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Imran S. Haque Profile picture
Imran S. Haque
@ImranSHaque
VP DataSci @RecursionPharma;ex-Freenome(CSO), Counsyl(VP Sci Aff), Stanford(PhD), forever Cal 🐻. Tweets my own, except when RTs; those prob someone else's!
Apr 26, 2023 • 10 tweets • 8 min read
More tweetorial! Let’s dig into the “proximity bias” we found @RecursionPharma confounding #CRISPR screens, what it means, and where it comes from.

You can always read along in the preprint here: biorxiv.org/content/10.110… Image If you missed the first tweetorial in the series, click here to understand what the red-and-blue heatmaps here mean, and how we use them to map the functions of genes at a genome-wide level:
Apr 25, 2023 • 10 tweets • 5 min read
Tweetorial time! We @RecursionPharma mapped consequences of #CRISPR screening of >17K human genes, found a systematic bias confounding all CRISPR screens, traced its molecular cause, and propose a debiasing algorithm. Image “But Imran,” you say, “I’d rather read your thrilling 41-page manuscript than read tweet threads!”

I can’t blame you, it’s great! (I may be a biased source.) Here ya go: biorxiv.org/content/10.110…
Aug 10, 2020 • 20 tweets • 8 min read
Happy Monday! In today's #tweetorial on our recent preprint describing @RecursionPharma's platform (biorxiv.org/content/10.110…), I'll explain the unusual 2-D drug response plots we use there and in our COVID-19 screen data at covid19.rxrx.ai..

in terms of jumping cat gifs. A primer: the @RecursionPharma platform takes images of cells under different conditions (disease agent, disease+drug, control, etc.), and feeds the images through a custom deep network to derive a high-dimensional (128-1024D) "embedding".
Apr 26, 2020 • 23 tweets • 11 min read
Very proud to be part of the team @RecursionPharma working on #Covid_19 and of our preprint today: biorxiv.org/content/10.110…. Brief #tweetorial :

We developed a human cell model of SARS-CoV-2 infection, compared it to the field-standard monkey cell model, and screened ~1700 drugs. Also: the entire cellular image dataset (~450GB of 5-channel microscopy) is available at rxrx.ai/rxrx19. 305,520 5-ch pics @ 1Mpx licensed CC-BY. Want some big image data for ML to help with the pandemic? Here it is. We've also released the DL image embeddings.