The 1+Million Genomes Minimal Dataset for Cancer

nature.com/articles/s4158…

'I can't believe I have to let go of another senior person. It's painful! What will the board say? What will happen to the stock? It will kill the morale. I don't do medicine here; I only deal with people.'

A few thoughts on breakups:

It's painful to let go of a senior member

Thanks Angelos Georgakis! Optimism is a CEO “superpower.” For me, it was a gift from my mother.

As she would say quoting the Ray Stevens song… “Everything is Beautiful!”

Layoff tracker: Mapping the close to 15,200 biotech and pharma layoffs in the first half of 2024 drugdiscoverytrends.com/mapping-2024-b…

I've used this and it's great!
Annotation of single cell T cells

Thanks Dylan Kotliar Soumya Raychaudhuri সৌম্য রায়চৌধুরী and team.

cc Ming "Tommy" Tang Amy Zhao Naftali Kaminski #singlcell

Accurate structure prediction of biomolecular interactions with AlphaFold 3 nature.com/articles/s4158… We used AlphaFold multimer to screen protein-protein interactions and it did not work well. Curious to see how AlphaFold3 performs.

Enjoy this tweet? follow me Ming "Tommy" Tang and join my newsletter to learn computational biology divingintogeneticsandgenomics.ck.page/newsletter

Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci | Genome Biology | Full Text genomebiology.biomedcentral.com/articles/10.11…

Robust differential expression testing for single-cell CRISPR screens at low multiplicity of infection | Genome Biology | Full Text genomebiology.biomedcentral.com/articles/10.11…

Our new study is now out in Nature Medicine! We introduce DEPLOY, a deep-learning model that enhances the diagnosis of CNS tumor subtypes. DEPLOY predicts methylation profiles from H&E slide images for classification. #CancerResearch #AI #DeepLearning shorturl.at/gjCOR 1/n

7/Watch a full video I made with real example on how to do GSEA in R with RNAseq data youtube.com/watch?v=IKCDQE… Do not forget to subscribe to the chatomics channel. Happy learning!

1/ When I was a beginner, I did not understand the difference between gene set over-representation analysis versus gene set enrichment analysis 🧵 to explain it 👇

Instrumentation at the Leading Edge of Proteomics pubs.acs.org/doi/10.1021/ac…

Dylan Kotliar It works really well- very user-friendly.

I'm having huge issues separating CD4 and CD8 T cells tho....and 0.8% are double positive.

Do we really believe that double positive CD4/CD8 exist?? (there is literature on this). How do we handle them?

Amy Zhao Ming "Tommy" Tang

*CAT seamlessly annotates continuous cGEPs and discrete labels for subset, activation, and more. Reach out if you want to make a catalog for other cell types or tissue. Our package makes it easy to use multiple reference catalogs in Python or R. github.com/immunogenomics…

11/12

Identification of hypoxic macrophages in glioblastoma with therapeutic potential for vasculature normalization dlvr.it/T72MJD

It's been a big week! What I'm reading this week in bioinformatics, synthetic biology, single cell omics, population genetics, microbial genomics, … 🧬🖥️🧵

Insanity is trying the same things repeatedly, even if things don't work out.

If your team isn't giving you feedback when you ask for it, it's time to switch things up.

One of my CEO clients (let's call him Jeff) tried to solve this problem. As the CEO with close to 1000