This issue has relevant content for #SingleCell data science: new foundation models, scGPT and scFoundation, GPT-4 for cell-type annotations (see N&V by Mo Lotfollahi), transformers, integration of datasets across species, variational autoencoders+biophysical models, and more!

📢 PHD STUDENTSHIPS - Applications are open worldwide for our 2024 #PhD programme at the Earlham Institute, as part of the NRPDTP. Find out more and apply at: okt.to/Sc29nN #findaphd #PhDChat UEA Norwich Research Park

Reminder! Today at 18:00 CET will be the last community meeting of the year! Lukas Heumos will talk about about pertpy, a Python-based modular framework for the analysis of large-scale perturbation single-cell experiments. Zoom link can be found here: scverse.zulipchat.com/#narrow/channe…

📢 Calling group leaders in the life sciences! We're collecting examples of successful job application materials for a workshop for postdocs applying to academic roles. Interested in sharing your materials? Drop us a line at [email protected] & we'll send you further info.

In this student-requested video, I demo the process of making a high quality publication-ready figure (from making a mockup to enhancing visual similarity in Illustrator) and narrate my general process. Follow along 📽️: youtube.com/watch?v=L9qo2X… #phdlife #AcademicTwitter #dataviz

Don’t miss: 🤖 Julio Saez-Rodriguez discussing machine learning for multi-omics data analysis 🔗 Evangelia Petsalaki on network-based approaches to integrate multi-omics data #FoG2025

New preprint from our group EMBL-EBI and the TVPLab ! We combined pseudotemporal ordering of cross sectional MASLD patient data with network analysis to describe the disease progression and identify a signature of 24 plasma biomarkers for patient staging biorxiv.org/content/10.110…

Check out the new preprint from Evangelia Petsalaki group and TVPLab on MASLD progression! Very grateful to have contributed to this amazing collaboration. More on the thread below ⬇️

The bioinformatics arm of the Functional Genomics Team and Expression Atlas will participate in the nf-core #hackathon at the Wellcome Genome Campus Campus Check out our challenge and join us, everyone is welcome! EMBL-EBI Wellcome Sanger Institute #nextflow #singlecell

A pre-trained SCVI model of our Tahoe-100M cell atlas is now available as a HubModel! It can be used for gene expression visualization, differential expression, or cell clustering. Available at Hugging Face with instructions on how to load it (see thread)

1/9 New preprint out! 🍳 Our team at @EMBL, DKFZ, and Memorial Sloan Kettering Cancer Center built #segger—a fast, accurate cell segmentation tool for ST. It’s a transcript-to-cell link predictor that matches transcripts to their cell origins in a snap!

Introducing SAVANA, a tool to detect somatic structural variants and copy number aberrations from long-read sequencing data with high sensitivity and specificity. nature.com/articles/s4159…

🔧 decoupler 2.0.6 is out thanks to Pau Badia i Mompel, now as a core scverse package scverse.org This release includes a streamlined API aligned with scverse standards, updated vignettes, and a new one on pseudotime enrichment analysis 👇 decoupler.readthedocs.io/en/latest/

My group, Rahuman Sheriff biomodels and Ellie McDonagh Open Targets EMBL-EBI are looking for an enthusiastic postdoc with skills in modelling to create Digital Twins for rare disease (CZI-funded). Exciting opportunity at the forefront of network biology, multiomics, AI and DT

CellMarker 2.0 An updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data http://117.50.127.228/CellMarker/index.html A nice resource for cell type markers for supervised clustering😁 Nucleic Acids Res 2023 academic.oup.com/nar/article/51…

DeepMind just dropped a 106-page paper unveiling AlphaGenome. This single model could completely redefine how we discover disease-causing mutations and drug targets. This is massive. 🧵

We have a curator position at EMBL-EBI to work with GSK within a project to understand fibrotic processes (no PhD required). Deadline 20th July. Please share 🙏 embl.wd103.myworkdayjobs.com/en-US/EMBL/job…

Our group is hiring a postdoc to work on Digital Twin development for rare diseases. Collaborate with me and a fantastic interdisciplinary team! Deadline coming up this Sunday!

We’re doing this. Come hang with us at Stanford in November. scverse people, real talks, and all things single-cell. Don’t miss it. 💪

People with #Eczema are 3x more likely to have #Depression and #Anxiety. Kids with eczema also show higher rates of #ADHD and other disorders. The science linking #SkinHealth and #MentalHealth is growing. Learn more: bit.ly/46WEBR0