Excited to share Nicheformer! Led by Alejandro Tejada Lapuerta & @AnnaCSchaar, Nicheformer is a foundation model for single-cell & spatial omics. Its innovation is going beyond disassociated analysis to capture & predict local tissue context at single-cell level. biorxiv.org/content/10.110…

Also today (May 8th, 4:30pm at Session 4)! Ask Luca Eyring, Dominik Klein and Théo Uscidda on how to utilize unbalanced optimal transport to handle undesired distribution shifts in unpaired translation tasks! With Giovanni Palla, Niki Kilbertus, Zeynep Akata, and Fabian Theis!

Tomorrow is the last day for the registration for #OME2024! ⏳ openmicroscopy.org/events/ome-com…

🚨Spatial enthousiasts wanted 🚨 You have a passion for spatial omics and you want to work in a thriving research environment? We are looking for a Postdoc, 2 PhD students and a software developer to join our team. Have a look at saeyslab.sites.vib.be/en/jobs #SpatialOmics24

Breaking the fourth wall with our own conference later this year! Especially exciting since it's the first edition. ↘️⬇️↙️ scverse.org/conference2024 ↗️⬆️↖️

What does the future of spatial omics data processing pipelines look like ? Meet Sparrow, our new human-in-the-loop interactive pipeline that facilitates better quality control, improves segmentation and leads to better downstream analysis Lotte Pollaris biorxiv.org/content/10.110…

Do you run functional assays? Wish you could get more results without having to scale? If you’re not using Prophet, you’re leaving potential on the table. (Warning: pitch not tweetorial)

1/8 Happy to share Prophet, done with Yuge Ji and Fabian Theis! We have trained a single model across more than 4.7M public cell experiments to predict phenotypic responses (IC50, Cell Painting morphology features, RNA expression, ...). One single model to predict everything.

Together with AI/ML experts, we explored how virtual cell models can advance scientific discovery. Rooted in community discussions, this 🆕 preprint lays out a roadmap for a large-scale, collaborative research agenda on AI-driven virtual cells bit.ly/3MP3mnx

David was an exceptional mentor during my PhD; I learned so much from him. I highly recommend applying to his lab!

our work on vitessce is out in Nature Methods!

Flexible differential expression analyses have always been neat in CZ #CellxGene. Now they’re next level! Quickly perform DE analysis across our entire data corpus. For ex: leveraging >125 relevant datasets to compare astrocytes with/without Alzheimer’s📷 bit.ly/4eDt9uU

Recently, we held the first #scverse SpatialData 3-day hackathon in Basel (Switzerland), where we brought together 20 developers from the Python, R, and web communities to work on interoperability, performance, and ergonomics for spatial omics data. Here is what we worked on!

We are excited that the Chan Zuckerberg Initiative Billion Cells Project will use our #UG100 sequencer and the 10x Genomics GEM-X tech to develop the largest #singlecell dataset ever. Collaboration and technology meet to accelerate AI in Biology. Learn more: prnewswire.com/news-releases/…

Creating the largest #singlecell dataset ever will take dedication, collaboration & high-performance tools. We’re thrilled the Chan Zuckerberg Initiative Billion Cells Project will pair GEM-X tech w/ Ultima Genomics sequencing to achieve this landmark scale: bit.ly/40Fu5ZW

“The Billion Cells Project will help clarify our understanding of the fundamental biology underpinning human health + disease while supercharging efforts at the intersection of AI & biology.” - Jonah Cool Learn more about the project czi.co/4hBZ5kM

Join our next #ICGEBCapeTown International seminar by Luca Marconato from EMBL Oliver Stegle Lab 📅 25 February 2025 🕛 Noon - SAST 🇿🇦 🔗 email: [email protected] for link to register

💰 Travel Grants Available for scverse conference 2025! 💰 Did you know we are offering grants to help anyone in financial need attend our annual conference? 🌍 🧵 #scverse #scverse2025 #SingleCell #Conference #StanfordUniversity #TravelGrant

Applications for Microsoft Research undergrad research internships for rising juniors and seniors are due Monday Oct 6! Apply to work with us in BioML 👉 aka.ms/msr-ugrad w/ Kevin K. Yang 楊凱筌, Alex Lu, Lorin Crawford, Kristen Severson, Neil Tenenholtz, Sarah Alamdari, and more!

Are you a PhD student interested in machine learning and biology or health? Come do an internship with me, Ava Amini, Alex Lu, Lorin Crawford, or Kristen Severson at @msrne! Applications are due Dec 1: make sure you include a research statement! jobs.careers.microsoft.com/global/en/job/…