shantanu-singh.cc - Profile | ThreadSky | a Reddit-style client for Bluesky

This is a room where we turn very modest salaries and budgets (and lots of coffee) into new knowledge, life-saving innovations, and technology that feeds business growth. It's literally the loom that spins hay into gold but these numpties are suddenly worried about the cost of hay.

submitted 20 days ago • 240 comments

Our paper “A genome-wide atlas of human cell morphology” is finally out today in @naturemethods.bsky.social ! www.nature.com/articles/s41... (I tweeted about our preprint in 2023 over at the bad place, but deactivated my account, so here we go again!)

submitted 35 days ago • 2 comments

🧪 Summer internship alert, Feb 7 deadline New URL: hsph.harvard.edu/fellowship-s... (+ @harvardchanschool.bsky.social is now on 🦋!)

submitted 54 days ago • 0 comments

Hey #StatsSky, what are you favorite papers to cite when you need to justify something that is obvious (I once had a reviewer ask we justify the use of logistic regression on a binary outcome) or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?

submitted 56 days ago • 68 comments

I don't think it's widely clear to the #RadiologyAI community just how poorly GPT-4V compares with the top report generation models on chest X-rays, like MedVersa or MAIRA-2. It's clear we need a way to track progress.

submitted 74 days ago • 1 comment

Instead of listing my publications, as the year draws to an end, I want to shine the spotlight on the commonplace assumption that productivity must always increase. Good research is disruptive and thinking time is central to high quality scholarship and necessary for disruptive research.

submitted 73 days ago • 21 comments

Taking pictures of cells with a microscope, then extracting thousands of features from them is uncannily effective for quantifying cell state, esp. for genes and chemicals (e.g., Cell Painting). But we often average the rich single-cell data to simplify analysis. Can we do better? #bioML 🧪 1/n

submitted 73 days ago • 1 comment

True luxury is found in the simplest moments.

submitted 74 days ago • 433 comments

“The climate crisis that is coming our way is not just about polar bears, and it’s not just about green jobs,” Mr. Whitehouse said. “It actually is coming through your mail slot, in the form of insurance cancellations, insurance nonrenewals and dramatic increases in insurance costs.” Gift link:

submitted 74 days ago • 11 comments

🧪 So proud of this work by the dream team of @johnarevalo.bsky.social and Ellen Su: a new graph dataset for predicting drug-target interactions, using information from Cell Painting. Stop by their poster in a few hours @ #NeurIPS! (details below) PS: John is on the job market 🚀 #bioML #MLSky

submitted 79 days ago • 0 comments

🎉 I'm starting my own lab at EMBL-EBI (Cambridge, UK; June 2025) 🎉 We will focus on identifying and characterizing chemical hazards to humans and ecosystems using computational biology methods. I am beginning the search for two postdocs now - stay tuned for more details! ewaldlab.org

submitted 80 days ago • 9 comments

Excited to present our spotlight paper at #NeurIPS! MOTIVE is a new dataset + benchmark for predicting drug-target interactions, using Cell Painting data Location: Fri 13 Dec 4:30 p.m. PST @ East Exhibit Hall A-C #4208 Poster: neurips.cc/virtual/2024... Paper: arxiv.org/abs/2406.08649

submitted 80 days ago • 0 comments

Related: Specialized Foundation Models Struggle to Beat Supervised Baselines arxiv.org/abs/2411.02796

submitted 81 days ago • 0 comments

Please join me in contributing to this worthy researcher's work (& support solar energy at the same time!)

submitted 81 days ago • 0 comments

A little fun with numbers on this Sunday, showing just how successful DNA really is. First, here's what DNA looks like. I'll draw your attention to the "rise" in DNA, that is, the distance between two basepairs, which is 3.4 Angstroms, also known as 3.4x10^-10 meters...

submitted 84 days ago • 4 comments

Now on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months www.biorxiv.org/content/10.1...

submitted 89 days ago • 1 comment

This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/

submitted 89 days ago • 9 comments

Reposting two starter packs with researchers working on AI4Science for those who are newly joining 🦋. So many wonderful folks on these lists, help me add more by sending names (including your own 😊). Starter Pack 2: go.bsky.app/GnFTUM6 Starter Pack 1: go.bsky.app/JeFdryY

submitted 90 days ago • 18 comments

Three BioML starter packs now! Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc Pack 3: go.bsky.app/NAKYUok DM if you want to be included (or nominate people who should be!)

submitted 90 days ago • 15 comments

My #I2K204 workshop is admittedly pretty specific, but if you're interested in accessing Cell Painting data on the Cell Painting Gallery, hopefully you find it helpful! Up on YouTube now. www.youtube.com/watch?v=ikzP... Thanks @bioimagingna.bsky.social for getting all the sessions up on YouTube!

submitted 96 days ago • 0 comments

PCPs on #MedSky must share this clear, compelling data with their >65 yo patients: getting last year’s COVID shot made you about 2.5 times less likely to end up in the hospital and 4 times less likely to die from COVID last winter—even if you’d had all the earlier shots and COVID before.

submitted 102 days ago • 0 comments

This is very interesting and highly relevant paper to clinical genetics and rare disease researchers. I wrote the accompanying News & Views piece. Free sharing link here: rdcu.be/d0VlK

submitted 102 days ago • 3 comments

One full year to get ready: join us next year in Berlin-Buch if you're into spatial biology, morphology and/or high-content perturbation screens! 🔬💻 #CytoData #Microscopy #ImageBasedProfiling

submitted 103 days ago • 1 comment

I must admit that this annotated Nature abstract remains a useful recipe for constructing a summary paragraph. I show it to my students every time we get started.

submitted 104 days ago • 13 comments

A delightful thread on the follow-up to the U-turn on double descent paper, extending explanations to neural network learning Context: 1. Seminal article on double descent arxiv.org/abs/2105.14368 2. U-turn paper, which ~demystified double descent (but not for NNs) arxiv.org/abs/2310.18988

submitted 104 days ago • 1 comment