Interested in working as a student research assistant (HiWi) at the Institute of Computational Biology at Helmholtz Zentrum Munich with Fabian Theis, setting your own goals and solving cutting edge problems in computational health? Apply here: jobs.helmholtz-muenchen.de/jobposting/b24…

What a great surprise to come back to after Christmas holidays to find our paper on benchmarking atlas-level single-cell data integration methods has finally been published. nature.com/articles/s4159… . A Tweetorial: 1/N

Finally published in Nature Methods: CellRank for directed #SingleCell fate mapping, our take on studying cellular dynamics using RNA velocity. Fantastic collab between labs of dana_peer @sloan_kettering and Fabian Theis Helmholtz Munich | @HelmholtzMunich, read at go.nature.com/3Fm17lt. 1/17

We’re thrilled to finally share the integrated Human Lung Cell Atlas (HLCA), a single-cell reference atlas of 444 individuals, and 2.2M cells! biorxiv.org/content/10.110… Human Cell Atlas Here’s a tweetorial on how we built it, and, most importantly, how you can use it: (1/20)

Interested in unlocking the full potential of Optimal Transport for temporal & spatial applications in sc genomics? Check out the recent MIA talk I gave with @CuturiMarco at the Broad Institute: youtu.be/qo-qvJPm7cY This was my first in-person talk in the PhD, so much fun!

Excited to share our work “Modeling fragment counts improves single-cell ATAC-seq analysis”, where we evaluate the effect of binarized versus count-based modeling on scATAC-seq analysis. Great collab between labs of gagneurlab and Fabian Theis Helmholtz Munich | @HelmholtzMunich, TU München

Exciting news: our story is now finally out in print and made it to the cover of Journals of The American Psychiatric Association. Using scRNA-seq we highlight the cell-type-specific effect of #glucocorticoids during brain development in #organoids. Cristiana Cruceanu Binder Lab Fabian Theis doi.org/10.1176/appi.a…

We are thrilled that our manuscript, out in print this month at Journals of The American Psychiatric Association, was featured in an editorial by Daniel R. Weinberger & Jennifer Erwin. Have a read of their thoughtful assessment of our work and the future of in vitro modelling of developmental risk: doi.org/10.1176/appi.a…

We are very excited to announce scverse (scverse.org), a new consortium around the core Python packages for single-cell omics data analysis. scverse is a cross-lab effort to ensure the longevity and interoperability of the single-cell analysis ecosystem in Python.

Today our Human Lung Cell Atlas (HLCA) paper came out in Nature Medicine nature.com/articles/s4159…! The HLCA includes 2.4M cells from 486 individuals and 49 datasets. Check out this tweetorial to learn more about how we built it, and how you can use it (1/21)

Is binarization of scATAC-seq data really necessary? The conclusion from our analysis is that a quantitative treatment is in fact beneficial. Now out in Nature Methods! gagneurlab Fabian Theis nature.com/articles/s4159… Many additions since the preprint 👇(1/n)

Our latest study exploring the effect of chronic glucocorticoids exposure on early brain development in an organoid system is now up on biorXiv. Big collaborative effort with @Binderlab @Fabian_Theis & @silvianeurompi led by the ever-curious Leander. biorxiv.org/content/10.110…

Super excited to share our Human Neural Organoid Atlas, now out in Nature! Led by ZhiSong He 何志嵩 Jonas (josch1@bsky) and myself, this resource was created from 36 scRNA-seq datasets—totalling over 1.7 million cells! 🔬✨ 🦋🧵-> bsky.app/profile/le-and… nature.com/articles/s4158…