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Congratulations, Viktor! Very proud of your efforts! 😀

Excited that veloVI is out Nature Methods! Led by Adam Gayoso & Philipp Weiler w awesome Yosef Lab, we combine deep generative modeling with a mechanistic single-cell transcriptional model for better RNA velocity analysis with uncertainty quantification. nature.com/articles/s4159…

Human brain atlas papers by Kimberly Siletti Alejandro Mossi Kawai Ernest Arenas Emelie Braun Miri Danan Gotthold Rebecca Hodge Trygve Bakken Ed Lein Lars Borm Elin Vinsland Erik Sundström and many others. With a stunning double cover illustration by Ivana Kapustová

Congrats to Teng on this outstanding effort to push the limits of allele-based CNV detection in order to characterize somatic variation in healthy tissues!

BARtab & bartools: an integrated Nextflow pipeline and R package for the analysis of synthetic cellular barcodes in the genome and transcriptome biorxiv.org/content/10.110…

✨#ImmuneDictionary✨is out today in nature! Paper nature.com/articles/s4158… Software immune-dictionary.org We created scRNA-seq dictionary of 17+ immune cell types responding to 86 cytokines in vivo, discovered the immune system is far more complex than previously known 1/

We profiled #scRNAseq of 386,703 cells and uncovered 17+ immune cell types in lymph nodes. Well-known cytokine-responsive genes, such as Il4i1 in response to IL-4, Tnfaip3 in response to TNF, are robustly upregulated in our dictionary. #ImmuneDictionary 6/

Very excited to share two papers published today in Cell describing stem cell plasticity in CRC. (1/22) cell.com/cell/fulltext/… cell.com/cell/fulltext/…

We are very excited to present a major breakthrough achievement – the de novo design of synthetic enhancers for selected tissues in fruit fly embryos in vivo using deep- and transfer learning, @deAlmeida_BPet al published today in nature nature.com/articles/s4158…. Thread 👇(1/N)

6 papers for ligand-receptor interaction for single-cell data 👇

Excited to share two new papers, published today in nature! Check them out here: (1) Slide-tags, a new method to unite single-cell and spatial profiling: nature.com/articles/s4158…

Our latest collaboration on metastatic renal cell carcinoma to the bone is published Genome Medicine. the bone metastatic environment is not well-defined, hindering progress towards therapeutic targets. Our group developed a unique translational research model. Congrats to our

Our latest out today in nature. We profiled 12 million single cells from mouse embryos spanning gastrulation to birth, defined cell type tree from zygote to birth, and unexpectedly found crazy fast changes within first hour of extrauterine life. OA PDF: rdcu.be/dyDAg

Just finished teaching another semester of genomic #datavisualization 🥳 Discover the awesome #dataviz made by students in the class for various #singlecell #spatialtranscriptomics data Check out the course notes + #Rstats code to explore for yourself: jef.works/genomic-data-v…

New preprint 🎉 led by Philipp Rentzsch 👇! We introduce an approach to prioritize biological driver genes by recalibrating differential expression fold changes with population variance. This extracts new meaning out of DE analysis, which is a cornerstone of computational biology!

How to pick a problem. Today in Cell. 1/53 cell.com/cell/fulltext/…

Great to be part of this collaboration with Ninib Baryawno and PeterK among others! Joint single-cell WGS/mRNA seq is an important tool to understand evolutionary processes in tumors!

Happy to see our work with Jimmie Ye's lab on coordinated variation of different cell types in healthy and diseased individuals published! At the core of it is the scITD tool for tensor decomposition, rotation and interpretation strategy. Great effort by Jonathan Mitchel et al.!

Our pre-print with Igor Adameyko on continuous spectra of progenitor fates during mammalian development. Using multiplexed clonal tracing, mosaic perturbations, and robust computational representations, we look at spatial and temporal modulation of cell fates in mouse embryos.

As part of our embryo clonal tracing and perturbation efforts with Igor Adameyko, a quick twittorial from Sergey on generating stable and informative representations of clonal fate variations from sparse and noisy barcode-based lineage tracing data.