Our Systema framework for evaluating genetic perturbation response prediction methods is now out in @natbiotech.nature.com ✨
Systema helps to evaluate perturbation response prediction methods by focusing on perturbation-specific effects rather than systematic variation 🎯
25.08.2025 18:36 — 👍 23 🔁 8 💬 1 📌 0
💥 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 🔁 59 💬 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 — 👍 5 🔁 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 — 👍 18 🔁 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 — 👍 10 🔁 3 💬 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 — 👍 15 🔁 7 💬 0 📌 1
Professor, Investigator, mom, frequent flyer.
Researcher @bayraktar_lab @teichlab @steglelab.bsky.social @sangerinstitute.bsky.social | Using models & AI to study cells, cell circuits & brains 🧠 | #SingleCell+spatial | 🌍+🇺🇦
Chromatin Enthusiasts 🧬 Epigenetics Researchers 🧬 Unlocking the secrets of #chromatin to understand cell state transitions in development 🧪 Focusing on Neural Stem Cells and Brain Organoids
located at #EPFL, #Campus_Biotech_Geneva, #Brain_Mind_Institute
Professor at Stanford & Director of Stanford Brain Organogenesis
Lab: https://pascalab.org
Center: http://www.brainorganogenesis.org
TED: https://go.ted.com/6WJy
Instagram: https://www.instagram.com/sergiu.p.pasca/
PhD student at EPFL
3D Vision | Underwater SLAM | AI for Conservation
http://josauder.github.io
Postdoc @ Stanford University
https://koloskova.github.io/
Research Scientist AI/ML @cziscience.bsky.social , PhD @www.helmholtz-munich.de , OSS @scverse.bsky.social
giovannipalla.com
Account of the Saez-Rodriguez lab at EMBL-EBI and Heidelberg University. We integrate #omics data with mechanistic molecular knowledge into #opensource #ML methods
Website: https://saezlab.org/
GitHub: https://github.com/saezlab/
computational biologist and statistician interested in how genes encode shape, form, and dynamics during development and regeneration; assistant professor @Columbia University https://www.morpho-lab.com/
Lipid cell biologist @EPFL
Professor of Computational Biology, Imperial College London
MRC Investigator, Computational Regulatory Genomics, MRC Laboratory of Medical Sciences
Interested in eukaryotic promoters, enhancers and long-range developmental regulation
Ph.D student in Computer Science and Engineering at the University of Washington working with Su-In Lee.
Executive Director of SIB Swiss Institute of Bioinformatics @sib.swiss and Professor at the University of Lausanne (UNIL), Switzerland. @cdessimoz and @dessimoz@mstdn.science elsewhere. Comparative Genomics, Phylogenetics, Evolution, Computational Biology.
Faculty at the ELLIS Institute Tübingen and Max Planck Institute for Intelligent Systems. Leading the AI Safety and Alignment group. PhD from EPFL supported by Google & OpenPhil PhD fellowships.
More details: https://www.andriushchenko.me/
VP, Genentech
Associate Professor at the Allen School of Computer Science and Engineering, University of Washington (on leave)
Faculty member at the Hebrew University, studying inference of spatial organization and dynamics from single-cell data, information processing, computation & self-organization in biology. www.nitzanlab.com
PhD student at Stanford CS; AI+Biomedicine
kexinhuang.com
Associate Professor at McGill University. Gene regulation, genomics, and bioinformatics. https://csg.lab.mcgill.ca/
