Maria Brbic

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve.

Preprint 📝: biorxiv.org/content/10.1...

🧵 1/n

21.07.2025 09:55 — 👍 91    🔁 58    💬 3    📌 2

ISMB/ECCB 2025:
Join us for the DREAM Challenges session on Monday, 21 July, 14:00 Explore community-driven benchmarking for Foundation Models—run a live experiment for LLMs.
@bowang87.bsky.social @anshulkundaje.bsky.social @cziscience.bsky.social @mariabrbic.bsky.social @juliosaezrod.bsky.social

20.07.2025 16:14 — 👍 4    🔁 3    💬 1    📌 0

Thrilled to share LUNA🌕 – our new generative AI model that reassembles tissue structures from dissociated cells! LUNA learns spatial priors over existing spatially resolved datasets with the aim to predict cell locations de novo.

Check out our paper here: www.biorxiv.org/content/10.1...

24.02.2025 15:29 — 👍 17    🔁 7    💬 0    📌 3

Latent spaces for tumour transcriptomes - Nature Biomedical Engineering Generating low-dimensional latent spaces for gene-expression data via unsupervised deep learning can unveil biological insight across cancers.

Honored to work with the exceptional @weiqiu.bsky.social @uwcse.bsky.social and brilliant co-senior author Kamila Naxerova @harvardmed.bsky.social! I still can’t believe I have the privilege of collaborating with them www.nature.com/articles/s41...

@weiqiu.bsky.social is on the academic job market!

19.01.2025 03:01 — 👍 11    🔁 4    💬 1    📌 1

Single cell – ENCODEHomo sapiens clickable body map

Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/

www.encodeproject.org/single-cell/...

07.01.2025 21:29 — 👍 288    🔁 86    💬 6    📌 0

GRETA graphical abstract

We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇
Paper: doi.org/10.1101/2024.12.20.629764
Code: github.com/saezlab/greta

23.12.2024 08:43 — 👍 126    🔁 46    💬 2    📌 5

Thank you!!

02.12.2024 19:56 — 👍 0    🔁 0    💬 0    📌 0

🎉 Four of our faculty members have been awarded the prestigious Swiss National Science Foundation SNSF "Starting Grant" for their groundbreaking research projects 🌟

Congratulations to @mariabrbic.bsky.social, Josie Hughues
@trackingactions.bsky.social and Philippe Schwaller! 🥳

02.12.2024 10:58 — 👍 10    🔁 2    💬 2    📌 0

Main - MLBio LAB Maria Brbic

🚀 We're #Hiring #PhD students at #MLBio Lab at
@EPFL through the #EDIC Program!
📅 Deadline: Dec 15

💥 We're part of School of Computer Science and School of Life Sciences at EPFL which gives access to excellent collaborators, network, and resources!

👉 Learn more at brbiclab.epfl.ch!

25.11.2024 17:19 — 👍 14    🔁 7    💬 0    📌 1

To expedite the development of a network focussed on single-cell and spatial genomics on this platform, I started to collect accounts of scientists & groups that are broadly active in these fields. This is work in progress, DM if you want to be added or have suggestions!

go.bsky.app/HZTJxbZ

20.11.2024 17:11 — 👍 45    🔁 15    💬 8    📌 0

Here’s the updated Computational Biology Starter Pack! Let me know if you'd like to be included.

go.bsky.app/QVPoZXp

24.11.2024 16:33 — 👍 174    🔁 78    💬 81    📌 5