Let’s play a little game. Let’s say that you’re the CSO at a cancer pharma company, and you have to choose a target to go after. Here’s a gene – high expression is associated with poor prognosis in brain cancer. Looks like a good candidate for an inhibitor right?

The recent discourse on t-SNE and UMAP applied to single-cell RNAseq data has distracted from reality: scRNA-seq experiments are complex, costly, and time-consuming projects that ultimately produce a cell type x condition x marker gene table. This distraction enables the

Kicked off my plastics project yesterday and hoping to have something to share next month. Please upvote the things you think we should test: plasticlist.org The main goals are to: (a) test a bunch of California food for various plastic chemicals and report the results,

How do enhancers work over distances that sometimes exceed megabases? Excited to share our work led by Grace Bower where we uncover a unique sequence signature globally associated with long-range enhancer-promoter interactions in developing limb buds: biorxiv.org/content/10.110… 1/

We analyzed all 5734 of the available WGS samples from The Cancer Genome Atlas, and find far, far smaller numbers of microbes than previous reports that appeared (with great fanfare) in nature and Cell. With Yuchen Ge et al biorxiv.org/content/10.110…

1/ We are launching SEAL Leaderboards—private, expert evaluations of leading frontier models. Our design principles: 🔒Private + Unexploitable. No overfitting on evals! 🎓Domain Expert Evals 🏆Continuously Updated w/new Data and Models Read more in 🧵 scale.com/leaderboard

We’re excited to release gReLU (github.com/Genentech/gReLU), a Python package for deep learning on DNA! gReLU covers all major steps in DNA sequence modeling: data processing, training, evaluation, interpretation, variant effect prediction, and ML-guided DNA sequence design. 1/13

Hello to all #bioinformatics #rustlang, I often copy code to generate data when writing tests. After 3 or 4 times, I got fed up and created biotest crates. biotest can generate fasta, fastq and vcf, I'm open to any suggestion, feedback or contribution. github.com/natir/biotest

Check out the marginaleffects.com website re-design. 30 free chapters of tutorials and case studies on how to interpret your statistical models in R and Python. Now with cute illustrations!

Ok academic Twitter: - Without judgment, what is one thing your PI did you admire, and think worked, and one thing they did you thought was not a good idea? Note - there are horror stories, but this one was more about lab policies. But we’re here to listen if you want to share.

Looking for the best color palette? 😔 Check the tool we just created with Joseph: 🎨 2500+ palettes 🐍 Python Library to get them 🔍 Easy-to-use application to find your perfect match python-graph-gallery.com/color-palette-… Feedback welcome, we're working hard on this right now!

🚀 Exciting News! 🚀 We're thrilled to announce that our longitudinal electronic health record (EHR) dataset, EHRSHOT, is now available for download! 🌟 📊 6,738 patients 📅 41.7M events 🩺 921,499 visits Details at: ehrshot.stanford.edu

Have you ever wondered why there are so many subtypes of immune cells? In our work published today at nature, we offer one possible reason – the capacity to evolve. 1/n nature.com/articles/s4158…

People are asking why this is a bad thing to do. Tumors are heterogeneous entities. What makes them different is also what makes them so adaptable, which is what makes them so aggressive. Striping away the differences between patients as "batches" removes valuable biology. Too

Our tutorial on diffusion & flows is out! We made every effort to simplify the math, while still being correct. Hope you enjoy! (Link below -- it's long but is split into 5 mostly-self-contained chapters). lots of fun working with Arwen Bradley Hattie Zhou Madhu Advani on this

Tidyomics offers a software ecosystem for omic data manipulation and analysis. Stefano Mangiola (Hiring!) Michael Love Prof Tony Papenfuss Timothée Keyes, PhD William Hutchison Bioconductor #tidyomics nature.com/articles/s4159…

🧹🤩 #tidyomics made it to Nature Methods! "The tidyomics ecosystem: Enhancing omic data analyses", 👏🏽, William Hutchison, Timothée Keyes, PhD, and Team! 32 researchers | 26 institutes | 10 countries | 4 continents A #crowd/#community-research success nature.com/articles/s4159… CZI Science

Class slides, notes, and problem sets for my Introduction to Data Science class (updated weekly) are publicly available here: datasciencelabs.github.io/2024/

RRG lab is recruiting grad students! Dr. Rachel Roberts-Galbraith is the BEST PI 🤗 Here’s a sneak peek of our totally real and not fabricated lab environment😉