Plate VI · News
New papers, tools and news, as posted by @fabian_theis. Replies and reposts are left out.
Want to annotate cells across whole organism? Led by @felix_f0097 with Villani lab, we propose scTab, a DL model for tabular single cell expr & show strong scaling behavior beyond linear. Comes with large benchmark useful for evaluating foundation models. biorxiv.org/content/10.110…
Met @adamgayoso for first time after collaborating for quite some time w @YosefLab. Nir presented MrVI, Adam’s now DrVI haha 😜
Traveling to #SCG2023 but train delayed and I missed first session, w @dana_peer handing out chocolate.. hope I still get some
View on X: post of 9 Oct 2023Shocked by the atrocities committed by Hamas against Israel 🇮🇱. It is so sad to see terrorism rise again. My thoughts are with my scientist friends, please be safe.
View on X: post of 9 Oct 2023Looking forward a lot to Single Cell Genomics 2023 in Engelberg 🇨🇭 next week, what a line up! conferences.weizmann.ac.il/SCG2023/single…
View on X: post of 7 Oct 2023Excited to share our integrated human neural organoid cell atlas (HNOCA). Led by @zhisong_he,@le_and_er& @josch_f, we integrate cells across organoid protocols + map to dev. brain. Awesome collab with @GrayCampLab,@TreutleinLab& @humancellatlas colleagues. biorxiv.org/content/10.110…
Excited that veloVI is out @naturemethods! Led by @adamgayoso & @PhilippWeiler7 w awesome @YosefLab, we combine deep generative modeling with a mechanistic single-cell transcriptional model for better RNA velocity analysis with uncertainty quantification. nature.com/articles/s4159…
Interesting opinion piece @PLOSBiology by @sarahteichmann1 et al @teichlab on what makes research institutes successful: ‚Everybody counts & everybody should be empowered to contribute‘. Ideas from admin to core facilities, recruiting, transfer & culture. journals.plos.org/plosbiology/ar…
Cool BC2 artwork competition in comp bio, won by Anastasia Sveshnikova.
Ido @IdoAmitLab talking at BC2 on single cell immunology and how to use single cell approaches for therapeutics, in particular for their new TREM2 antagonists in glioblastoma.
Visiting Basel for SIB BC2 conference- and meeting w @MariusLange8 for typical Basel outdoor activity - Rhein swimming with a ‘wrap fish’ to take clothes 😅
Happy that our mouse islet atlas (MIA) across many single-cell transcriptomic datasets is out @NatMetabolism. Led by @KHrovatin & w @LickertHeiko lab, you can use this atlas to explore β-cell heterogeneity in healthy+disease. Read rdcu.be/dlRRH & nature.com/articles/s4225…
Excited about the possibilities that future foundation models could hold in single cell analysis. I however find it confusing when ‘FM’ is used synonymously with ‘LLMs’, in particular when in sc analysis ‘transformers’ may be more adequate, no? Example: biorxiv.org/content/10.110…
View on X: post of 9 Sept 2023Single-cell multiplexing (hashing/genetics) is key for upscaling scRNA-seq. We introduce hadge, a Nextflow pipeline combining existing comp analysis methods with new metrics & rescue mode for efficient deconvolution. Led by F Curion, X Wu & @LukasHeumos. biorxiv.org/content/10.110…
Maria Leptin @mleptin, @ERC_Research president, giving talk @HelmholtzMunich townhall. Key point is that economic growth is driven by technology, which *needs* strong fundamental science; here example of mRNA vaccines, based on decade long basic research. Great to have the ERC!
Want to learn cell state dynamics beyond RNA velocity? Led by @PhilippWeiler7 & @MariusLange8, and with @dana_peer, our new CellRank 2 enable fate mapping leveraging pseudotime, gene scores, time points or metabolic labeling in multi-view single-cell data. biorxiv.org/content/10.110…
Kick-off of ‚M1’, the Munich Medicine Alliance by @MarkusBlume and others. Brings together @HelmholtzMunich, @TU_Muenchen & @LMU_Muenchen and their clinics in a single legal unit, with efficient data sharing amongst others.
Opening of our new @PioneerCampus building @HelmholtzMunich - excited to have this fantastic mixture of wetlab and computational spaces for bioengineering efforts of the future. Please come visit
Ed Lein presenting at #HCA2023GM on brain atlassing efforts, highlighting amongst others this guide to access + navigate BICCN data sets. journals.plos.org/plosbiology/ar…
View on X: post of 10 Jul 2023Malte @MDLuecken presenting HCA integration team approach and state @humancellatlas meeting. #hca2023gm.
Human cell atlas network strongly increasing #HCA2023GM with equally exploding data sets across most organs.
Conference/meeting trip through Paris, NYC, and Boston, met up with current and/or former lab members at each place - so honored to know&work with such talented, nice and fun people. ☺️
Great to be back @broadinstitute after quite some time thanks to kind invite by Caroline Uhler. Boston feels a bit like coming home again, so nice. New Broad building very fancy though, great view too.
Excited to visit @dana_peer lab, meeting talented students and giving an outlook talk today. And look at the view of lower Manhattan!
Enjoyed giving keynote & discussing @institutpasteur, Paris, at an AI and biology conference - and great to see so many diverse application areas but with often very exciting and related methods such as the inclusion of simulations into then ML models. Thanks for the invite!
Glad to have Nils @ngehlenborg visiting us today, talking @CompHealthMuc seminar about his awesome visualization tools, in particular in single and spatial omics.
Long term sysbio hero @UriAlonWeizmann ‚simulating’ dynamic systems for wound healing vs fibrosis by pen on the whiteboard - great fun conceptual talk @SBHDConference 2023!
