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CellRank 2, our latest work on cell-state dynamics from single-cell data, is out in Nature Methods and won the first Helmholtz Software Award in the category “Scientific originality”. To date, the software has been downloaded over 120,000 times from PyPI and is used by biologists around the world to gain a deeper understanding into complex biological processes including cancer, regeneration, development and reprogramming.

Are you an MSc student in Computer Science, Physics, Maths, Bioinformatics, or a related discipline with strong coding/ML skills and an interest in biological questions? This thesis project might be interesting for you!

Happy to share that we released our preprint presenting CellRank 2, a unified framework to study cellular fate decisions. CellRank 2 comes with a modular interface that makes it easy to learn transition probabilities among cells based on various data modalities or views; currently, these include any Pseudotime, developmental potential, real-time information, and metabolic labeling data.

We’ve just released moscot, our new computational framework that maps single cells across time and space using efficient optimal transport algorithms. Importantly, moscot makes use of multi-modal information consistently across all applications, scales to atlases, and comes with a modular and extensible implementation.

We’ve just released moslin, our new computational tool that maps single cells across time points based on lineage and gene expression information. To find out more, see the tweetorial or read the full preprint at bioRxiv.

On October 24th, I successfully defended my PhD thesis with summa cum laude. My committee consisted of Fabian Theis, Dana Pe’er and Samantha Morris and was chaired by Donna Ankerst. I’m extremely thankful for all the support I received throughout my PhD from my supervisor Fabian, the office at the institute, my colleagues, collaboration partners, friends, family and mentors.

Starting August 1st, I’ll go on a 3-months partial end-of-PhD leave. I’ll reduce my working hours to one day a week; this means it will take me a bit longer to react to emails.

Proud to share Philipp Weiler’s upcoming seminar at the Sydney Precision Bioinformatics Alliance (SPBA). He will be presenting our joint work with Michal Klein and Fabian Theis on CellRank2. Watch the talk to find out how we’re improving CellRank and how you might benefit from these new features.

I’m excited to give a talk on CellRank and recent extensions featured in CellRank2 on June 14th at 10am ET in the Einstein-Montefiore Omics Club of Albert Einstein College of Medicine in New York.