Marianna Rapsomaniki

New preprint 🧫🧬

Spatial transcriptomics (~550,000 cells, 2,432 patient-derived organoids): we map gene expression, shape, and function in space to understand cancer biology and drug response. w/ @marianna-raps.bsky.social @khomicsko.bsky.social and Maxim Norkin

www.biorxiv.org/content/10.6...

Looking to start your lab in generative biology / AI?
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty

📢 4 #PhD positions in #Quantitative #Biology are available!
⚠️ Application deadline: 30.11.2025

More info 👉 career5.successfactors.eu/career?compa...

@ciriellolab.bsky.social @marianna-raps.bsky.social

Thank you @isabellease.bsky.social 🙏

🔥 18-19/9/25 🔥 Computational Biology Symposium in Lausanne! Meet the speakers: Mo Lotfollahi @sangerinstitute.bsky.social is expert of cutting-edge #AI approaches to study #singlecell biology , #generativeAI, and #spatialbiology lotfollahi.com

🎤 It’s a pleasure to welcome @stephaniehicks.bsky.social from the @jhubiostat.bsky.social to present at the [BC]2 conference.
🔹Session chairs: @marianna-raps.bsky.social (@unil.bsky.social, CHUV) & @julienroux.bsky.social (@unibas.ch)
👉Register: tinyurl.com/3edr5hy6
#bc2basel

Towards generalizable single-cell perturbation modeling via the Conditional Monge Gap Learning the response of single-cells to various treatments offers great potential to enable targeted therapies. In this context, neural optimal transport (OT) has emerged as a principled methodologic...

🚨 Our new paper: Conditional Optimal Transport generalizes well to unseen drugs. Big step forward, thanks to conditional Monge Gap! Even better: conditional models often beat local, non-conditional ones. arxiv.org/abs/2504.08328. Code public! Thanks to all co-authors
@marianna-raps.bsky.social

Looking forward to 2 days full of exciting CompBio research @unil.bsky.social
this September 🧬🧫🔬
Hurry up and register!

#IDWGS — Day of Women and Girls in Science 👩‍🔬 🚀 🏛️
To strengthen the leadership qualities of women researchers, the SNSF ran the #PRIMA #Leadership Programme for five years. Now, some of the participants have written a book to share some of their stories.
📆 Book launch: 29 September 2025

Precision Dermatology 2.0: #DataScience + #Immunology + #Genomics + #Clinical Science. Interdisciplinary collaboration at its best at the @CHUV.
www.chuv.ch/fr/chuv-home... Paper on @naturecomms.bsky.social www.nature.com/articles/s41...

If you're @neuripsconf.bsky.social and into #OptimalTransport & bio, dont miss on Alice Driessen's spotlight talk on #ConditionalMongeGap for modeling CAR Response. Today #AIDrugX workshop!

Positive results on OOD perturbations -> accurate gene expression prediction. Paper: ibm.biz/carot-pre

Huge congrats Philippe - so well deserved 🙌🏻

We are hiring (resharing appreciated)!

Given recent successful grant applications (I got my SNSF Starting Grant 🚀), we are extending the LIAC team with multiple openings (PhD/postdoc) for 2025.

Apply now (deadline: December 20th) by filling in this form: forms.fillout.com/t/eq5ADAw3kkus.
#ChemSky

Hiring! I'm looking for a postdoc in machine learning of spatial single-cell data. Exciting project to develop methods for modelling cellular circuits in disease and regeneration of heart, liver and bone marrow using Xenium data from our lab.
tinyurl.com/ymkvk7vn

Immune organization in sentinel lymph nodes of melanoma patients is prognostic of distant metastases Sentinel lymph node (sLN) biopsy is part of melanoma staging, as involved LNs indicate a higher risk of recurrence. However, how the sLN is shaped by the tumor and reciprocally affects metastatic prog...

Preprint alert! We profiled immune organization in sentinel lymph nodes (sLNs) of melanoma patients using spatial proteomics and spatial transcriptomics, and found that it is prognostic of distant metastases. biorxiv.org/cgi/content/...

Super interesting work Leeat - looking forward to reading it!

🚀 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!

Women are under-represented at senior levels in #academia globally, & across all #science 🧪 disciplines, as shown by these "scissor-shaped curves" ✂️

So how can we ever achieve #gender #equality?

We discuss various strategies in this #Cell Commentary

#WomeninSTEM

www.cell.com/cell/fulltex...
🧵 1/

If you are considering creating a Python package I strongly suggest cookiecutter-scverse by @scverse.bsky.social

It’s a template that already incorporates many useful features.

github.com/scverse/cook...

Not a #science post but somehow the perfect #firstblueskypost.. Somewhere in the Swiss Alps, the year of our Lord 2024 😎 Ladies, stay classy!

Sign of the times, no more bluebird on the biorxiv engagement tab..

Fist real post here — so pay attention, folks!
Below is (yet another) nice study from our neighbours in the Oudelaar lab and peers SPP2202 and SFB1565, to which we added bottom-up MD simulations to further rationalise experimental data.
Read on in @mariekeoudelaar.bsky.social ‘s thread!

Learning on compressed molecular representations Last year, a preprint gained notoriety, proposing that a k-nearest neighbour classifier is able to outperform large-language models using compressed text as input and normalised compression distance (...

Fresh off the presses:
In "Learning on compressed molecular representations" Jan Weinreich and I looked into whether GZIP performed better than Neural Networks in chemical machine learning tasks. Yes, you've read that right.

TL;DR: Yes, GZIP can perform better than baseline GNNs and MLPs. It can ..

Highly Cited Researchers | Clarivate The Highly Cited Researchers 2024 list identifies and celebrates individuals who have demonstrated significant and broad influence in their fields of research. Through rigorous selection criteria and ...

Thank you for this incredible honor! 🙏 A huge shoutout to the trainees in my lab—this achievement is thanks to you. Excited for what’s ahead from our Biomedical #DataScience Center at UNIL/CHUV 🚀 #Teamwork #Innovation #AI #HighlyCited2024
clarivate.com/highly-cited... @unil.bsky.social

It’s great advice, if it’s followed up by tips on how to get these ideas funded!

Interested in #singlecell and #spatial #metabolomics? Then book your calendar for December 10th! – Our online, free event will summarize major achievements of the field in 2024. #metabolism #omics #MALDI #EPFL With Giovanni D'Angelo and our #PhD students we prepared for you a fantastic lineup. 🧵 1/5

Alma Dal Co at her microscope

Alma Dal Co was an incredible scientist and a wonderful person who left us far too soon.
Last Friday, Sven Bergmann and the Alma Dal Co foundation organized a very special 2nd Memorial Symposium. It was mind-blowing to see how Alma‘s ideas continue to be a huge influence on all of us who knew her.

So many nice starter packs.. I couldn't find one related to spatial biology yet, so I started one 🧬🔬! Here's who I’ve included so far—let me know if you'd like to be added or suggest other must-follow accounts! #SpatialBiology

go.bsky.app/SU34ELC

Machine Learning on Graphs Join the conversation

Here is an initial starter pack list on Machine Learning on Graphs: go.bsky.app/HN2MTzp

Inspired by the other amazing starter packs - here's one for cancer researchers!

I tried to make this broad - from immunology to genomics to cell biology and so much more..

This list also includes organizations & institutes supporting cancer researchers 🧪🔬⚕️🩺

Hope its useful!

go.bsky.app/FEoaJMc