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Reposted by Mark Robinson

Ana Conesa @anaconesa.bsky.social · 6d

Looking for scientists working with long-read transcriptomics technologies to join a COST action proposal. Contact us!!! @nanoporetech.com @pacbio.bsky.social

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Mark Robinson @markrobinsonca.bsky.social · 8d

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.

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Reposted by Mark Robinson

Wolfgang Huber @wkhuber.bsky.social · 20d

Martin Emons on SpatialFDA - searching for differential colocalization in spatial omics data

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Reposted by Mark Robinson

Bioconductor @bioconductor.bsky.social · 20d

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

EuroBioC2025 group photo on PRBB terrace with sea in background.

EuroBioC2025 welcome in PRBB auditorium by host Robert Castelo, showing slides with conference sticker and sponsor logos.

EuroBioC2025 hexwall banner with the hexwall creator Kevin Rue-Albrecht standing beside it.

EuroBioC2025 carved wooden keyring, a gift for all participants, created by Annekathrin Nedwed.

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Reposted by Mark Robinson

Martin Emons @martinemons.bsky.social · 27d

We are excited to share the publication of our paper on exploratory spatial statistics for spatial omics data

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

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Reposted by Mark Robinson

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 12

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

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Reposted by Mark Robinson

Martin Emons @martinemons.bsky.social · Jun 27

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

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

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Reposted by Mark Robinson

Nav @naveed-ishaque.bsky.social · Jul 2

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...

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

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Reposted by Mark Robinson

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 2

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

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Reposted by Mark Robinson

Javier Santoyo @jsantoyo.bsky.social · Jul 1

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...

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Reposted by Mark Robinson

SIB Swiss Institute of Bioinformatics @sib.swiss · Jul 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...

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Reposted by Mark Robinson

🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Jun 12

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

[2025-06-11] Pseudobulk DGE statistical methods journal club

YouTube video by Leonardo Collado Torres

youtu.be

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Mark Robinson @markrobinsonca.bsky.social · Apr 29

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

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Mark Robinson @markrobinsonca.bsky.social · Apr 29

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

Call for papers - Benchmarks v2.0

www.biomedcentral.com

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Mark Robinson @markrobinsonca.bsky.social · Mar 24

@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/...

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 ...

journals.sagepub.com

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Reposted by Mark Robinson

Ana Conesa @anaconesa.bsky.social · Mar 24

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

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Reposted by Mark Robinson

BF Francis Ouellette @bffo.bsky.social · Mar 20

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...

Eleven quick tips for writing a Bioconductor package

journals.plos.org

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Mark Robinson @markrobinsonca.bsky.social · Mar 5

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.

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Reposted by Mark Robinson

Davide Risso @davi1893.bsky.social · Jan 27

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!

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Reposted by Mark Robinson

Neuron @cp-neuron.bsky.social · Dec 20

snRNA-seq stratifies multiple sclerosis patients into distinct white matter glial responses

Macnair and Calini et al. analyze 632,000 snRNA-seq profiles from multiple sclerosis and control brain samples, identifying distinct cellular responses in white and gray matter. They stratify MS patients into groups based on patterns of gene expression in…

dlvr.it

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Mark Robinson @markrobinsonca.bsky.social · Dec 5

We look forward your feedback!

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Mark Robinson @markrobinsonca.bsky.social · Dec 5

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

Mark Robinson @markrobinsonca.bsky.social · Dec 5

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!

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Mark Robinson @markrobinsonca.bsky.social · Dec 5

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 ..

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Mark Robinson @markrobinsonca.bsky.social · Dec 5

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

Siyuan Luo @siyuanluo.bsky.social · Dec 5

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...

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

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