Jonas Verhellen

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Are you curious to see what my team and I are up to? Check out our group website here: peptide-discovery.ethz.ch

The New York Times visual journalism story thumbnails

Our team is looking for a visual journalist to report, design and code stories with us. You'll be able to learn from our skilled colleagues. I joined this team in 2021 and have continued to learn ever since. It's definitely a great work environment. Learn more about it or apply here: bit.ly/4kG33L6

If you're near Copenhagen, I'd love to host you for a talk!

#ICCS25

GENEOnet: Accurate Protein Binding Pocket Detection

#ICCS25

A Chemoinformatics Journey (in 17 parts) by Mike Lynch Awardee Val Gillet.

Made it to @intconfchemstr.social.edu.nl.ap.brid.gy just in time for the Mike Lynch Award (after about 6 hours of public transport).

“I’ve studied McCarthyism’s impact on higher education for 50 years. What’s happening now is worse.” -Ellen Schrecker, historian

Academic freedom in the United States has found itself periodically under siege, but the current attacks from the federal government raise a new level of alarm. nyer.cm/u405qvQ

Thank you!

Big news! I've received a DKK 2.97 million postdoc grant from the Lundbeck Foundation to kick off my independent research at the University of Copenhagen!

lundbeckfonden.com/news/young-t...

#neuroscience #postdoc #LundbeckFoundation #mentalhealth

It was about time. 😉

I was very happy to discover Copenhagen has a statue for @janhjensen.bsky.social! 🦉🦉🦉

NeurIPS participation in Europe We seek to understand if there is interest in being able to attend NeurIPS in Europe, i.e. without travelling to San Diego, US. In the following, assume that it is possible to present accepted papers ...

Would you present your next NeurIPS paper in Europe instead of traveling to San Diego (US) if this was an option? Søren Hauberg (DTU) and I would love to hear the answer through this poll: (1/6)

Learn more about #NordicAIR at our new website: nordicpartnership.ai (3/3)

Introducing olmOCR, our open-source tool to extract clean plain text from PDFs!

Built for scale, olmOCR handles many document types with high throughput. Run it on your own GPU for free—at over 3000 token/s, equivalent to $190 per million pages, or 1/32 the cost of GPT-4o!

FYI @kl4sp.bsky.social :)

The Allen Institute for AI

Come work with me!
We are looking to bring on more top talent to our language modeling workstream at @ai2.bsky.social building the open ecosystem. We are hiring:
* Research scientists
* Senior research engineers
* Post docs (Young investigators)
* Pre docs

job-boards.greenhouse.io/thealleninst...

Happy Valentine's day! And for all of us who need some extra love today - especially the NIH folks - here's a happy oxytocin molecule! 💞🧪

The day will come ... it always does. 💪

1 week left to apply for this fully funded #compchem PhD opportunity part of the EU Marie Curie Doctoral Network, “CATALOOP”
🗓 Deadline: 31/01/2025
📥 How to Apply: submit your application via the university portal shorturl.at/nHyAo

New preprint from my group: Enhancing Chemical Synthesis Planning: Automated Quantum Mechanics-Based Regioselectivity Prediction for C-H Activation with Directing Groups doi.org/10.26434/che... #compchem

😯 — 🙏

CatFlow: An Automated Workflow for Training Machine Learning Potentials to Compute Free Energies in Dynamic Catalysis Dynamic effects of catalysts play a crucial role in catalytic reactions, necessitating the incorporation of statistical sampling and understanding of the impact of dynamic structures in free energy calculations. However, the complexity of catalytic systems poses challenges in effectively exploring the vast configurational space effectively. In this work, we propose CatFlow, an automated workflow for training machine learning potentials (MLPs) to compute free energies of catalytic reactions. CatFlow combines constrained molecular dynamics (MD) simulation with concurrent training of MLPs and sequential calculation of free energies with well trained MLPs. By rapidly generating reliable MLPs, CatFlow facilitates rigorous free energy calculations, enabling the determination of the reaction profiles in an end-to-end manner. We showcased the capabilities of CatFlow by investigating the activation of O2 catalyzed by Pt clusters and demonstrated the effects of phase transition on the activities of the catalytic reaction. CatFlow offers an efficient and automated solution for studying the catalytic elementary reaction processes. It reduces the need for human intervention and provides researchers with a powerful tool to investigate free energies of dynamic catalysis.

Active-learning ML approach for catalytic free-energy calculations by Liu et al.: An MLP “committee” and constrained MD refine data, capturing reaction pathways 10^6× faster than ab initio. Their scheme ensures robust coverage of transitions and near-DFT precision. pubs.acs.org/doi/10.1021/...

Ooh this looks nice! ✨ I was looking for something of this kind before the holidays. 😊

Two PhD or Postdoc positions in computational off-target analysis of siRNA and small peptides

Please forward to good candidates jobportal.ku.dk/videnskabeli...

YouTube video by Oceandreams313 Studio 60 O Holy Night

I used to share this video on the other place every year at Christmas ... time for a new tradition. Happy holidays BlueSky!

youtu.be/Etflv7R6NKA?...

People playing the board game "Tokado" with candles in the background.

I opened BlueSky during someone else's turn and your post was the first thing I saw. 😊🎄😂

Come join us on an exciting joint PhD project on ML for protein function with @kailalab.bsky.social -- We are looking for a strong quantitative candidate with prior experience in ML. The position is based in Gothenburg and is fully funded for 5 years.

www.chalmers.se/en/about-cha...

Definitely worth considering. Also checking for repeats (different smiles somehow but same compound) and inconsistencies. There's quite a few issues with most of these (compiled) datatsets. I think Pat Walters has had a blog post about this. Can't remember exactly.

Despite decades of research, people suffering from severe mental health disorders still face an average 10 to 15 year reduction in life expectancy. In part due to current medical limitations and in part due the severity of the comorbidities.