social has a new look! 👀

talus.bio

Talus Bio | Unlocking the Regulome for Drug Discovery

Talus Bio makes the regulome—the control layer of gene expression—visible, measuring and modulating gene regulators in live cells to access new drug targets and enable first-in-class medicines.

talus.bio

2

Will Fondrie @willfondrie.com · Jun 10

Nothing deflates a mood faster than a flat tire with no tube or patch 😔 🚲

Reposted by Will Fondrie

asher newsome @iondoctor.bsky.social · Jun 8

Remember to send out your reprints from #ASMS2025! From the home screen, select "More", then "My Reprint Requests". You can email to yourself the names and addresses of everyone who requested. Android has a bug but iPhone and the desktop work.
The desktop site is: eppro01.ativ.me/web/planner....

2 7

Reposted by Will Fondrie

Yasset Perez-Riverol @ypriverol.bsky.social · Jun 6

We 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...

6 13

Reposted by Will Fondrie

Will Fondrie @willfondrie.com · Jun 5

Stop by poster ThP 289 to… calmly discuss… metadata collection and management with Anastasiya 👏

#ASMS2025

2 4 21