Posts on X

Excited to share our scVelo manuscript - led by @VolkerBergen and @falexwolf, we generalize the beautiful RNA velocity concept from @KharchenkoLab and @slinnarsson to transient cell states through dynamical modeling. biorxiv.org/content/10.110… and scvelo.org #scRNAseq

@wbialek talking at @czbiohub meeting about optimization principles in genetic networks with example fruit fly segmentation. Nice: "quantitative biology is all about fitting big models"

Fun run this morning across Berkeley hills (quite smokey because of wild fires), and then came by this true temple of the life sciences @UCBerkeley

Stephen Quake @czbiohub kicking off the two-day meeting ‘beyond the cell atlas’ at Berkeley. Looking forward to a fun meeting, and of course to ‘the golden age of cell biology’ we are currently entering acc. to Steve.

If you are interested in doing a PhD in data science, maybe in comp bio, please consider applying to the Munich School of Data Science. mu-ds.de

@MunichDS

17 days to go...

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Excited to host a workshop on spatial transcriptomics by @10xGenomics next Tuesday, Oct 22, 9-11am @ICBmunich @HelmholtzMunich. Few places left to register for free: bit.ly/2W3nya5

The evaluation of #scRNA-seq pipelines from Enard&@IHellmann labs out now in @NatureComms. Using simulations, they compare 5 scRNA-seq techniques, 3 mapping, 4 imputation, 7 normalisation and 4 differential expression tools, and find normalisation is key: nature.com/articles/s4146…

Exciting junior group leader positions in #AI at @helmholtz_ai!

@FeestChristoph

👉budding scientist in #MachineLearning and #ArtificialIntelligence with bold and unconventional💡ideas? ambitious? non-incremental? check our @helmholtz_ai @fabian_theis latest opening go.nature.com/2MElmBj

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Really excited to see that our Bavarian state government with MP @Markus_Soeder will be investing €2B into research and innovation, in particular into #AI (100 new professorships), more than @BMBF_Bund. themunicheye.com/two-billion-eu…

@leeat_keren and @gc_yuan talking @humancellatlas Spain breakout session on analyzing spatial omics data sets. Many new (and some old) fun computational challenges!

Musa @mhlangalab reporting on @humancellatlas equity group and efforts on how to realize HCA’s egalitarian principles - first HCA meetings and projects happening in low and middle income countries.

Chloe and Peter @KharchenkoLab digging into the conference dinner @humancellatlas Spain.

@dana_peer @humancellatlas Barcelona pe’ering into the abyss of data analysis. 😂

Sample numbers with >1M cells and ~>50 individuals in each of the 6 exemplary organs of the @humancellatlas

3 years of @humancellatlas already - wow. Great community and scientific effort!

Looking forward to an exciting #humancellatlas meeting, this time in Barcelona. In the Science Museum, really cool, eg with artificial rain forest. Thx @hoheyn for organizing this!

Excited to share our recent work on generative modeling for unpaired data using a ‚transformer VAE’. Led by @MohammadLotfol1 and @falexwolf, we extend scGen using a conditional VAE together with an MMD regularization. Applications for images and scRNA-seq. arxiv.org/abs/1910.01791

@ahmedElkoussy from @LUMC talking @ICBmunich‘s seminar on collaborations of geneticists and neurobiologists, using single cell genomics.

Data analysis in single cell genomics goes through many steps, mostly still manually supervised, at least after count matrices. Who is using workflow systems for this already, and can give recommendations? (@slinnarsson) Nice overview here: nature.com/articles/d4158…

Somewhat anecdotal piece on reviewing @sciencemagazine with some true points. But "keep in mind that writing in a second language is even harder"? We all know, after all the great majority of researchers are non-native English speakers. science.sciencemag.org/content/366/64…

Looming #Brexit already impacting research and collaborations between UK and (rest-)EU says @sciencemagazine, with less joint consortia and less ERC-like grants over past 4 years. science.sciencemag.org/content/366/64…

@Uber_Ger: tried your e-scooter @JUMPbyUber @muenchen today. It was comically bad. Speed not faster than walking, no clear advice where to park and then +25€ service charge you did not announce in the app. Plus: no support contact other than public tweets. Why?

@Munich of the future, @Munich of the past - youtu.be/diI0Tb3V2Cs 😂

PhD project management: fight "analysis paralysis" and make "progress by by failing early". This is good advice for PIs as well. nature.com/articles/d4158…

Great #Bioinformatics student presentations in our joint master with @TU_Muenchen and @LMU_Muenchen - also, did you notice it is Octoberfest time?

Beautiful poster session @ICBmunich‘s retreat at Spitzing Lake in the Bavarian alps. Phds and postdocs presenting great research leading to fun discussions.

Great review authored amongst others by my fantastic colleague @EleZeggini

@EricTopol

Precision medicine, translational #genomics well reviewed: "this progress has been made possible by technological advances in genomics and analytics and by the digital revolution." science.sciencemag.org/content/365/64… @EleZeggini @LouiseVwain @annagloyn @UoMMskResearch w/@ScienceVisuals

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Interesting read - #AI in healthcare faces two major issues: politicals and data availability/fragmentation. Amen to that.

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@dana_peer at #scg2019 on single cell genomics for real clinical data and the somewhat common ‘tSNE tea leave reading’ 😂

Guoji Guo speaking at #SCG2019 on cell landscape mapping. His 2010 Dev Cell paper at Robson lab got me into single cell genomics. 48 genes, 500 cells. Good old times, when all things were easier. Just not the biology 😀