Yosef Lab

🇨🇭 In January 2027, I'm starting the Computational Cellular Dynamics Lab at the University of Basel, in the Department of Biomedicine and the Basel Research Centre for Child Health. I'm now looking for people to build it with. 🧬 We'll develop generative models of how human tissues develop, mature and regenerate, and of what goes wrong in disease, with a focus on child health. The models learn from single-cell and spatial genomics, and we generate much of that data ourselves, together with partners at Basel's hospitals, universities and institutes. Some of the questions we'll work on: - How do cells and tissues respond when their signaling environment changes? - Can flow and diffusion models learn the gene regulation behind cellular dynamics? - Which perturbations and measurements should we run next, and how can models keep learning as new data come in? Open positions: 🎓 PhD – four years, fully funded. Apply via the University of Basel portal: https://lnkd.in/ePxZTKFa 🔬 Postdoc – funding available, and I'm happy to support fellowship applications. 📩 For the postdoc, email me at marius.lange@unibas.ch with your CV, contact details of two or three references, your GitHub and a short statement on your past research and what you want to work on next. I'm looking for people with a strong background in machine learning, mathematics, physics, statistics or computational biology, some exposure to biological data, and a wish to apply those skills to real biological questions. Sharing is very much appreciated! #hiring #PhD #postdoc #MachineLearning #SingleCell #ComputationalBiology

I’m excited to share that I have joined The Julius Maximilians University of Würzburg as a Junior Professor of Systems Immunology and Computational Health Center | Helmholtz Munich as a Principal Investigator. Across both sites, my lab will develop new machine-learning methods to study how individual disease trajectories emerge in immune-mediated diseases. We are hiring! I am recruiting PhD students and software engineers. If you are excited about computational immunology, machine learning, personalized medicine, or open-source software development, please reach out or share within your network: https://lnkd.in/eWCbdj6Y. Check out our currently open MUDS - Munich School for Data Science PhD call: https://lnkd.in/e3qykXZJ And stay tuned for updates from scverse or join us in Copenhagen: https://lnkd.in/eWYiv7CC #SystemsImmunology #PersonalizedMedicine #SingleCell #SpatialOmics #OpenSource #MachineLearning

https://lnkd.in/eehkF_fn

We're #hiring a new Independent AI Fellow-PhD graduates ONLY in Rehovot, Center District. Apply today or share this post with your network.

I’m excited to share our new bioRxiv preprint: “NovaClone: A Network-Based Algorithm for Clonal and Subclonal Genotyping of Barcoded Transgene Integrations” Accurate clone calling is a critical first step in lineage tracing analysis, as errors at this stage influence all downstream analyses. However, technical noise and sequencing errors make reliable clonal reconstruction particularly challenging. In this work, we developed NovaClone, a network-based algorithm for hierarchical clone calling in single-cell lineage tracing data. The algorithm and our new suite of QC metrics are now available as an open-source Python package. Proud to have co-led this work with Sebastián Prillo, who I learned a lot from along the way, and truly grateful for the guidance and mentorship of Nir Yosef. Read the preprint here: https://lnkd.in/dnHVrybQ Yosef Lab Yun S. Song #SingleCell #LineageTracing #CloneCalling #Bioinformatics 

I'm excited to share our new paper, now published in Cancer Cell by Cell Press! “Tumor-antigen-independent targeting of solid tumors by armored macrophage-directed anti-TREM2 CAR T cells” Solid tumors remain a significant challenge for CAR T therapy, largely due to the highly immunosuppressive nature of the tumor microenvironment. In this work, we targeted TREM2⁺ tumor-associated macrophages with a macrophage-directed CAR T approach, "armoring" the cells with activation-dependent IL-12 secretion to drive immune infiltration and activation within the TME. I had the honor to be the a co-first author and the bioinformatician on this project, working from discovery to validation. I'm proud to have contributed to such an amazing project! I want to thank prof. Ido Amit and my colleagues at the Amit Lab at Weizmann Institute of Science, who worked with me days and nights on this research. We are also honored to be published back-to-back with the significant study from the Brian D. Brown and Miriam Merad, MD, PhD labs, collectively highlighting the importance of macrophage-targeting immunotherapies and their potential in the clinic. Read the full paper here: https://lnkd.in/eUSfn2Gp Gal Yagel Michelle von Locquenghien Pascale Zwicky #CancerCell #Immunotherapy #CART #Bioinformatics #CancerResearch #TME #CancerImmunotherapy