How do >1600 transcription factors (TFs) bind across hundreds of cell types? Experimentally profiling every combination isn't practically doable. But relying on DNA motifs isn't a great alternative -- they lack both sensitivity and specificity. #Genomics #GeneRegulation 👇

The program is up for the first 1st Interdisciplinary Symposium on Meta Science for Methods Research and it promises to be a BANGER! crsuzh.pages.uzh.ch/msmr/program/

Check out the great program of the *1st Interdisciplinary Symposium on Meta Science for Methods Research* organized 31 August and 1 September in Zürich! Ton of cool speakers and meta-methodological reseach! crsuzh.pages.uzh.ch/msmr/program/ (registration still open)

This was a fun effort from our lab retreat (!) to recreate a "arms-length" benchmark (i.e., one that someone else created) using our Omnibenchmark framework. We all learned a lot in the process ..

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 3mo ago

Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation https://www.biorxiv.org/content/10.64898/2026.05.01.722166v1

Still ~3 days left to submit an abstract to MSMR (Meta Science for Methods Research) 2026 in Zurich .. scicomm.xyz/@SamuelPawel... crsuzh.pages.uzh.ch/msmr/ Come join us and discuss how quantitative/computational methods are developed, evaluated (benchmarked!) ..

We are excited to share our latest preprint on spatialFDA, a method for the statistical analysis of spatial omics data. bioconductor.org/packages/3.2...

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 4mo ago

Differential co-localisation analysis of multi-sample and multi-condition experiments with spatialFDA https://www.biorxiv.org/content/10.64898/2026.04.13.718197v1

scprocess is the result of an *unbelievable* amount of hard work by Maruša Koderman, PhD at University of Zürich co-supervised by me and @markrobinsonca.bsky.social. Maruša did so much: ideas, writing so much code, testing and debugging, writing all of the docs, tolerating me changing my mind... 🙈

😅 We are also excited to be presenting a Omnibenchmark workshop at ECCB in Geneva in Aug/Sept .. eccb2026.org/tutorials-wo...

Mark Robinson@markrobinsonca.bsky.social · 6mo ago

So, this should be quite interesting! We just posted a BIG update to our Omnibenchmark "framework", basically a software layer to help you manage, build, standardize, and orchestrate reproducible and extensible (computational method) benchmarks .. (quite a mouthful) .. arxiv.org/abs/2409.17038

So, this should be quite interesting! We just posted a BIG update to our Omnibenchmark "framework", basically a software layer to help you manage, build, standardize, and orchestrate reproducible and extensible (computational method) benchmarks .. (quite a mouthful) .. arxiv.org/abs/2409.17038

Omnibenchmark: transparent, reproducible, extensible and standardized orchestration of solo and collaborative benchmarks

Benchmarking involves designing, running and disseminating rigorous performance assessments of methods, most often for data analysis and software tools, but the process can also be applied to experime...

arxiv.org

"Bulk RNA-seq to the rescue of differential expression analysis in single-cell transcriptomics" 🧫 📑 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 is…

doi.org

Orchestrating Spatial Transcriptomics Analysis with Bioconductor (including interoperability with Python) Paper: www.biorxiv.org/content/10.1... Book: bioconductor.org/books/OSTA/ #Rstats

Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA. Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions). It’s been a joy working with you @estellayixingdong.bsky.social!

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 9mo ago

Orchestrating Spatial Transcriptomics Analysis with Bioconductor https://www.biorxiv.org/content/10.1101/2025.11.20.688607v1

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

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...

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

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

DESpace2: detection of differential spatial patterns in spatial omics data. #SpatialOmics #DifferentialSpatialPatterns #scRNAseq #Genomics #Bioinformatics @biorxivpreprint.bsky.social 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…

biorxiv.org

🧬 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

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...

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 10mo ago

Analysis of anatomical multi-cellular structures from spatial omics data using sosta https://www.biorxiv.org/content/10.1101/2025.10.13.682065v1

Analysis of anatomical multi-cellular structures from spatial omics data using sosta https://www.biorxiv.org/content/10.1101/2025.10.13.682065v1

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

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

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

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

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

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

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...

biorxiv.org

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...

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