Single Cell Omics Germany (SCOG)

Connecting researchers using & developing single cell technologies. Providing a collaborative platform, organizing workshops & hackathons, exchanging expertise.

[MDC-BIMSB @BIMSB_MDC]

Save the date for the 17th Berlin Summer Meeting: AI’s Adventures in Genomics, 6-7 June 2024!
Speakers include Vikram Agarwal @vagar112, @BurkholzRebekka, Julien Gagneur @gagneurlab, Andreas Keller @CCB_CBI, Georg Seelig @seeliglab, @ewa_szczurek & Josh Welch @LabWelch
#mdcBerlin

[Karin Hrovatin @KHrovatin]

1/5 Integration of scRNA-seq data is key for cross-dataset comparison. Yet, substantial batch effects can't be sufficiently removed without losing too much biological information. We show how to improve the integration of substantial batch effects https://t.co/LQLbD9U3av

[Fabian Theis @fabian_theis]

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.
https://t.co/JiuExwvG0n

[The German Human Genome-Phenome Archive @GHGA_DE]

It's a wrap! Our two day annual meeting has come to an end. As everyone is heading home, we would like to thank all the speakers, our SAB, and the team for an enganging and productive meeting. Until next time! 👋 #GHGAtalks

[Helmholtz Munich | @HelmholtzMunich @HelmholtzMunich]

#AI accelerates & enables #therapies!

👉Learn how Prof. @fabian_theis & team at #HelmholtzMunich & @TU_Muenchen transform info of #BigData into medical #applications:
🔗Einzelzell-Atlas der Lunge:
https://t.co/u6JT1bJZnZ
🔗Passionate about AI in #Health: https://t.co/QKhvkQ6k9r

[Mo Lotfollahi @mo_lotfollahi]

(1/n)scPoli is now published in @naturemethods https://t.co/sWXY6tZ2qF; see below. scPoli is an open-world learner for multi-scale analysis of scRNAseq/ATAC-seq across samples and species with cell types and conditions hierarchies. With scPoli you can:

[Gray Camp @GrayCampLab]

36 datasets, 26 protocols, 1.7 million harmonized cells! First edition Human Neural Organoid Cell Atlas. Important work from @zhisong_he @josch_f Leander Dony @TreutleinLab @fabian_theis. Strong community effort @Sergiu_P_Pasca @GiorgiaQuadrato. #organoids @ETH_BSSE @IHB_Research

[Saez-Rodriguez Group @saezlab]

📢LIANA+, our all-in-one cell-cell communication framework for multi-condition single-cell and spatial data, is now part of the @scverse_team. In the same spirit, we are open to suggestions, requests and contributions👩‍💻👨‍💻https://t.co/MsFr5uWCJi
Here's a list of tutorials 👇

[Nature Biotechnology @NatureBiotech]

Supervised discovery of interpretable gene programs from single-cell data https://t.co/8a6Fw6GCxt

[Mo Lotfollahi @mo_lotfollahi]

GET: a foundation model of transcription across human cell types

Scalable training across single-cell ATAC and RNA+ATAC datasets

https://t.co/H9Sszcczqf

[Nature Methods @naturemethods]

A workflow developed by @N_Rajewsky, @ILegnini and colleagues combines optogenetic perturbations and spatial transcriptomics to enable insights into cell fates and spatiotemporal gene patterns in organoids.

OA paper: https://t.co/BAyOpfxOS0

[Fabian Theis @fabian_theis]

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. https://t.co/EaBpcqwexi

[Single Cell Omics Germany (SCOG) @singlecellomics]

#singlecelljob in Barcelona

[Holger Heyn @hoheyn]

PLEASE consider joining our #singlecell #spatial genomics group @cnag_eu in beautiful Barcelona! #lifeisbetteratthebeach

Senior Laboratory Technician
https://t.co/5qN8pZzTRT

Postdoctoral Computational Biologist
https://t.co/o8QzM5Rsjm

Please RT.

[Eric Topol @EricTopol]

The latest on human total body cell count and cell size derived from >1,500 sources @PNASNews
Men ~36 trillion cells
Women ~28 trillion cells
an inverse relationship between cell size and count
https://t.co/i9qKqFOaVB

[biohub @biohub]

We are planning to build a high-performance computing cluster with 1000+ GPUs to accelerate AI for biomedical science, including advancing the development of new virtual cell 👇🪡https://t.co/fFDt7Y81I0

[The Knoblich Lab @Knoblich_lab]

We are thrilled to share our latest work, a collaborative effort with @TreutleinLab, in Nature (https://t.co/pChgPCFEOM). We introduce CHOOSE, a powerful screening system within cerebral organoids, through which we identified developmental defects associated with autism.
🧵1/7

[Matthias Mann Lab @labs_mann]

Our journey of multiplexed DIA, encompassing applications in spatial #singlecell #proteomics, is showcased on the cover of the latest issue of @MolSystBiol. We are excited about the prospects of sensitivity, reproducibility and high-throughput applications in clinical proteomics.

[Karin Hrovatin @KHrovatin]

To ease understanding of diabetes, which is complicated by bio and technical factors affecting the regulators of blood glucose – the pancreatic islets, we created a comprehensive mouse islet atlas (MIA) by integrating multiple single-cell transcriptomic (scRNA-seq) datasets.

[MDC-BIMSB @BIMSB_MDC]

We thank the speakers, organizers and ca. 200 participants of the 16th Berlin Summer Meeting 'The MDC Celebrates 15 Years of BIMSB', 6-7 Sept 2023, for 2 days of superb presentations & discussions on the latest exciting findings in systems biology!
@MDC_Berlin #mdcBIMSB2023

[Single Cell Omics Germany (SCOG) @singlecellomics]

📢 Starting now! Don't miss Céline's lecture "Mechanisms of cell plasticity in breast cancer".
@VallotCeline, @institut_curie, #SCOGVLS

✏️ Register: https://t.co/oGXJaNK1Pw

[Single Cell Omics Germany (SCOG) @singlecellomics]

📢 Join SCOG Virtual Lecture #55 - TOMORROW
⏰ September 6, 4:00-4:45pm CEST

💬 Céline Vallot (@VallotCeline, @institut_curie)
💡"Mechanisms of cell plasticity in breast cancer"
✏️ Registration: https://t.co/oGXJaNK1Pw
#SCOGVLS @fabian_theis