🔥The 9th Round of Easy Loan, Earn $40 Reward is in progress❗️ ⏰ Promotion Period: January 15th - Feburary 15th, 2025 👉 Register now and check more details at gate.io/campaigns/358

"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-toxic-…

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.

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/ne…

Absolutely. To me, Gold OA is one of the most discouraging and wasteful aspects of practising science, propagating enormous inequality, gatekeeping, and Matthew effects.

We are #hiring! Join our Department of Molecular Life Sciences University of Zurich as Assistant Professor #tenuretrack in "BioImaging and Data Analysis"! jobs.uzh.ch/offene-stellen… Apply until 30th June 2024 at mnf.uzh.ch/bioimaging! #BioVisionCenter #imageanalysis #computervision #AI #ML

*DifferentialRegulation* out in Biostatistics: doi.org/10.1093/biosta… 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/Diffe…

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_ch… genomebiology.biomedcentral.com/articles/10.11…

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/weekly-recap…

Yes!!! @EurekaPrizes WEHI (Walter and Eliza Hall Institute)

biorxiv.org/content/10.110… 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/

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/

Come join us for a 1w SIB spatial omics workshop in beautiful Lausanne 🇨🇭 > t.ly/ilpUr < featuring Lars Borm Ahmed Mahfouz Mark R@markrobinsonca@{genomic.social,bsky.social} Yvan Saeys Rasool Saghaleyni @AnnaCSchaar Marco Varrone & more - deadline: Nov 1st.

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/v5FJ21oLcJQokw…

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/10.1101/2024.1…

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/ascona202… There are few registration slots left, so if you are interested to join us, get in touch.

Looking forward to giving my talk on community-driven benchmarking via Open Problems tomorrow at the first Ascona benchmarking meeting. Mark R@markrobinsonca@{genomic.social,bsky.social} really knows how to put on a conference in this beautiful location! Half of my lab came along :).