Mark Robinson
@markrobinsonca.bsky.social
statistical bioinformatics; canadian / swiss; #methodsmatter #rstats; open science advocate; grumpy towards prestige worshippers, excessive admin and bros; will sacrifice sleep for a sunrise.
https://robinsonlabuzh.github.io/
https://robinsonlabuzh.github.io/
Reposted by Mark Robinson
We are so excited to announce that our latest paper is out in @jem.org
By combining single-cell RNA sequencing and 3D imaging, we reveal striking structural and molecular differences between human and mouse dermal lymphatic vasculature, opening up new perspectives on #Lymphatics and #HumanBiology
By combining single-cell RNA sequencing and 3D imaging, we reveal striking structural and molecular differences between human and mouse dermal lymphatic vasculature, opening up new perspectives on #Lymphatics and #HumanBiology
Transcriptomics- and 3D imaging–based characterization of the lymphatic vasculature in human skin | Journal of Experimental Medicine | Rockefeller University Press
This study reveals how the structure and cellular morphology of human dermal afferent lymphatic vessels differ from the current, primarily mouse tissue–bas
rupress.org
November 15, 2025 at 10:07 PM
We are so excited to announce that our latest paper is out in @jem.org
By combining single-cell RNA sequencing and 3D imaging, we reveal striking structural and molecular differences between human and mouse dermal lymphatic vasculature, opening up new perspectives on #Lymphatics and #HumanBiology
By combining single-cell RNA sequencing and 3D imaging, we reveal striking structural and molecular differences between human and mouse dermal lymphatic vasculature, opening up new perspectives on #Lymphatics and #HumanBiology
Reposted by Mark Robinson
From @csoneson.bsky.social , @markrobinsonca.bsky.social & colleagues in @plos.org #Computational #Biology | Building a continuous #benchmarking ecosystem in #bioinformatics | #Education 🧬 🖥️ 🧪 🔓
⬇️
journals.plos.org/ploscompbiol...
⬇️
journals.plos.org/ploscompbiol...
Building a continuous benchmarking ecosystem in bioinformatics
Benchmarking, which involves collecting reference datasets and demonstrating method performance, is a requirement for the development of new computational tools, but also becomes a domain of its own t...
journals.plos.org
November 15, 2025 at 5:11 PM
From @csoneson.bsky.social , @markrobinsonca.bsky.social & colleagues in @plos.org #Computational #Biology | Building a continuous #benchmarking ecosystem in #bioinformatics | #Education 🧬 🖥️ 🧪 🔓
⬇️
journals.plos.org/ploscompbiol...
⬇️
journals.plos.org/ploscompbiol...
Reposted by Mark Robinson
Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.11.06.686971v1
https://www.biorxiv.org/content/10.1101/2025.11.06.686971v1
November 7, 2025 at 8:00 AM
Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.11.06.686971v1
https://www.biorxiv.org/content/10.1101/2025.11.06.686971v1
Reposted by Mark Robinson
DESpace2: detection of differential spatial patterns in spatial omics data. #SpatialOmics #DifferentialSpatialPatterns #scRNAseq #Genomics #Bioinformatics @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
DESpace2: detection of differential spatial patterns in spatial omics data
Spatially resolved transcriptomics (SRT) enables the investigation of mRNA expression in a spatial context. While several SRT analysis frameworks have been developed, the vast majority of them focus…
www.biorxiv.org
November 8, 2025 at 6:05 PM
DESpace2: detection of differential spatial patterns in spatial omics data. #SpatialOmics #DifferentialSpatialPatterns #scRNAseq #Genomics #Bioinformatics @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Mark Robinson
🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
October 29, 2025 at 9:02 AM
🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Reposted by Mark Robinson
I'm very excited to share our latest preprint!
We introduce structure-based analysis of spatial omics data – an approach that focuses on multi-cellular anatomical structures rather than single cells.
We also present sosta to facilitate this type of analysis: bioconductor.org/packages/sos...
We introduce structure-based analysis of spatial omics data – an approach that focuses on multi-cellular anatomical structures rather than single cells.
We also present sosta to facilitate this type of analysis: bioconductor.org/packages/sos...
Analysis of anatomical multi-cellular structures from spatial omics data using sosta https://www.biorxiv.org/content/10.1101/2025.10.13.682065v1
October 14, 2025 at 3:11 PM
I'm very excited to share our latest preprint!
We introduce structure-based analysis of spatial omics data – an approach that focuses on multi-cellular anatomical structures rather than single cells.
We also present sosta to facilitate this type of analysis: bioconductor.org/packages/sos...
We introduce structure-based analysis of spatial omics data – an approach that focuses on multi-cellular anatomical structures rather than single cells.
We also present sosta to facilitate this type of analysis: bioconductor.org/packages/sos...
Reposted by Mark Robinson
Analysis of anatomical multi-cellular structures from spatial omics data using sosta https://www.biorxiv.org/content/10.1101/2025.10.13.682065v1
October 14, 2025 at 2:48 PM
Analysis of anatomical multi-cellular structures from spatial omics data using sosta https://www.biorxiv.org/content/10.1101/2025.10.13.682065v1
Reposted by Mark Robinson
Looking for scientists working with long-read transcriptomics technologies to join a COST action proposal. Contact us!!! @nanoporetech.com @pacbio.bsky.social
October 2, 2025 at 5:25 PM
Looking for scientists working with long-read transcriptomics technologies to join a COST action proposal. Contact us!!! @nanoporetech.com @pacbio.bsky.social
Reposted by Mark Robinson
Martin Emons on SpatialFDA - searching for differential colocalization in spatial omics data
September 18, 2025 at 9:46 AM
Martin Emons on SpatialFDA - searching for differential colocalization in spatial omics data
Reposted by Mark Robinson
EuroBioC2025 is in full swing here in Barcelona!
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
September 18, 2025 at 9:53 AM
EuroBioC2025 is in full swing here in Barcelona!
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for what’s ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
Reposted by Mark Robinson
We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Harnessing the potential of spatial statistics for spatial omics data with pasta
Abstract. Spatial omics allow for the molecular characterization of cells in their spatial context. Notably, the two main technological streams, imaging-ba
academic.oup.com
September 11, 2025 at 7:04 AM
We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data
academic.oup.com/nar/article/...
academic.oup.com/nar/article/...
Reposted by Mark Robinson
MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments https://www.biorxiv.org/content/10.1101/2025.07.08.663623v1
July 12, 2025 at 5:47 AM
MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments https://www.biorxiv.org/content/10.1101/2025.07.08.663623v1
Reposted by Mark Robinson
Update: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”.
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...
arxiv.org
June 27, 2025 at 1:28 PM
Update: We greatly revised our paper and renamed it “Harnessing the Potential of Spatial Statistics for Spatial Omics Data with pasta”.
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
We discuss the broad range of exploratory spatial statistics options for spatial Omics technologies and show relevant use cases.
arxiv.org/abs/2412.01561
Reposted by Mark Robinson
Did you ever notice discrepancies in benchmarking of bioinformatics tools? We did too! Setting out to benchmark spatial clustering methods, we encountered major reproducibility issues in previous benchmarks and questionable "ground truths".
More in our preprint: www.biorxiv.org/content/10.1...
More in our preprint: www.biorxiv.org/content/10.1...
Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering
Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcript...
www.biorxiv.org
July 2, 2025 at 12:05 PM
Did you ever notice discrepancies in benchmarking of bioinformatics tools? We did too! Setting out to benchmark spatial clustering methods, we encountered major reproducibility issues in previous benchmarks and questionable "ground truths".
More in our preprint: www.biorxiv.org/content/10.1...
More in our preprint: www.biorxiv.org/content/10.1...
Reposted by Mark Robinson
DESpace2: detection of differential spatial patterns in spatial omics data https://www.biorxiv.org/content/10.1101/2025.06.30.662268v1
July 2, 2025 at 5:46 PM
DESpace2: detection of differential spatial patterns in spatial omics data https://www.biorxiv.org/content/10.1101/2025.06.30.662268v1
Reposted by Mark Robinson
A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification. #HiFi #LongReads #Sequencing #Transcriptomics
@pacbio.bsky.social @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
@pacbio.bsky.social @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
July 1, 2025 at 9:15 AM
A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification. #HiFi #LongReads #Sequencing #Transcriptomics
@pacbio.bsky.social @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
@pacbio.bsky.social @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Mark Robinson
🤖 SIB supplies the foundation of transformational AI by providing:
⭐ gold-standard training data through curated databases
🔗 connected information through knowledge representation
💪 trustworthy evaluation through benchmarking.
See how in the #SIBProfile 2025: issuu.com/sibswissinst...
⭐ gold-standard training data through curated databases
🔗 connected information through knowledge representation
💪 trustworthy evaluation through benchmarking.
See how in the #SIBProfile 2025: issuu.com/sibswissinst...
July 1, 2025 at 9:16 AM
🤖 SIB supplies the foundation of transformational AI by providing:
⭐ gold-standard training data through curated databases
🔗 connected information through knowledge representation
💪 trustworthy evaluation through benchmarking.
See how in the #SIBProfile 2025: issuu.com/sibswissinst...
⭐ gold-standard training data through curated databases
🔗 connected information through knowledge representation
💪 trustworthy evaluation through benchmarking.
See how in the #SIBProfile 2025: issuu.com/sibswissinst...
Reposted by Mark Robinson
Pseudobulk DGE #RStats journal club
* #muscat doi.org/10.1038/s414... @helucro.bsky.social
* pbDD doi.org/10.1101/2023... @davi1893.bsky.social
* #dreamlet doi.org/10.1101/2023... @panosroussos.bsky.social
* #distinct doi.org/10.1214/22-A... @markrobinsonca.bsky.social
youtu.be/TB9dfKPfns8
* #muscat doi.org/10.1038/s414... @helucro.bsky.social
* pbDD doi.org/10.1101/2023... @davi1893.bsky.social
* #dreamlet doi.org/10.1101/2023... @panosroussos.bsky.social
* #distinct doi.org/10.1214/22-A... @markrobinsonca.bsky.social
youtu.be/TB9dfKPfns8
[2025-06-11] Pseudobulk DGE statistical methods journal club
YouTube video by Leonardo Collado Torres
youtu.be
June 12, 2025 at 6:51 PM
Pseudobulk DGE #RStats journal club
* #muscat doi.org/10.1038/s414... @helucro.bsky.social
* pbDD doi.org/10.1101/2023... @davi1893.bsky.social
* #dreamlet doi.org/10.1101/2023... @panosroussos.bsky.social
* #distinct doi.org/10.1214/22-A... @markrobinsonca.bsky.social
youtu.be/TB9dfKPfns8
* #muscat doi.org/10.1038/s414... @helucro.bsky.social
* pbDD doi.org/10.1101/2023... @davi1893.bsky.social
* #dreamlet doi.org/10.1101/2023... @panosroussos.bsky.social
* #distinct doi.org/10.1214/22-A... @markrobinsonca.bsky.social
youtu.be/TB9dfKPfns8
Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"):
www.biomedcentral.com/collections/...
www.biomedcentral.com/collections/...
Call for papers - Benchmarks v2.0
www.biomedcentral.com
April 29, 2025 at 7:08 AM
Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"):
www.biomedcentral.com/collections/...
www.biomedcentral.com/collections/...
Reposted by Mark Robinson
Honored to deliver the opening keynote talk at the Modern Benchmarking Conferene in Ascona a very much needed meeting organizad by @markrobinsonca.bsky.social @iscb.bsky.social sites.google.com/view/ascona2...
Ascona 2025
Modern Benchmarking: Advancing Computational Methods in Molecular Biology is an event dedicated to bringing together researchers and students from bioinformatics, computational biology, molecular biol...
sites.google.com
March 24, 2025 at 9:07 AM
Honored to deliver the opening keynote talk at the Modern Benchmarking Conferene in Ascona a very much needed meeting organizad by @markrobinsonca.bsky.social @iscb.bsky.social sites.google.com/view/ascona2...
Reposted by Mark Robinson
From @csoneson.bsky.social , @mramos148.bsky.social, @jorainer.bsky.social & colleagues in @plos.org #Computational #Biology | Eleven quick tips for writing a #Bioconductor package | #Bioinformatics #Education #Rstats #PLOSCBQT 🧬 🖥️ 🧪 🔓
⬇️
journals.plos.org/ploscompbiol...
⬇️
journals.plos.org/ploscompbiol...
Eleven quick tips for writing a Bioconductor package
journals.plos.org
March 20, 2025 at 11:53 AM
From @csoneson.bsky.social , @mramos148.bsky.social, @jorainer.bsky.social & colleagues in @plos.org #Computational #Biology | Eleven quick tips for writing a #Bioconductor package | #Bioinformatics #Education #Rstats #PLOSCBQT 🧬 🖥️ 🧪 🔓
⬇️
journals.plos.org/ploscompbiol...
⬇️
journals.plos.org/ploscompbiol...
Quick update. We have a pretty exciting lineup of topics/speakers in and around benchmarking that will be presented in Ascona at the end of the month:
sites.google.com/view/ascona2...
There are few registration slots left, so if you are interested to join us, get in touch.
sites.google.com/view/ascona2...
There are few registration slots left, so if you are interested to join us, get in touch.
March 5, 2025 at 1:56 PM
Quick update. We have a pretty exciting lineup of topics/speakers in and around benchmarking that will be presented in Ascona at the end of the month:
sites.google.com/view/ascona2...
There are few registration slots left, so if you are interested to join us, get in touch.
sites.google.com/view/ascona2...
There are few registration slots left, so if you are interested to join us, get in touch.
Reposted by Mark Robinson
Do you want to learn more about the statistical analysis of proteomics, metabolomics, single-cell and spatial transcriptomics? Do you want to up your game with R and Bioconductor? All of this while enjoying summer in the beautiful Italian Alps? Join us for the 21st edition of CSAMA July 6-11!
January 27, 2025 at 8:16 AM
Do you want to learn more about the statistical analysis of proteomics, metabolomics, single-cell and spatial transcriptomics? Do you want to up your game with R and Bioconductor? All of this while enjoying summer in the beautiful Italian Alps? Join us for the 21st edition of CSAMA July 6-11!
Reposted by Mark Robinson
Another preprint from our group this week .. see @siyuanluo.bsky.social's explainer below ..
Excited to share our preprint on selecting validation metrics for single-cell and spatial omics! Explore how to evaluate embeddings, graphs, clustering, and spatial domains with biological relevance in mind. Plus, discover poem, our R package with new spatially-aware metrics!
doi.org/10.1101/2024...
doi.org/10.1101/2024...
On metrics for subpopulation detection in single-cell and spatial omics data
Benchmarks are crucial to understanding the strengths and weaknesses of the growing number of tools for single-cell and spatial omics analysis. A key task is to distinguish subpopulations within compl...
doi.org
December 5, 2024 at 12:52 PM
Another preprint from our group this week .. see @siyuanluo.bsky.social's explainer below ..