iiinova — where your digital self keeps evolving

Ahmet Sarigun

@asarigun.bsky.social

29 followers 106 following 8 posts

curious explorer - asarigun.github.io

Posts Replies Media

Reposted by Ahmet Sarigun

Ahmet Sureyya Rifaioglu @ahmetrifaioglu.bsky.social · 17/12/2025

🎉 Happy to share our new work SpaCEy, now available🧬 SpaCEy is an explainable method for learning clinically relevant spatial tissue organization directly from spatial omics data—without predefined cell types or regions. 📄 Paper: www.biorxiv.org/content/10.6... 💻 Code repo: github.com/saezlab/SpaCEy

biorxiv.org

121

Reposted by Ahmet Sarigun

Matthieu da Costa @mdc-biocat.bsky.social · 31/08/2025

With the release of Boltz 2, is there already a review comparing the efficiency of different (new) docking tools? (I’ve already tried Pocket Vina, which is actually quite good for high-throughput)

031

Reposted by Ahmet Sarigun

Max Delbrück Center @mdc-berlin.bsky.social · 12/09/2025

Nearly 50 new cancer drugs are approved each year – but which one fits which patient? At the #mdcBerlin, @al2na.bsky.social’s team built Flexynesis, a deep learning toolkit to guide precision cancer care. Learn more: 👉 www.mdc-berlin.de/news/press/u... 👈

Illustration with overlaid text: The image shows a cancer cell in the bloodstream. The overlaid text appears in white, all-caps sans-serif font inside a dark blue rectangular box at the top left. It reads: “USING DEEP LEARNING FOR PRECISION CANCER THERAPY.” A small credit at the bottom right reads: “© Annie Cavanagh / Wellcome Collection.”

094

Reposted by Ahmet Sarigun

Gina El Nesr @ginaelnesr.bsky.social · 13/07/2025

is this how small molecules bind?? 😼

151

Reposted by Ahmet Sarigun

Radoslav Krivak @rdkbio.bsky.social · 27/06/2025

🚀 GPU-accelerated docking to P2Rank-predicted pockets

054

Ahmet Sarigun @asarigun.bsky.social · 26/06/2025

I'm excited to share our new preprint: PocketVina — a fast, scalable, and accurate multi-pocket molecular docking method. Docking remains essential in early-stage drug discovery, but recent deep learning–based approaches still face limitations in generating... Thread - (1/n)

144

Reposted by Ahmet Sarigun

Open Free Energy @openfree.energy · 04/02/2025

We're changing the field of #compchem by creating free and open-source software for performing alchemical free energy calculations. Our flagship protocol calculates relative binding free energies of protein-ligand systems. Try it out in your browser: colab.research.google.com/github/OpenF...

Artistic rendering of a biochemical model: a small molecule ligand, shown as a ball-and-stick model colored by element, is bound in a pocket in a protein surface, shown as a space filling model colored off-white.

03014

Reposted by Ahmet Sarigun

Leif S. Ludwig @leifludwig.bsky.social · 31/01/2025

Join us to connect with the vibrant #singlecell community. 📢Register for the #ISCO'25 Conference "Innovations in #SingleCell #OMICS" in Berlin! 🗓️ 12-13 May 2025 🎤 Fantastic Keynote and Invited Speakers 🫵🏿 Many slots for talks: submit your abstract 🔗http://isco-conference.eu Please spread the word!

1149

Reposted by Ahmet Sarigun

Pia Rautenstrauch @prauten.bsky.social · 24/01/2025

1/4 🧵 Preprint alert: In "Metrics Matter: Why We Need to Stop Using Silhouette in #SingleCell #Benchmarking," we reveal critical flaws in common #Evaluation metrics for #Integration and propose robust alternatives. @uweohler.bsky.social www.biorxiv.org/content/10.1...

biorxiv.org

Metrics Matter: Why We Need to Stop Using Silhouette in Single-Cell Benchmarking

Current-day single-cell studies comprise complex data sets affected by nested batch effects caused by technical and biological factors, relying on advanced integration methods. Silhouette is an establ...

1167