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CellOracle: Dissecting cell identity via network inference and in silico gene perturbation nature.com/articles/s4158…

I'm excited to share that I'll be joining MIT Biology as an Asst Prof. in Jan 2024! Come join us! 🤓🧪🖥️🧬

Check out our latest work on a new algorithm for protein clustering and the discovery of new CRISPR systems! More on this soon. So grateful to have this work published by Science Magazine !

For anyone interested in generating publication-quality secondary structure diagrams from PDB files, SSDraw is available and now published by proteinsociety onlinelibrary.wiley.com/doi/full/10.10…

Is binarization of scATAC-seq data really necessary? The conclusion from our analysis is that a quantitative treatment is in fact beneficial. Now out in Nature Methods! gagneurlab Fabian Theis nature.com/articles/s4159… Many additions since the preprint 👇(1/n)

Dorado v0.5 NCM release 🎉 - new simplex models - faster - higher accuracy - easier to use (auto model selection) - hemi-methylation (duplex mods) - primer & adapter trimming - custom barcodes #nanoporeconf github.com/nanoporetech/d…

We're looking for a PhD student interesting in protein design and tech development. Exciting project interfacing protein VIB_StructuralBiologyBrussels and solid-state nanopores imec. Computational design of hybrid nanopore sensors. Apply by December 15th! imec-int.com/en/work-at-ime…

Expanding protein pore palette beyond biology. Computational design of protein pores with various shapes and sizes. (Potential applications: Nanopore sensing, DNA/Protein sequencing, Custom pores for selective membranes and ligand-gated channels for cellular delivery.....)

We are hiring! Come join us for a PhD in Computational Language Evolution ETH Zürich in Basel D-BSSE, ETH Zurich and the National Research Program on Evolving Language NCCR Evolving Language. We are looking forward to receiving your application jobs.ethz.ch/job/view/JOPG_…

#openposition Exciting opportunity for a #postdoc: be part of the partnership ETH Zurich and Roche and become a Next-Gen Bioengineer > u.ethz.ch/m4Lwj Thanks for sharing!

Beautiful work by the talented Kiera Sumida and Reyes! Their findings on the quantitative tradeoff between seq conservation, designability and function (fig. 3f/g) is particularly insightful, and will be useful for many future protein engineering efforts!

LigandMPNN preprint: biorxiv.org/content/10.110… LigandMPNN inference code + model weights (including ProteinMPNN, SolubleMPNN etc): github.com/dauparas/Ligan…

The commentary I wrote is now live at Nature Biotech: nature.com/articles/s4158… (free version rdcu.be/dwSSy).

Continuous directed evolution is so cool 🥹

I keep on preaching to my lab about the usefulness ChatGPT for coding, but real-life demos might be more effective. A thread on a neural network we quickly developed to classify antibiotics sensitivity 🧵 (1/10)

Short summary thread of our recent review on de novo protein design: (Poster-sized figure (36 x 48 inches) for printing: drive.google.com/file/d/1sG3OlE…)

Super excited to share our paper “Design of amyloidogenic peptide traps” is out now! 🧠 nature.com/articles/s4158… Special thanks to Ewa Andrzejewska , Danny Sahtoe and David Baker