Mark Robinson

MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments https://www.biorxiv.org/content/10.1101/2025.07.08.663623v1

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...

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

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...

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...

DESpace2: detection of differential spatial patterns in spatial omics data https://www.biorxiv.org/content/10.1101/2025.06.30.662268v1

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...

🤖 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...

YouTube video by Leonardo Collado Torres [2025-06-11] Pseudobulk DGE statistical methods journal club

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

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

Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"):
www.biomedcentral.com/collections/...

Many Analysts, One Data Set: Making Transparent How Variations in Analytic Choices Affect Results - R. Silberzahn, E. L. Uhlmann, D. P. Martin, P. Anselmi, F. Aust, E. Awtrey, Š. Bahník, F. Bai, C. Ba... Twenty-nine teams involving 61 analysts used the same data set to address the same research question: whether soccer referees are more likely to give red cards ...

@jeffmold.bsky.social @willmacnair.bsky.social would be very interesting indeed. Here is the classic study doing something along these lines (not in genomics):
journals.sagepub.com/doi/10.1177/...

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...

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...

Eleven quick tips for writing a Bioconductor package

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...

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.

CSAMA 2025 flyer

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!

We look forward your feedback!

As @siyuanluo.bsky.social said, feedback is welcome.

for spatial omics data, we should really think about using SPATIALLY-AWARE METRICS, e.g., for evaluating domain detection! For example, when clustering into domains, it's probably fine to give less weight to boundaries. We provide some spatially-aware and some nice toy examples!

There are several gems in there (e.g., you should look at scores on embeddings or graphs of your single cell data! not just partition-based metrics), but also ..

Another preprint from our group this week .. see @siyuanluo.bsky.social's explainer below ..

source: https://www.biorxiv.org/content/10.1101/2024.01.21.576131v2.full Figure 2: The edgeR workflow. The diagram shows the main steps in an edgeR analysis. Individual functions involved in each step are shown on the right.

edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. #EdgeR #DifferentialAnalysis #Bioinformatics #Genomics @biorxivpreprint.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...

A little piece that's been in the works with former MSc, now PhD student, Jiayi Wang & @markrobinsonca.bsky.social in the multi-sample/-condition/-subpopulation theme: ...

Another fresh preprint from our group about spatial statistics for spatial omics data .. @samuelgunz.bsky.social gives a nice explainer below.

pasta: Pattern Analysis for Spatial Omics Data 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...

Interested in spatial statistics for spatial omics data? Check out our new resource: pasta.

We show how different technologies lead to different data modalities give and overview of point-pattern and lattice-based spatial analysis. Feedback welcome!

arxiv.org/abs/2412.01561

Thread below from @helucro.bsky.social on a new preprint from us .. trying to separate "type" from "state" genes at the feature selection step ..

2. The reviewer culture makes it difficult to get funding for proposals that are genuinely high risk: where little of the work has been done in advance. But also proposals that are meaningfully low risk: the benchmarking and maintenance of important tools.

so one last call .. abstracts due today (6pm, time zone of your choice 😀) ..

Ascona, Switzerland in March 2025 .. conference about all things benchmarking:
sites.google.com/view/ascona2...

Abstract submission link:
t.co/zGGZ9Xd60E

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...

Deadline for abstracts for this exciting meeting on benchmarking in computational biology is this Monday @markrobinsonca.bsky.social @SIB.mstdn.science.ap.brid.gy
sites.google.com/view/ascona2...
#bioinformatics #ComputationalBiology