Marco Varrone
@marcovarrone.bsky.social
Postdoc in Computational Biology at @CirielloLab @dbc_unil.
Machine Learning for spatial omics.
https://batcheffect.com
Machine Learning for spatial omics.
https://batcheffect.com
Pinned
CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity - Natu...
CellCharter is a flexible, platform-agnostic method for identifying cell niches in spatially resolved data. Analysis of lung cancers demonstrates the importance of considering spatial information, exe...
www.nature.com
Excited that our paper "CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity" is finally out!
CellCharter is a computational framework to identify and study cellular niches in large-scale spatial transcriptomics, proteomics, and even epigenomics data.
CellCharter is a computational framework to identify and study cellular niches in large-scale spatial transcriptomics, proteomics, and even epigenomics data.
A few weeks ago, we released CellCharter v0.3.5.
Among some bug fixes, we received our first contribution from an external contributor: @loggas.bsky.social !
He designed a new metric called Relative Component Size (RCS).
Among some bug fixes, we received our first contribution from an external contributor: @loggas.bsky.social !
He designed a new metric called Relative Component Size (RCS).
GitHub - CSOgroup/cellcharter: A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data. - CSOgroup/cellcharter
github.com
July 15, 2025 at 1:31 PM
A few weeks ago, we released CellCharter v0.3.5.
Among some bug fixes, we received our first contribution from an external contributor: @loggas.bsky.social !
He designed a new metric called Relative Component Size (RCS).
Among some bug fixes, we received our first contribution from an external contributor: @loggas.bsky.social !
He designed a new metric called Relative Component Size (RCS).
Reposted by Marco Varrone
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 1:09 PM
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
Last year I completed my PhD and my father recorded my public defense 📹
So I decided to share it!
I talked about the communities of cells in our bodies and how we develop algorithms to study them.
Hope you enjoy it!
So I decided to share it!
I talked about the communities of cells in our bodies and how we develop algorithms to study them.
Hope you enjoy it!
Computational models to characterize spatial intra-tumor heterogeneity | Marco Varrone
YouTube video by Marco Varrone
youtu.be
March 12, 2025 at 7:46 AM
Last year I completed my PhD and my father recorded my public defense 📹
So I decided to share it!
I talked about the communities of cells in our bodies and how we develop algorithms to study them.
Hope you enjoy it!
So I decided to share it!
I talked about the communities of cells in our bodies and how we develop algorithms to study them.
Hope you enjoy it!
Reposted by Marco Varrone
The only sort of gatekeeper I wish we saw more of were those who wanted better software. Who cares if your model performs the best if it's unusable, or if your pipeline aligs reads faster if it only works on your local work computer? Or if there's no documentation on how to use any of it.
January 6, 2025 at 10:27 AM
The only sort of gatekeeper I wish we saw more of were those who wanted better software. Who cares if your model performs the best if it's unusable, or if your pipeline aligs reads faster if it only works on your local work computer? Or if there's no documentation on how to use any of it.
The scverse ecosystem is one of the best things that could have ever happened to the single-cell and spatial fields.
Smoother computational analyses mean faster and better research
Smoother computational analyses mean faster and better research
Closing 2024, scverse celebrates growth and collaboration! Huge thanks to everyone on this journey and our core team & board (@fabiantheis.bsky.social, @francescafinotello.bsky.social, @steglelab.bsky.social, Nir Yosef, @panosroussos.bsky.social, @robp.bsky.social). Here's to an inspiring 2025!
December 19, 2024 at 4:12 PM
The scverse ecosystem is one of the best things that could have ever happened to the single-cell and spatial fields.
Smoother computational analyses mean faster and better research
Smoother computational analyses mean faster and better research
Contributing to this project has been very cool!
Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density.
Switched to DeepCell Mesmer and it worked like a charm!
Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density.
Switched to DeepCell Mesmer and it worked like a charm!
Just before the holidays, here is the latest from the Oricchio lab. In collaboration with the hemato-oncology team, we established a new model to test therapies on lymphoma patient samples by preserving the tissue composition and architecture of the original tumors. www.nature.com/articles/s41...
Development of patient-derived lymphomoids with preserved tumor architecture for lymphoma therapy screening - Nature Communications
Choosing the most effective anti-cancer therapy is difficult due to the high degree of tumour cell and tumour microenvironment heterogeneity. Here, the authors develop a platform for the generation of...
www.nature.com
December 18, 2024 at 3:10 PM
Contributing to this project has been very cool!
Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density.
Switched to DeepCell Mesmer and it worked like a charm!
Quick tip for anyone interested in cell segmentation: I started with StarDist but it failed to detect nuclei in samples with regions of very different cell density.
Switched to DeepCell Mesmer and it worked like a charm!
Reposted by Marco Varrone
To bring to light data science topics that usually don’t make it into publications I started a blog on this topic: hrovatin.github.io By interviewing different researchers, I plan to find out what is going on in the community.
Karin Hrovatin
Data science blog on topics that don’t get published.
hrovatin.github.io
December 16, 2024 at 6:59 AM
To bring to light data science topics that usually don’t make it into publications I started a blog on this topic: hrovatin.github.io By interviewing different researchers, I plan to find out what is going on in the community.
We are used to thinking that, when an organism has cancer, all other cells will fight it.
We are now realizing that this is not true, and some of these cells may even help it.
In the fourth Batch Effect post I talked about 4 aspects:
We are now realizing that this is not true, and some of these cells may even help it.
In the fourth Batch Effect post I talked about 4 aspects:
The hidden allies of cancer
How spatial omics is bringing normal cell interactions into focus
www.batcheffect.com
December 12, 2024 at 7:00 AM
We are used to thinking that, when an organism has cancer, all other cells will fight it.
We are now realizing that this is not true, and some of these cells may even help it.
In the fourth Batch Effect post I talked about 4 aspects:
We are now realizing that this is not true, and some of these cells may even help it.
In the fourth Batch Effect post I talked about 4 aspects:
🔬 Spatial omics: revolutionary breakthrough or just incremental progress?
In the third Batch Effect blog post, I compared this emerging technology to the historic hype around interferon therapy.
Is this time going to be different?
www.batcheffect.com/p/breakthrou...
In the third Batch Effect blog post, I compared this emerging technology to the historic hype around interferon therapy.
Is this time going to be different?
www.batcheffect.com/p/breakthrou...
Breakthrough or incremental progress?
Why spatial omics is revolutionary for biology and medicine
www.batcheffect.com
December 5, 2024 at 7:12 AM
🔬 Spatial omics: revolutionary breakthrough or just incremental progress?
In the third Batch Effect blog post, I compared this emerging technology to the historic hype around interferon therapy.
Is this time going to be different?
www.batcheffect.com/p/breakthrou...
In the third Batch Effect blog post, I compared this emerging technology to the historic hype around interferon therapy.
Is this time going to be different?
www.batcheffect.com/p/breakthrou...
What do fruit pies 🥧, lego sets🧩, and cities🏙️ have in common?
They are all metaphors used to describe spatial transcriptomics.
In the second Batch Effect blog post I explored the best metaphor to make anyone understand what is spatial transcriptomics
www.batcheffect.com/p/the-best-m...
They are all metaphors used to describe spatial transcriptomics.
In the second Batch Effect blog post I explored the best metaphor to make anyone understand what is spatial transcriptomics
www.batcheffect.com/p/the-best-m...
The best metaphor for spatial transcriptomics
How everyone can understand what is spatial transcriptomics
www.batcheffect.com
November 27, 2024 at 6:56 AM
What do fruit pies 🥧, lego sets🧩, and cities🏙️ have in common?
They are all metaphors used to describe spatial transcriptomics.
In the second Batch Effect blog post I explored the best metaphor to make anyone understand what is spatial transcriptomics
www.batcheffect.com/p/the-best-m...
They are all metaphors used to describe spatial transcriptomics.
In the second Batch Effect blog post I explored the best metaphor to make anyone understand what is spatial transcriptomics
www.batcheffect.com/p/the-best-m...
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...
The Human Cell Atlas: towards a first draft atlas.
I often read people complaining about "yet another atlas" published, but they are an important component of modern cell biology.
They drive discovery, enable reproducibility, and I use them in nearly every project I work on.
I often read people complaining about "yet another atlas" published, but they are an important component of modern cell biology.
They drive discovery, enable reproducibility, and I use them in nearly every project I work on.
The Human Cell Atlas: towards a first draft atlas
In a collection of research articles and related content, the Human Cell Atlas consortium presents tools, data and ideas towards the generation of their first draft atlas of cells in the human body.
www.nature.com
November 21, 2024 at 6:43 AM
The Human Cell Atlas: towards a first draft atlas.
I often read people complaining about "yet another atlas" published, but they are an important component of modern cell biology.
They drive discovery, enable reproducibility, and I use them in nearly every project I work on.
I often read people complaining about "yet another atlas" published, but they are an important component of modern cell biology.
They drive discovery, enable reproducibility, and I use them in nearly every project I work on.
A few months ago, I started Batch Effect, a blog on the latest in cancer research under the lens of computational biology and spatial omics.
I never shared here, so I'll start posting one old article every week.
Hopefully we'll catch up just in time for a new series I am working on!
I never shared here, so I'll start posting one old article every week.
Hopefully we'll catch up just in time for a new series I am working on!
Welcome to Batch Effect
A blog on the new frontiers of Computational Biology for cancer research
www.batcheffect.com
November 18, 2024 at 6:29 AM
A few months ago, I started Batch Effect, a blog on the latest in cancer research under the lens of computational biology and spatial omics.
I never shared here, so I'll start posting one old article every week.
Hopefully we'll catch up just in time for a new series I am working on!
I never shared here, so I'll start posting one old article every week.
Hopefully we'll catch up just in time for a new series I am working on!
🎉 We released CellCharter v0.3.2!
- Now part of the Scverse ecosystem
- More efficient differential neighborhood enrichment
- Peak finding for cluster stability
- Compatible with the latest PyTorch
A few lessons learned along the way 🧵 1/4
github.com/CSOgroup/cel...
- Now part of the Scverse ecosystem
- More efficient differential neighborhood enrichment
- Peak finding for cluster stability
- Compatible with the latest PyTorch
A few lessons learned along the way 🧵 1/4
github.com/CSOgroup/cel...
GitHub - CSOgroup/cellcharter: A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data. - CSOgroup/cellcharter
github.com
November 12, 2024 at 7:24 AM
🎉 We released CellCharter v0.3.2!
- Now part of the Scverse ecosystem
- More efficient differential neighborhood enrichment
- Peak finding for cluster stability
- Compatible with the latest PyTorch
A few lessons learned along the way 🧵 1/4
github.com/CSOgroup/cel...
- Now part of the Scverse ecosystem
- More efficient differential neighborhood enrichment
- Peak finding for cluster stability
- Compatible with the latest PyTorch
A few lessons learned along the way 🧵 1/4
github.com/CSOgroup/cel...
Excited that our paper "CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity" is finally out!
CellCharter is a computational framework to identify and study cellular niches in large-scale spatial transcriptomics, proteomics, and even epigenomics data.
CellCharter is a computational framework to identify and study cellular niches in large-scale spatial transcriptomics, proteomics, and even epigenomics data.
CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity - Natu...
CellCharter is a flexible, platform-agnostic method for identifying cell niches in spatially resolved data. Analysis of lung cancers demonstrates the importance of considering spatial information, exe...
www.nature.com
December 8, 2023 at 2:38 PM
Excited that our paper "CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity" is finally out!
CellCharter is a computational framework to identify and study cellular niches in large-scale spatial transcriptomics, proteomics, and even epigenomics data.
CellCharter is a computational framework to identify and study cellular niches in large-scale spatial transcriptomics, proteomics, and even epigenomics data.
Hello there 👋 I'm Marco, a computer engineer turned computational biologist. In my PhD I'm currently exploring spatial omics data to study cancer.
I have learned a lot about it in the last 3 years and I would love to share it, but I still don't know in which format (posts, blogs or videos).
I have learned a lot about it in the last 3 years and I would love to share it, but I still don't know in which format (posts, blogs or videos).
October 12, 2023 at 1:16 PM
Hello there 👋 I'm Marco, a computer engineer turned computational biologist. In my PhD I'm currently exploring spatial omics data to study cancer.
I have learned a lot about it in the last 3 years and I would love to share it, but I still don't know in which format (posts, blogs or videos).
I have learned a lot about it in the last 3 years and I would love to share it, but I still don't know in which format (posts, blogs or videos).