I’m beyond excited to share work from my PhD, co-led with Alicia Braxton, out today in Nature! We used CODA to map the anatomic and genomic properties of pancreatic cancer precursors. Led by the amazing Laura DeLong Wood and Denis Wirtz ! nature.com/articles/s4158…

Today, May 12, is Mother’s Day. A special mother and brilliant mathematician was also born today: Maryam Mirzakhani, the first female Fields medalist (and to date, one of only two female Fields medalists). In her honor, her birthday, which is on May 12, is now celebrated as Women

Severin, Isaac Virshup, Ilan Gold and Felix teamed up at the #OpenHackathons in Görlitz, hosted by @casusscience with NVIDIA & HZDR support. They advanced a multi-GPU rapids-singlecell project, propelling bioinformatics innovation. Stay tuned for more with OpenACC!

I'm super happy to see part of our lab's work out this week in Cell Systems. Emily Laubscher's work presents a compelling, deep learning-based solution for image-based spatial transcriptomics. cell.com/cell-systems/f…

Truly happy to see this out NEJM - translational work from Tobias B. Huber and my lab on autoantibodies in nephrotic syndrome with first author Felicitas Hengel. Big thanks to @pi_ronco Markus Rinschen Moritz Lassé and all other collaborators! UKE Hamburg

We are looking for an Xarray community developer to work at Earthmover to focus on building connections, both technical and social, between the Xarray project and the biomedical research community. jobs.gusto.com/postings/earth…

The end of an era! The PhD is now gone but everything I’ve learned and the people I’ve met will stay! What a nice reflection moment of the past years. I would do it all over again, alongside Lars Juhl Jensen. Thank you for everything!

Our scverse zulip chat recently crossed 500 members. It's super cool to have so many developers and users in one place to discuss how to best move forward with all things scverse. Please consider joining: scverse.zulipchat.com

i am so excited about our open source inexpensive, sub-cellular capture, do-it-yourself Open-ST that transforms tissues into virtual tissue blocks in 3D - IDing pathways & gene programs driving phenotypes. a huge congratz to the team! cell.com/cell/abstract/…

🌟 Join me at #Scverse2024 for the "GPU-Accelerated Single-Cell Analysis with rapids-singlecell" workshop! 📍 Munich, Germany 🗓️ Sept 10-12 Don't miss out! Register now: [scverse.org/conference2024/] Explore the toolkit: [github.com/scverse/rapids…] scverse

So proud of my intern Rotem Shalita for her work at the #AiHub on deciphering T cell homing signatures for optimized CAR T cell engineering for neurodegeneration!

Systematic comparison of sequencing-based spatial transcriptomic methods | Nature Methods nature.com/articles/s4159…

Somatic mutation tracing with single-cell data is a fairly niche but growing field. We can learn more from each other via open analyses and direct communication than waiting for published papers and journal peer reviews. Let’s make it happen. 8/n

I'm stoked to announce our new end-to-end framework for perturbation analysis! Our scverse advisory committee highlighted that a maintained and well-documented framework for perturbation analysis is missing. Pertpy is our attempt to satisfy this request biorxiv.org/content/10.110…

Earlier this week we carried out a preliminary analysis of our first 10x Genomics Xenium prime (5,000 gene) run. We had designed this experiment to get a sense of how the prime chemistry performed compared to the Xenium V1 chemistry.

First conference, first selfie with some of the incredible scverse core and volunteers! Feeling so grateful to be part of this amazing community pushing the boundaries of single cell analysis. 🖤🤍 #scverse2024

The first scverse community survey is LIVE!📋🐍🧑‍💻 Do you use or contribute to scverse tools for omics analysis? Your feedback will help us improve support resources and shape future community initiatives and events. Fill out the survey before Oct 15th 👉forms.gle/cJpTFJLkQ6SBsq…

Big thanks to Luke Zappia for being part of the first-ever #scverse2024 conference and for the amazing summary and sketchnotes! 🙌 It's always a pleasure to see charismatic people with even more charisma! Check out his fantastic summary here: lazappi.id.au/posts/2024-09-…

Excited to share our work on a new spatial-lineage platform for tumor evolution analysis led by very talented postdocs Matt Jones & Sun_Dawei. A great collaboration with Jonathan Weissman's Lab Fei Chen Lab Yosef Lab. ❗️Matt is on the job market and he will be a wonderful colleague to have

Important topic, but this is more of a quick-start guide. For cutting-edge research on LLM evals, see these papers using Prediction-Powered Inference to incorporate synthetic data and model predictions for narrower CIs. 👇 Gemini already knows about them!