Just merged in a nice PR to xsra this morning to increase streaming support with named pipes (FIFO). You can stream your R1/R2 directly to other tools and skip the intermediate write step. It works with both on- and off-disk accessions Give it a shot! github.com/arcInstitute/x…

Thanks to Noam's clean code & Rust's readability, I was able to help Noam integrate this in short order! This is a feature I've long wanted from fastq-dump/fasterq-dump, it took xsra to get it! Stream multiple segments from xsra directly to your downstream preprocessing tools!

CERN Scientists today:

Genomes encode biological complexity, which is determined by combinations of DNA mutations across millions of bases In new Arc Institute work, we report the discovery and engineering of the first programmable DNA recombinases capable of megabase-scale human genome rearrangement

Slides from my talk (with Kamil Jaron) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kmers…

Ten years after Rust 1.0, we need to stop thinking of it as just "systems programming." That label carries historic baggage and scares away teams who could benefit from Rust. corrode.dev/blog/foundatio… #rustlang #rust

Excited to share the Kernel Hub, optimized CUDA kernels, plug-and-play from the Hugging Face Hub. No boilerplate, just speed. huggingface.co/blog/hello-hf-…

0 citations but one can only hope this becomes industry standard for sequencing data biorxiv.org/content/10.110…

Introducing Arc Institute’s first virtual cell model: STATE

Today Arc Institute releases State, our first perturbation prediction AI model and an important step towards our goal of a virtual cell State is designed to learn how to shift cells between states (e.g. “diseased” to “healthy”) using drugs, cytokines, or genetic perturbations

Cells are dynamic, messy and context dependent. Scaling models across diverse states needs flexibility to capture heterogeneity Introducing State, a transformer that predicts perturbation effects by training over sets of cells Team effort led by the unstoppable Abhinav Adduri

Register today for the Virtual Cell Challenge and use AI to solve one of biology’s most complex problems. Announced in Cell, the competition is hosted by Arc Institute and sponsored by NVIDIA, 10x Genomics, and Ultima Genomics.

I use this all the time! Great for quick inspections without loading up a jupyter notebook I actually submitted a PR to uv a while back so the `--with` flag accepts a CSV list so you can run a simple oneliner `uvx --with numpy,polars,seaborn ipython`

Dropped the Virtual Cell Challenge Primer on HF. We are shipping transformers support for STATE (the SOTA model for predicting perturbation response) very soon!

Computing x engineering biology is a playground for systems. Come join us for round three of the SF systems reading group with a focus on biotech. - Noam Teyssier (Arc Institute): BINSEQ: A Family of High Performance Binary Formats for Nucleotide Sequences ​- Aidan Abdullali

writing CUDA kernels is fun. getting them to actually ship is pain. we built kernel-builder so you can skip the pain → huggingface.co/blog/kernel-bu…

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024.0…

I’m super excited to announce our preprint on Transcriptional regulation of disease-relevant microglial activation programs. To determine regulators of microglia activation states, we performed six transcription factor-wide CRISPRi screens. biorxiv.org/content/10.110…