statistical bioinformatics; canadian/swiss; #methodsmatter #rstats; open science advocate; grumpy towards prestige worshippers, excessive admin and bros.
Joined October 2011
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Interested in benchmarking computational methods in computational biology, generally?
Save the date, submit an abstract, join us next March in Ascona!
Conference website:
sites.google.com/view/ascona…
Please retweet and/or tell your colleagues!
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
1 Dec 2025
📝 A recommendation of this preprint from @GermainPl, Jiayi Wang, and @markrobinsonca
: doi.org/10.1101/2025.04.15.6…
Thank you to the recommender and two reviewers for evaluating this manuscript! 🙌
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
22 Nov 2025
We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor” (OSTA)!
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
14 Oct 2025
Analysis of anatomical multi-cellular structures from spatial omics data using sosta biorxiv.org/content/10.1101/… #biorxiv_bioinfo
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
3 Jul 2025
DESpace2: a novel framework to compare spatial expression patterns between conditions (e.g., healthy vs. diseased), from spatial omics data.
Aim: identifying genes with distinct spatial structures (DSP) between groups of samples.
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Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"):
biomedcentral.com/collection…
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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 R@markrobinsonca@{genomic.social,bsky.social} retweeted
24 Mar 2025
Looking forward to giving my talk on community-driven benchmarking via Open Problems tomorrow at the first Ascona benchmarking meeting. @markrobinsonca really knows how to put on a conference in this beautiful location! Half of my lab came along :).
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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/ascona…
There are few registration slots left, so if you are interested to join us, get in touch.
Interested in benchmarking computational methods in computational biology, generally?
Save the date, submit an abstract, join us next March in Ascona!
Conference website:
sites.google.com/view/ascona…
Please retweet and/or tell your colleagues!
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
5 Dec 2024
Excited to share our work on selecting validation metrics for single-cell and spatial omics! Learn to evaluate embeddings, graphs, clustering, and spatial domains with biological relevance. Discover poem, our R package with new spatially-aware metrics! doi.org/10.1101/2024.11.28.6…
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This is getting exciting. Over 20 abstracts submitted. The committee will be looking at them next week. Looking forward to these discussions.
There is still time to submit (due Monday 18th).
Google form link:
forms.gle/v5FJ21oLcJQokwkd7
Interested in benchmarking computational methods in computational biology, generally?
Save the date, submit an abstract, join us next March in Ascona!
Conference website:
sites.google.com/view/ascona…
Please retweet and/or tell your colleagues!
3
10
1,831
Interested in benchmarking computational methods in computational biology, generally?
Save the date, submit an abstract, join us next March in Ascona!
Conference website:
sites.google.com/view/ascona…
Please retweet and/or tell your colleagues!
1
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Abstract submission and pre-registration is now open:
forms.gle/v5FJ21oLcJQokwkd7
(due November 18th 2024, 6pm, time zone of your choice)
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
21 Sep 2024
biorxiv.org/content/10.1101/…
Nice benchmark of single cell "foundation models" (scGPT, scFoundation) and GEARS (a GNN model) further hyped as "virtual cell models" against linear baselines on perturbation prediction.
Long-story short: they can't beat the linear baselines. 1/
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
21 Sep 2024
Before folks jump to the next level with even bigger, more complex models, can u plz come together with others who have expertise on how to set up benchmarks & baselines to really test whether u r actually making progress? 3/
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
4 Sep 2024
Yes!!!
@EurekaPrizes
@WEHI_research
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
30 Aug 2024
Weekly recap: What I'm reading this week in de-extinction and patent law, ATAC-seq benchmarking, large animal genomes, SV genotyping with long reads, cell type-specific enhancer prediction, AI in biosecurity, blog.stephenturner.us/p/week…
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
18 Aug 2024
New benchmarking study of 8 pipelines and 5 widely used methods for scATAC data analysis..includes embedding, graph and partition-based metrics and useful recommendations by data complexity and downstream tasks. Snakemake workflow: github.com/RoseYuan/sc_chrom… genomebiology.biomedcentral.…
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
19 Jun 2024
*DifferentialRegulation* out in Biostatistics: doi.org/10.1093/biostatistic…
A Bayesian hierarchical method to identify differences in splicing dynamics (i.e. gene regulation) between conditions.
It works on bulk and single-cell RNA-seq.
Also on Bioconductor: bioconductor.org/packages/Di…
18 Aug 2023
DifferentialRegulation pre-print online -> doi.org/10.1101/2023.08.17.5…
*DifferentialRegulation* studies how splicing dynamics change between experimental conditions.
It is based on a Bayesian hierarchical method (multiple samples) with latent states (for multi-mapping reads).
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
21 May 2024
We are #hiring!
Join our Department of Molecular Life Sciences @UZH_en as Assistant Professor #tenuretrack in "BioImaging and Data Analysis"!
jobs.uzh.ch/offene-stellen/a…
Apply until 30th June 2024 at mnf.uzh.ch/bioimaging!
#BioVisionCenter #imageanalysis #computervision #AI #ML
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
16 Mar 2024
Absolutely. To me, Gold OA is one of the most discouraging and wasteful aspects of practising science, propagating enormous inequality, gatekeeping, and Matthew effects.
16 Mar 2024
The "pay to publish model" has been terrible for sci publishing. And no, it was not initially popularized by commercial publishers.
In fact, many publishers, including numerous society ones, would be happy to go back to subs 😅 (with all the problems it also has)
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