statistical bioinformatics; canadian/swiss; #methodsmatter #rstats; open science advocate; grumpy towards prestige worshippers, excessive admin and bros.
Zurich, CH
Joined October 2011
- Tweets2.6K
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Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
📝 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! 🙌
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor” (OSTA)!
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
Analysis of anatomical multi-cellular structures from spatial omics data using sosta biorxiv.org/content/10.1101/… #biorxiv_bioinfo
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
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 :).
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
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…
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
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/
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
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/
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
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…
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
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.…
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
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
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
Absolutely. To me, Gold OA is one of the most discouraging and wasteful aspects of practising science, propagating enormous inequality, gatekeeping, and Matthew effects.
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
UZH has decided to withdraw from the Times Higher Education World University Ranking. The ranking is not able to reflect the wide range of activities in teaching and research undertaken by universities. news.uzh.ch/en/articles/news…
ALT UZH main building
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
"In some labs, the culture fosters a dynamic where students who produce desired results are favored, regardless of quality of the work or even research integrity" kamounlab.medium.com/whats-a…
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
Want a simple rule? Does the lab judge its success by where it publishes? Does it consider a Science, Cell or Nature paper to be the highest accomplishment? If so, it's not serious about doing science right. You should join a lab that's fighting the system, not playing in it.
"In some labs, the culture fosters a dynamic where students who produce desired results are favored, regardless of quality of the work or even research integrity" kamounlab.medium.com/whats-a…
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
If you want to check out Oarfish and other isoform quantification tools for @PacBio Kinnex RNA data here’s the webinar link
programs.pacb.com/l/1652/202… – at San Francisco, CA
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
The statement is so silly I felt I should not only disagree privately but also publicly. Being highly cited now has next to nothing to do with having carried out robust, rigorous science in the last 10yrs that will turn out to have made an important contribution in 10yrs.
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
this would be funnier if it weren't so common
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
Publication by the Allain, Panse & @markrobinsonca Labs w/ 1st authors Ahmed Moursy & @AcleryClery "#RNA recognition by Npl3p reveals U2 snRNA-binding compatible with a chaperone role during #splicing" @NatureComms
bit.ly/3NAKERp
#NMR #NMRchat
@Seb_Campagne @DrDuszczyk
Mark R@markrobinsonca@{genomic.social,bsky.social} retweeted
I just published: Scientists, have we lost the plot?
Open science and transparency serve as antidotes to the epidemic of flawed and fraudulent research. And the journey toward open science begins with preprinting.
#academicchatter #Phdchat
link.medium.com/G7LEQjmDKEb
