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
"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 𧫠π A new PCI Genomics recommendation by @mireyaplass.bsky.social: doi.org/10.24072/pci...
Bulk RNA-seq to the rescue of differential expression analysis i...
Due to the costs of single-cell sequencing, sample sizes are often relatively limited, sometimes leading to poorly reproducible results. In many contexts, however, larger bulk RNAseq data isβ¦
doi.org
December 1, 2025 at 8:30 AM
"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 𧫠π A new PCI Genomics recommendation by @mireyaplass.bsky.social: doi.org/10.24072/pci...
Reposted by Mark Robinson
Orchestrating Spatial Transcriptomics Analysis with Bioconductor
(including interoperability with Python)
Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/
#Rstats
(including interoperability with Python)
Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/
#Rstats
November 21, 2025 at 5:39 PM
Orchestrating Spatial Transcriptomics Analysis with Bioconductor
(including interoperability with Python)
Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/
#Rstats
(including interoperability with Python)
Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/
#Rstats
Reposted by Mark Robinson
Many people hours, calls and messages later: OSTA is now βin (pre)printβ, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
Itβs been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
Itβs been a joy working with you @estellayixingdong.bsky.social!
November 21, 2025 at 5:31 PM
Many people hours, calls and messages later: OSTA is now βin (pre)printβ, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
Itβs been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
Itβs been a joy working with you @estellayixingdong.bsky.social!
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 imagingβbased 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 tissueβbas
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 𧬠π₯οΈ π§ͺ π Β
β¬οΈ
journals.plos.org/ploscompbiol...
β¬οΈ
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 𧬠π₯οΈ π§ͺ π Β
β¬οΈ
journals.plos.org/ploscompbiol...
β¬οΈ
journals.plos.org/ploscompbiol...
Reposted by Mark Robinson
Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution #SingleCell π§ͺπ§¬π₯οΈ
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 π§ͺπ§¬π₯οΈ
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 focusβ¦
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
𧬠EuroBioC2026 is coming to Turku, Finland, from June 3β5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
π 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.
π More details soon at eurobioc2026.bioconductor.org
October 29, 2025 at 9:02 AM
𧬠EuroBioC2026 is coming to Turku, Finland, from June 3β5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
π 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.
π More details soon at eurobioc2026.bioconductor.org
.. where some compelling demonstration of performance/usefulness is made (ideally done in a way that is interoperable with community efforts) .. and over the longer term, communities complement/consolidate with continuous benchmarks. In principle, Omnibenchmark supports both use cases.
October 24, 2025 at 2:38 PM
.. where some compelling demonstration of performance/usefulness is made (ideally done in a way that is interoperable with community efforts) .. and over the longer term, communities complement/consolidate with continuous benchmarks. In principle, Omnibenchmark supports both use cases.
Interesting discussion! I agree that "extensive" benchmarks within method papers are not really the priority/essential. But at the same time, it would be tough to motivate having benchmark-less methods papers. I think we need a middle ground ..
October 24, 2025 at 2:38 PM
Interesting discussion! I agree that "extensive" benchmarks within method papers are not really the priority/essential. But at the same time, it would be tough to motivate having benchmark-less methods papers. I think we need a middle ground ..
Reposted by Mark Robinson
I'm very excited to share our latest preprint!
We introduce structure-based analysis of spatial omics data β 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 β 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 β 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 β 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
There are some similarities, but also some differences.
Scale: cells versus regions, but probably more importantly, Feature Space: segmentation focuses a lot on DNA and cell membrane markers (possibly transcript locations), while SAC is more about multi-cellular / neighbourhoods.
Scale: cells versus regions, but probably more importantly, Feature Space: segmentation focuses a lot on DNA and cell membrane markers (possibly transcript locations), while SAC is more about multi-cellular / neighbourhoods.
September 30, 2025 at 12:28 PM
There are some similarities, but also some differences.
Scale: cells versus regions, but probably more importantly, Feature Space: segmentation focuses a lot on DNA and cell membrane markers (possibly transcript locations), while SAC is more about multi-cellular / neighbourhoods.
Scale: cells versus regions, but probably more importantly, Feature Space: segmentation focuses a lot on DNA and cell membrane markers (possibly transcript locations), while SAC is more about multi-cellular / neighbourhoods.
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 whatβs ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for whatβs 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 whatβs ahead today and tomorrow!
#EuroBioC2025 #Bioconductor #OpenScience #Community
Day 1 was full of great talks, conversations, and that amazing Bioconductor community energy. Excited for whatβs 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 βHarnessing the Potential of Spatial Statistics for Spatial Omics Data with pastaβ.
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 βHarnessing the Potential of Spatial Statistics for Spatial Omics Data with pastaβ.
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
π€ SIB supplies the foundation of transformational AI by providing:
β gold-standard training data through curated databases
π connected information through knowledge representation
πͺ trustworthy evaluation through benchmarking.
See how in the #SIBProfile 2025: issuu.com/sibswissinst...
β gold-standard training data through curated databases
π connected information through knowledge representation
πͺ trustworthy evaluation through benchmarking.
See how in the #SIBProfile 2025: issuu.com/sibswissinst...
July 1, 2025 at 9:16 AM
π€ SIB supplies the foundation of transformational AI by providing:
β gold-standard training data through curated databases
π connected information through knowledge representation
πͺ trustworthy evaluation through benchmarking.
See how in the #SIBProfile 2025: issuu.com/sibswissinst...
β gold-standard training data through curated databases
π connected information through knowledge representation
πͺ 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... βͺ@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... βͺ@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... βͺ@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... βͺ@panosroussos.bsky.social
* #distinct doi.org/10.1214/22-A... @markrobinsonca.bsky.social
youtu.be/TB9dfKPfns8
Guest Editors:
Mark Robinson, University of Zurich
Fritz Joachim Sedlazeck, Baylor College of Medicine
Hong-Bin Shen, Shanghai Jiao Tong University
Jean Yee Hwa Yang, The University of Sydney
Xin Maizie Zhou, Vanderbilt University
Mark Robinson, University of Zurich
Fritz Joachim Sedlazeck, Baylor College of Medicine
Hong-Bin Shen, Shanghai Jiao Tong University
Jean Yee Hwa Yang, The University of Sydney
Xin Maizie Zhou, Vanderbilt University
April 29, 2025 at 7:08 AM
Guest Editors:
Mark Robinson, University of Zurich
Fritz Joachim Sedlazeck, Baylor College of Medicine
Hong-Bin Shen, Shanghai Jiao Tong University
Jean Yee Hwa Yang, The University of Sydney
Xin Maizie Zhou, Vanderbilt University
Mark Robinson, University of Zurich
Fritz Joachim Sedlazeck, Baylor College of Medicine
Hong-Bin Shen, Shanghai Jiao Tong University
Jean Yee Hwa Yang, The University of Sydney
Xin Maizie Zhou, Vanderbilt University