Henrik Köppke

I am so happy to share that our paperis officially published in Cell Genomics! In this paper, we describe TESLA-seq, which combines pooled CRISPR activation with targeted single-cell RNA-seq to map enhancer-gene connections at high sensitivity.

Link to the full story: www.cell.com/cell-genomic...

Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology Silhouette score is unsuitable as a metric for single-cell data integration.

Shortcomings of silhouette in single-cell integration benchmarking - @uweohler.bsky.social @prauten.bsky.social @mdc-bimsb.bsky.social @mdc-berlin.bsky.social @humboldtuni.bsky.social go.nature.com/4fcQzZr

#Spatialtranscriptomics is revolutionizing gene expression profiling at subcellular resolution!

🔬These 'molecular microscopes' can unlock disease mechanisms & guide therapies...but how to bring ST to the clinic?

Our thoughts w @N_Rajewsky & @nukappa.bsky.social out @annualreviews.bsky.social

🧵👇

As far as I know, the PromethION 2 Solo with the same package cost just under $10K a few days ago, before the recent price increase on Nanopore products. And now, with a grant, you’re paying $15K?

Metrics Matter: Why We Need to Stop Using Silhouette in Single-Cell Benchmarking Current-day single-cell studies comprise complex data sets affected by nested batch effects caused by technical and biological factors, relying on advanced integration methods. Silhouette is an establ...

1/4 🧵 Preprint alert: In "Metrics Matter: Why We Need to Stop Using Silhouette in #SingleCell #Benchmarking," we reveal critical flaws in common #Evaluation metrics for #Integration and propose robust alternatives. @uweohler.bsky.social
www.biorxiv.org/content/10.1...