Marianna Rapsomaniki
@marianna-raps.bsky.social
Assistant Professor at the Biomedical Data Science Center at University of Lausanne (UNIL) and Lausanne University Hospital (CHUV). AI/ML for single-cell and spatial biology with a focus on oncology.
Reposted by Marianna Rapsomaniki
🔥 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
June 3, 2025 at 2:10 PM
🔥 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
Reposted by Marianna Rapsomaniki
🎤 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
🔹Session chairs: @marianna-raps.bsky.social (@unil.bsky.social, CHUV) & @julienroux.bsky.social (@unibas.ch)
👉Register: tinyurl.com/3edr5hy6
#bc2basel
April 30, 2025 at 9:00 AM
🎤 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
🔹Session chairs: @marianna-raps.bsky.social (@unil.bsky.social, CHUV) & @julienroux.bsky.social (@unibas.ch)
👉Register: tinyurl.com/3edr5hy6
#bc2basel
Reposted by Marianna Rapsomaniki
🚨 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
@marianna-raps.bsky.social
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...
arxiv.org
April 21, 2025 at 3:43 PM
🚨 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
@marianna-raps.bsky.social
Looking forward to 2 days full of exciting CompBio research @unil.bsky.social
this September 🧬🧫🔬
Hurry up and register!
this September 🧬🧫🔬
Hurry up and register!
After 6 (healthy) months of hiatus from social media, first post with a brand new conference announcement!! 🔥COMPUTATIONAL BIOLOGY IS EVERYWHERE! Join us in Lausanne for the first international Computational Biology Symposium! 18-19 September 2025 Registrations are OPEN! cbiosymposium.unil.ch
Computational Biology Symposium
cbiosymposium.unil.ch
March 18, 2025 at 8:27 PM
Looking forward to 2 days full of exciting CompBio research @unil.bsky.social
this September 🧬🧫🔬
Hurry up and register!
this September 🧬🧫🔬
Hurry up and register!
Reposted by Marianna Rapsomaniki
#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
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
February 11, 2025 at 8:19 AM
#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
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
Reposted by Marianna Rapsomaniki
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...
www.chuv.ch/fr/chuv-home... Paper on @naturecomms.bsky.social www.nature.com/articles/s41...
Eczéma, psoriasis, lupus et autres maladies inflammatoires de la peau : des signatures génomiques pour améliorer le diagnostic et le traitement
www.chuv.ch
December 22, 2024 at 7:22 AM
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...
www.chuv.ch/fr/chuv-home... Paper on @naturecomms.bsky.social www.nature.com/articles/s41...
Reposted by Marianna Rapsomaniki
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
Positive results on OOD perturbations -> accurate gene expression prediction. Paper: ibm.biz/carot-pre
December 15, 2024 at 9:29 PM
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
Positive results on OOD perturbations -> accurate gene expression prediction. Paper: ibm.biz/carot-pre
Reposted by Marianna Rapsomaniki
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
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
December 2, 2024 at 10:33 AM
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
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
Reposted by Marianna Rapsomaniki
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
tinyurl.com/ymkvk7vn
November 20, 2024 at 8:07 AM
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
tinyurl.com/ymkvk7vn
Reposted by Marianna Rapsomaniki
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/...
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...
biorxiv.org
November 27, 2024 at 2:58 PM
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/...
Reposted by Marianna Rapsomaniki
🚀 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!
@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!
Main - MLBio LAB
Maria Brbic
brbiclab.epfl.ch
November 25, 2024 at 5:19 PM
🚀 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!
@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!
Reposted by Marianna Rapsomaniki
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/
So how can we ever achieve #gender #equality?
We discuss various strategies in this #Cell Commentary
#WomeninSTEM
www.cell.com/cell/fulltex...
🧵 1/
November 25, 2024 at 12:38 PM
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/
So how can we ever achieve #gender #equality?
We discuss various strategies in this #Cell Commentary
#WomeninSTEM
www.cell.com/cell/fulltex...
🧵 1/
Reposted by Marianna Rapsomaniki
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...
It’s a template that already incorporates many useful features.
github.com/scverse/cook...
November 25, 2024 at 4:51 PM
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...
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!
November 24, 2024 at 5:41 PM
Not a #science post but somehow the perfect #firstblueskypost.. Somewhere in the Swiss Alps, the year of our Lord 2024 😎 Ladies, stay classy!
Reposted by Marianna Rapsomaniki
Sign of the times, no more bluebird on the biorxiv engagement tab..
November 24, 2024 at 9:59 AM
Sign of the times, no more bluebird on the biorxiv engagement tab..
Reposted by Marianna Rapsomaniki
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!
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!
📣 Preprint alert! We have studied the formation of pair-wise and multi-way enhancer-promoter interactions in the #3Dgenome in a lymphoid-to-myeloid transdifferentiation system and learned interesting new things about their function in #GeneRegulation. 1/10
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 22, 2024 at 2:38 PM
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!
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!
Reposted by Marianna Rapsomaniki
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 ..
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 ..
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 (...
pubs.rsc.org
November 21, 2024 at 12:58 PM
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 ..
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 ..
Reposted by Marianna Rapsomaniki
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
clarivate.com/highly-cited... @unil.bsky.social
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 ...
clarivate.com
November 20, 2024 at 1:59 PM
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
clarivate.com/highly-cited... @unil.bsky.social
Reposted by Marianna Rapsomaniki
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
November 19, 2024 at 5:04 PM
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
Reposted by Marianna Rapsomaniki
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.
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.
November 17, 2024 at 5:58 AM
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.
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.
Reposted by Marianna Rapsomaniki
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
go.bsky.app/SU34ELC
November 16, 2024 at 10:13 PM
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
go.bsky.app/SU34ELC
Reposted by Marianna Rapsomaniki
Here is an initial starter pack list on Machine Learning on Graphs: go.bsky.app/HN2MTzp
Machine Learning on Graphs
Join the conversation
go.bsky.app
November 16, 2024 at 1:09 AM
Here is an initial starter pack list on Machine Learning on Graphs: go.bsky.app/HN2MTzp
Reposted by Marianna Rapsomaniki
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
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
November 14, 2024 at 9:44 PM
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
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
Reposted by Marianna Rapsomaniki
🧠Le 23 novembre aura lieu la Journée de l’intelligence artificielle organisée par l’UNIL et l’EPFL. L’occasion de parcourir ses bénéfices et risques dans les sciences biomédicales, glaciologiques et criminelles. À lire dans l'uniscope 👉 go.unil.ch/sMZUc
November 15, 2024 at 12:08 PM
🧠Le 23 novembre aura lieu la Journée de l’intelligence artificielle organisée par l’UNIL et l’EPFL. L’occasion de parcourir ses bénéfices et risques dans les sciences biomédicales, glaciologiques et criminelles. À lire dans l'uniscope 👉 go.unil.ch/sMZUc
Reposted by Marianna Rapsomaniki
in case this is useful to someone in this massive platform migration: a starting pack for single-cell omics computational methods
go.bsky.app/GmS1cH
go.bsky.app/GmS1cH
single-cell computational methods
Join the conversation
go.bsky.app
November 15, 2024 at 11:11 AM
in case this is useful to someone in this massive platform migration: a starting pack for single-cell omics computational methods
go.bsky.app/GmS1cH
go.bsky.app/GmS1cH