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Alex Federation

@afederation.bsky.social
93 followers 149 following 29 posts

Co-founder, CEO of Talus Bio. Drugging "undruggable" transcription factors with proteomics #chembio. Scientist, mountain runner, new dad. readout.substack.com

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Reposted by Alex Federation
Will Fondrie @willfondrie.com · 30/07/2026
New @talusbio.bsky.social #AI preprint just dropped 🚀 Meet Ptarmigan-1. It predicts which small molecules bind a protein, and which residues they hit, from sequence and 2D chemistry alone. No structures, no docking, no poses. www.biorxiv.org/content/10.6... Time for a 🧵 (1/13)
biorxiv.org
Structure-free, site-resolved contrastive learning extends small-molecule discovery beyond the reach of structure-based modeling
Virtual screening asks which molecules, among an enormous space of drug-like chemistry, are worth synthesizing and testing against a protein target. Most modern methods answer by building and scoring ...
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Alex Federation @afederation.bsky.social · 10/07/2025
I just ran the first n=1 dynamic regulome experiment. On myself. A 72-hour fast where we tracked all 4,000+ components of the genome regulatory 'software' to see how they respond And over 30% changed, most never mentioned in fasting literature Why does this matter?
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Reposted by Alex Federation
EuBIC-MS @eubic-ms.org · 03/02/2025
The EUBIC-MS Developers Meeting 2025 in Brixen is off to a great start with keynotes by Pavel Sinitcyn, Katerina Nastou, and @willfondrie.com. #EuBIC2025
Audience in lecture hallPavel Sinitcyn presentingKaterina Nastou presentingWill Fondrie presenting
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Reposted by Alex Federation
Sri Kosuri @srikosuri.bsky.social · 08/02/2025
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
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Alex Federation @afederation.bsky.social · 08/02/2025
Some diseases are too rare to be VC-fundable. Without grant funding, these patients get nothing—that’s unacceptable. NIH grants fund our work on a rare cancer with no approved treatments. Every year, we pay out of pocket for a third-party audit to prove there’s no waste, no fraud—just science.
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Alex Federation @afederation.bsky.social · 07/02/2025
Does anyone know if the savings will be re-invested into more grants? Or is this just slashing the overall budget of the NIH?
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Alex Federation @afederation.bsky.social · 28/01/2025
Love to see more teams getting into the multidimensional drug screening game with DIA proteomics. 380 kinases in one assay - pubs.acs.org/doi/10.1021/...
pubs.acs.org
Automated High-Throughput Affinity Capture-Mass Spectrometry Platform with Data-Independent Acquisition
Affinity capture (AC) combined with mass spectrometry (MS)-based proteomics is highly utilized throughout the drug discovery pipeline to determine small-molecule target selectivity and engagement. How...
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Reposted by Alex Federation
Lindsay K Pino @lindsaykpino.com · 27/01/2025
Getting a bit tight in the hallways #teamMassSpec #proteomics
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Alex Federation @afederation.bsky.social · 27/01/2025
That seems... like a reasonable number? I'm surprised it's not higher, especially since a postdoc will usually double their salary going into industry www.nature.com/articles/d41...
nature.com
More than 40% of postdocs leave academia, study reveals
Publishing highly cited papers helps postdoctoral researchers to land a faculty job.
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Alex Federation @afederation.bsky.social · 26/01/2025
Cancer might be the most creative biologist - it's evolutionary "job" is to stress test every biological mechanism in our cells are see if promoted survival/fitness Apparently tumors can tunnel into lymphocytes and dump their mutated mitochondria? What a wild world
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Alex Federation @afederation.bsky.social · 25/01/2025
This is the perspective I was waiting for after seeing all the new transcription factor footprinting papers 👇
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Alex Federation @afederation.bsky.social · 23/01/2025
Nice discussion here - we're doing our part building the first proteomics search engine that can handle the scale needed for drug discovery www.nautilus.bio/blog/transla...
nautilus.bio
Translating Proteomics Episode 15: Combating the Reproducibility Crisis in Computational Proteomics
Discover new ways to improve the reproducibility of proteomic and multiomic analyses.
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Alex Federation @afederation.bsky.social · 12/01/2025
I'm not sure how I missed this, but apparently there's a flash of light when the egg gets fertilized!? Pretty wild www.nature.com/articles/sre...
nature.com
The zinc spark is an inorganic signature of human egg activation - Scientific Reports
Scientific Reports - The zinc spark is an inorganic signature of human egg activation
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Reposted by Alex Federation
Derek Lowe @dereklowe.bsky.social · 06/01/2025
Re-upping this reply thread from last night. Drugs don't come from nowhere, folks. And we're not ripping off the NIH, either.
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Alex Federation @afederation.bsky.social · 05/01/2025
New Drug Approval: Opdivo Qvantig from BMS www.drugs.com/newdrugs/fda...
drugs.com
FDA Approves Opdivo Qvantig (nivolumab and hyaluronidase-nvhy) Subcutaneous Injection for Use in Most Previously Approved Solid Tumor Opdivo (nivolumab) Indications
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Alex Federation @afederation.bsky.social · 03/01/2025
Lots of really cool molecules here. The menin inhibitors are super important. No new transcription factor inhibitors, sadly. On to 2025 🚀
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Reposted by Alex Federation
Emma Chory, Ph.D. @chorye.bsky.social · 02/01/2025
First @chorylab.bsky.social blog post! chorylab.substack.com/p/new-year-n...
chorylab.substack.com
New Year, New Lab: Automating Your Lab Life with Zapier 🎉
Freezers fail. Robots tantrum. Automation saves the day.
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Alex Federation @afederation.bsky.social · 28/12/2024
Don't think I've ever read something this moving about gene regulation before
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Alex Federation @afederation.bsky.social · 27/12/2024
Wow. Very impressive work with in vivo dTAG looking at KRAS G12V. Lots more to learn with this technology, this is only the start. Congratulations Behnam and team!
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Reposted by Alex Federation
Derek Thompson @dkthomp.bsky.social · 21/12/2024
People sometimes make fun of science that sounds stupid and random. Meanwhile, a study of lizard saliva turned into a peptide medication, which was turned into a diabetes medication, which was turned into a GLP1 weight loss drug, that just became the first therapy every approved for … sleep apnea
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Alex Federation @afederation.bsky.social · 12/12/2024
Spatial proteomics wins method of the year! Our team at @talusbio.bsky.social isn't using IF-based spatial proteomics, TF-Scan does provide a surrogate of protein localization within the nucleus, with enough throughput to be useful for drug discovery. www.nature.com/articles/s41...
nature.com
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
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Reposted by Alex Federation
Will Fondrie @willfondrie.com · 11/12/2024
One of the reasons I joined @talusbio.bsky.social was @afederation.bsky.social and @lkpino.bsky.social's commitment to open science 👏 One of the first posts on our new company blog is a repost from my own blog on #OSS in #proteomics. Check it out here: blog.talus.bio/p/the-case-f...
blog.talus.bio
The Case for Open-Source Scientific Software
Papers without code are just advertisements.
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Alex Federation @afederation.bsky.social · 10/12/2024
Really cool pipeline, excited to play around with this (someday)
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Alex Federation @afederation.bsky.social · 09/12/2024
Where would genomics be if the BAM/SAM file format was proprietary and Bamtools/Bowtie was closed source and prohibitively expensive? That's where the proteomics field is right now. Talus Bio's @willfondrie.com and a group of industry+academia leaders share -
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Reposted by Alex Federation
Gabriele Corso @gcorso.bsky.social · 08/12/2024
You may have seen a recent pre-print [1] from Jain et al. with strongly worded claims against the experimental results in our DiffDock paper [2]. We initially declined to respond as we saw that this preprint contained falsehoods, misleading comparisons, seemingly deliberate omissions, ...1/n
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Alex Federation @afederation.bsky.social · 06/12/2024
😮 "And the preprint highlights a major problem behind the DiffDock team's approach. As a training set, they used roughly 98% of the known small-molecule-bound structures in the literature, and reserved the other 2% to evaluate the program's performance as a test set."
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