Victor Manna
@victormanna.bsky.social
PhD Student @Charité Berlin
Reposted by Victor Manna
Just released Proseg 3, which has some major performance improvements, support for Visium HD, and can output directly zarr formatted spatialdata objects.
crates.io/crates/proseg
crates.io/crates/proseg
crates.io: Rust Package Registry
crates.io
August 7, 2025 at 9:44 PM
Just released Proseg 3, which has some major performance improvements, support for Visium HD, and can output directly zarr formatted spatialdata objects.
crates.io/crates/proseg
crates.io/crates/proseg
Reposted by Victor Manna
Contrary to popular belief, what is important in science is as much its spirit as its product: it is as much the openmindedness, the primacy of criticism, the submission to the unforeseen, however upsetting, as the result, however new that may be. – Francois Jacob
www.nature.com/articles/s41...
www.nature.com/articles/s41...
April 7, 2025 at 1:07 AM
Contrary to popular belief, what is important in science is as much its spirit as its product: it is as much the openmindedness, the primacy of criticism, the submission to the unforeseen, however upsetting, as the result, however new that may be. – Francois Jacob
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Victor Manna
Thanks for coming to visit us @joshuabull.bsky.social and presenting your www.muspan.co.uk spatial analysis platform. Very impressive. Lots of interest here in using it to dig into cancer ecology and evolution.
February 27, 2025 at 7:14 AM
Thanks for coming to visit us @joshuabull.bsky.social and presenting your www.muspan.co.uk spatial analysis platform. Very impressive. Lots of interest here in using it to dig into cancer ecology and evolution.
Reposted by Victor Manna
👉 We Are Hiring! Looking for a motivated Postdoc and Computational Biologist to join our lab! If you're passionate about single-cell and spatial omics, this is an exciting opportunity.
📩 Get in touch to know more about the project and apply here:
qmul-jobs.tal.net/vx/mobile-0/...
📩 Get in touch to know more about the project and apply here:
qmul-jobs.tal.net/vx/mobile-0/...
Quick Check Needed
qmul-jobs.tal.net
March 25, 2025 at 12:20 PM
👉 We Are Hiring! Looking for a motivated Postdoc and Computational Biologist to join our lab! If you're passionate about single-cell and spatial omics, this is an exciting opportunity.
📩 Get in touch to know more about the project and apply here:
qmul-jobs.tal.net/vx/mobile-0/...
📩 Get in touch to know more about the project and apply here:
qmul-jobs.tal.net/vx/mobile-0/...
Reposted by Victor Manna
Quite an essay on the basis of cancer entitled "The End of the Genetic Paradigm of Cancer" @plosbiology.org arguing against the primacy of somatic mutations (traditional model) and cells, invoking gene regulatory networks and tissue
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
March 18, 2025 at 6:25 PM
Quite an essay on the basis of cancer entitled "The End of the Genetic Paradigm of Cancer" @plosbiology.org arguing against the primacy of somatic mutations (traditional model) and cells, invoking gene regulatory networks and tissue
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Reposted by Victor Manna
7/ Data cleaning is often the hardest part of bioinformatics. Before fancy models, learn to tidy metadata. It’ll save you hours later.
March 19, 2025 at 1:15 PM
7/ Data cleaning is often the hardest part of bioinformatics. Before fancy models, learn to tidy metadata. It’ll save you hours later.
Reposted by Victor Manna
Reposted by Victor Manna
Spatial transcriptomics holds great promise to understand biological tissue function, but the assignment of transcripts to cells has been a substantial bottleneck.
For this reason, Elyas Heidari, a student in my lab and in @steglelab.bsky.social built segger.
www.biorxiv.org/content/10.1...
For this reason, Elyas Heidari, a student in my lab and in @steglelab.bsky.social built segger.
www.biorxiv.org/content/10.1...
March 17, 2025 at 4:19 PM
Spatial transcriptomics holds great promise to understand biological tissue function, but the assignment of transcripts to cells has been a substantial bottleneck.
For this reason, Elyas Heidari, a student in my lab and in @steglelab.bsky.social built segger.
www.biorxiv.org/content/10.1...
For this reason, Elyas Heidari, a student in my lab and in @steglelab.bsky.social built segger.
www.biorxiv.org/content/10.1...
Reposted by Victor Manna
Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!
Documentation here!
docs.nimbusimage.com
Documentation here!
docs.nimbusimage.com
NimbusImage
NimbusImage.com
March 17, 2025 at 2:46 PM
Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!
Documentation here!
docs.nimbusimage.com
Documentation here!
docs.nimbusimage.com
Reposted by Victor Manna
🧬If you work with @10xgenomics.bsky.social Xenium, this might be of your interest.
Our new study on Xenium exploration best practice and comparing it with other commercial platforms is now out in @naturemethods.bsky.social
www.nature.com/articles/s41...
Our new study on Xenium exploration best practice and comparing it with other commercial platforms is now out in @naturemethods.bsky.social
www.nature.com/articles/s41...
Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows - Nature Methods
This study presents a comprehensive evaluation of Xenium In Situ datasets and provides recommendations on analysis workflows.
www.nature.com
March 14, 2025 at 2:38 PM
🧬If you work with @10xgenomics.bsky.social Xenium, this might be of your interest.
Our new study on Xenium exploration best practice and comparing it with other commercial platforms is now out in @naturemethods.bsky.social
www.nature.com/articles/s41...
Our new study on Xenium exploration best practice and comparing it with other commercial platforms is now out in @naturemethods.bsky.social
www.nature.com/articles/s41...
Reposted by Victor Manna
Thrilled to share new work led by @jieyang437.bsky.social in the lab published today in @Nature. We find that Aspirin prevents metastasis by releasing T cells from immune suppression by platelet TXA2. @Cambridge_Uni @CRUKCamCentre rdcu.be/eci1U
March 5, 2025 at 6:56 PM
Thrilled to share new work led by @jieyang437.bsky.social in the lab published today in @Nature. We find that Aspirin prevents metastasis by releasing T cells from immune suppression by platelet TXA2. @Cambridge_Uni @CRUKCamCentre rdcu.be/eci1U
Reposted by Victor Manna
The analogy of omics data normalization and cooking:
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
February 27, 2025 at 8:01 AM
The analogy of omics data normalization and cooking:
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
Reposted by Victor Manna
I have been trying to find the time to move away from the polical hellscape we find ourselves in to finish and share a bluetorial about science.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
the word irony is written on a white background
ALT: the word irony is written on a white background
media.tenor.com
February 22, 2025 at 10:19 AM
I have been trying to find the time to move away from the polical hellscape we find ourselves in to finish and share a bluetorial about science.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
This helps me remember what this is all about.
Ironically, it is about the treatment of pain.
Reposted by Victor Manna
Best practices for single-cell analysis across modalities go.nature.com/4gJkk3c #ExpertRecommendation by @lukasheumos.bsky.social et al. (from the @fabiantheis.bsky.social lab) - now nearing 250k accesses!
Free to read here: rdcu.be/eabUB
Free to read here: rdcu.be/eabUB
Best practices for single-cell analysis across modalities - Nature Reviews Genetics
Practitioners in the field of single-cell omics are now faced with diverse options for analytical tools to process and integrate data from various molecular modalities. In an Expert Recommendation art...
go.nature.com
February 17, 2025 at 12:15 PM
Best practices for single-cell analysis across modalities go.nature.com/4gJkk3c #ExpertRecommendation by @lukasheumos.bsky.social et al. (from the @fabiantheis.bsky.social lab) - now nearing 250k accesses!
Free to read here: rdcu.be/eabUB
Free to read here: rdcu.be/eabUB
Reposted by Victor Manna
🚨 New paper alert! 🚨
Excited to share our latest work in Nature Communications spearheaded by brilliant @omaiques.bsky.social and thanks to all our collaborators—we show how matrix mechano-sensing at the invasive front induces a cytoskeletal and transcriptional memory that supports metastasis! 🧵⬇️
Excited to share our latest work in Nature Communications spearheaded by brilliant @omaiques.bsky.social and thanks to all our collaborators—we show how matrix mechano-sensing at the invasive front induces a cytoskeletal and transcriptional memory that supports metastasis! 🧵⬇️
February 14, 2025 at 12:36 PM
🚨 New paper alert! 🚨
Excited to share our latest work in Nature Communications spearheaded by brilliant @omaiques.bsky.social and thanks to all our collaborators—we show how matrix mechano-sensing at the invasive front induces a cytoskeletal and transcriptional memory that supports metastasis! 🧵⬇️
Excited to share our latest work in Nature Communications spearheaded by brilliant @omaiques.bsky.social and thanks to all our collaborators—we show how matrix mechano-sensing at the invasive front induces a cytoskeletal and transcriptional memory that supports metastasis! 🧵⬇️
Reposted by Victor Manna
Miriam Merad & Co @sinaiimmuno.bsky.social
outline the molecular basis of #DendriticCell maturation and the mechanisms through which cancer impairs #DC maturation and consider the potential for DC-focused cancer #immunotherapeutics.
📖 ⬇️
outline the molecular basis of #DendriticCell maturation and the mechanisms through which cancer impairs #DC maturation and consider the potential for DC-focused cancer #immunotherapeutics.
📖 ⬇️
#REVIEW 🚨
bit.ly
February 12, 2025 at 5:23 PM
Miriam Merad & Co @sinaiimmuno.bsky.social
outline the molecular basis of #DendriticCell maturation and the mechanisms through which cancer impairs #DC maturation and consider the potential for DC-focused cancer #immunotherapeutics.
📖 ⬇️
outline the molecular basis of #DendriticCell maturation and the mechanisms through which cancer impairs #DC maturation and consider the potential for DC-focused cancer #immunotherapeutics.
📖 ⬇️
Reposted by Victor Manna
Please share.
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
February 12, 2025 at 2:40 PM
Please share.
Reposted by Victor Manna
NEW Review: Trained immunity in chronic inflammatory diseases and cancer
by George Hajishengallis, Mihai Netea & Triantafyllos Chavakis
Explores the concept of 'maladaptive' TRIM - the potential to increase severity of or susceptibility to chronic inflammation and cancer.
#immunosky #immunology
by George Hajishengallis, Mihai Netea & Triantafyllos Chavakis
Explores the concept of 'maladaptive' TRIM - the potential to increase severity of or susceptibility to chronic inflammation and cancer.
#immunosky #immunology
Trained immunity in chronic inflammatory diseases and cancer - Nature Reviews Immunology
Besides its beneficial effects against infection, trained immunity has recently been implicated in inflammation-related disorders and is being exploited in cancer immunotherapy. These advances may ena...
www.nature.com
February 4, 2025 at 9:38 AM
NEW Review: Trained immunity in chronic inflammatory diseases and cancer
by George Hajishengallis, Mihai Netea & Triantafyllos Chavakis
Explores the concept of 'maladaptive' TRIM - the potential to increase severity of or susceptibility to chronic inflammation and cancer.
#immunosky #immunology
by George Hajishengallis, Mihai Netea & Triantafyllos Chavakis
Explores the concept of 'maladaptive' TRIM - the potential to increase severity of or susceptibility to chronic inflammation and cancer.
#immunosky #immunology
Reposted by Victor Manna
Gene expression topography analysis by GASTON portrays domain organization and spatial gradients of gene expression and cell type composition using spatially resolved transcriptomics data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 23, 2025 at 4:37 PM
Gene expression topography analysis by GASTON portrays domain organization and spatial gradients of gene expression and cell type composition using spatially resolved transcriptomics data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Victor Manna
From the teams of Hadi Nia, Rakesh Jain and Lance Munn, this Review defines the four physical hallmarks of cancers and discusses the methods and technologies for assessing each hallmark.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
January 16, 2025 at 10:02 PM
From the teams of Hadi Nia, Rakesh Jain and Lance Munn, this Review defines the four physical hallmarks of cancers and discusses the methods and technologies for assessing each hallmark.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Victor Manna
Microscopy Nodes is now up on bioRxiv! 🚀
This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).
High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬
www.biorxiv.org/content/10.1...
This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).
High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬
www.biorxiv.org/content/10.1...
January 15, 2025 at 1:39 PM
Microscopy Nodes is now up on bioRxiv! 🚀
This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).
High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬
www.biorxiv.org/content/10.1...
This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).
High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬
www.biorxiv.org/content/10.1...
Reposted by Victor Manna
If you hate statistics like I do, then you'll love my free lectures. Putting science before statistics, 20 lectures from basics of inference & causal modeling to multilevel models & dynamic state space models. It's all free, made with love and sympathy. 🧪 #stats www.youtube.com/playlist?lis...
September 19, 2024 at 10:56 AM
If you hate statistics like I do, then you'll love my free lectures. Putting science before statistics, 20 lectures from basics of inference & causal modeling to multilevel models & dynamic state space models. It's all free, made with love and sympathy. 🧪 #stats www.youtube.com/playlist?lis...
Reposted by Victor Manna
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics
Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...
doi.org
January 3, 2025 at 7:18 PM
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Reposted by Victor Manna
Cancers may arise in tissues with a low mutational burden. It’s up to the microenvironment! We discussed this in @natrevcancer.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Beyond genetics: driving cancer with the tumour microenvironment behind the wheel - Nature Reviews Cancer
In their Review article, Fuchs and colleagues discuss how a single or a few mutations in adult cells can lead to invasive cancers without a high mutational burden, demonstrating that non-genetic ...
www.nature.com
December 31, 2024 at 1:44 PM
Cancers may arise in tissues with a low mutational burden. It’s up to the microenvironment! We discussed this in @natrevcancer.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Victor Manna
Tao of Night Science: it’s best to be like water. Go with the flow of the project, think conceptually, seek questions, enjoy the process, value the friendship, be generous, and don't argue over credit.
open.spotify.com/episode/7FgV...
open.spotify.com/episode/7FgV...
December 31, 2024 at 8:57 PM
Tao of Night Science: it’s best to be like water. Go with the flow of the project, think conceptually, seek questions, enjoy the process, value the friendship, be generous, and don't argue over credit.
open.spotify.com/episode/7FgV...
open.spotify.com/episode/7FgV...