Siva

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 🧬🖥️

Overview of the LEMUR steps: (1) subspace alignment, (2) differential expression, (3) DE neighborhoods, (4) pseudobulking.

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 Abstract. Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integ

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/

High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...

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....
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Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome Postdoctoral Researcher in Bioinformatics of the Human Gut Microbiome

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

Generating a scRNA-seq count matrix with simpleaf Simpleaf is a command line toolkit written in rust that exposes a unified and simplified interface for processing scRNA-seq datasets using the alevin-fry pipeline. It encapsulates the whole alevin-fry...

While it's a limiting step, you can simply add your collaborator in cc and you would get access.

I have never tried it on parse data, but Simpleaf could be an option combine-lab.github.io/alevin-fry-t...

YouTube video by Google DeepMind Science in the Age of AI | AI for Science Forum

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...