Thank you @training.ebi.embl.org for putting together an insightful program and bringing in a very diverse group of participants, both in terms of countries and experience levels. I'm leaving with a rich support network who were all readily sharing ideas and solutions.

Ah, here it is. bsky.app/profile/sara...

We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!

Biologist, stop putting UMAP plots in papers! Blogpost here: simplystatistics.org/posts/2024-1...

Interested in learning about the single cell advances? Tune in to this event from SatijaLab. satijalab.org/scgd #SingleCell 🧬🖥️

After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳 www.nature.com/articles/s41... LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space. Some highlights⬇️

🎆4 years in the making! Thrilled to share the 1st spatial single cell aging clock ⏰ www.nature.com/articles/s41... We use #AI + spatial transcriptomics to discover what makes some cells age faster/slower in the brain 🧠 Led by Eric Sun and awesome collaboration w/ @brunetlab.bsky.social🧵

Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools. #GeneExpression #SingleCell #scRNAseq #NAR 🧬 🖥️ academic.oup.com/nar/advance-...

Noor (@noorpratap.bsky.social) has been working on this for quite some time! It took a bit of work to figure out, but now you can map your scATAC-seq reads directly to the genome and sort and dedup them with alevin-fry-atac. You get a BED file with counts ready for downstream analysis! 1/

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8

There’s an open postdoc position in our EIC funded project FIBRE-MATCH at the University of Helsinki, Finland. Further information in the ad. jobs.helsinki.fi/job-invite/3...

That's a cool and trendy way to advertise

New work reveals the impact of anxiety & depression on PhD students. "Anxiety and depression can have a substantially detrimental impact on graduate students’ experiences [..] and likely also contribute to increased time to degree and student attrition." nature.com/articles/s41...

I'm writing up a brief history of the tidyverse? What do you want to know about it? #rstats

I created a starter pack including people working in #bioinformatics core facilities 🧬 🖥️ I am sure I missed a lot of relevant people, so if you'd like to be added or know people who should be in there, let me know! go.bsky.app/LfGCpSX

I was forced to think about a friendlier color scheme during the revision of my first paper. Perhaps, the journals should start emphasizing on adapting color blind friendly color schemes.

For nearly 20 years, I've posted all my teaching slides & materials on my dedicated teaching website Do check it out! If you want to use anything, no need to ask for permission - just use with credit! www.teachepi.org

My panel in London this week on accelerating science with A.I. @deep-mind.bsky.social www.youtube.com/watch?v=QK_U...

A big day of output for the Human Cell Atlas, a global collaborative project with 100 countries to understand our ~37 trillion cells A Wikipedia of our cells, a "remarkable achievement" nature.com/articles/d41... nature.com/immersive/d4...