Henrik Köppke
@henrikkoe.bsky.social
PhD candidate at Max Delbrück Center - Berlin Institute for Medical Systems Biology (MDC-BIMSB). Interested in genomics, 3D chromatin organisation and method development.
Reposted by 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...
Link to the full story: www.cell.com/cell-genomic...
September 9, 2025 at 3:29 PM
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...
Link to the full story: www.cell.com/cell-genomic...
Reposted by Henrik Köppke
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
Shortcomings of silhouette in single-cell integration benchmarking - Nature Biotechnology
Silhouette score is unsuitable as a metric for single-cell data integration.
go.nature.com
July 30, 2025 at 3:26 PM
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
Reposted by Henrik Köppke
#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
🧵👇
🔬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
🧵👇
February 18, 2025 at 1:02 PM
#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
🧵👇
🔬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
🧵👇
Reposted by Henrik Köppke
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
January 24, 2025 at 5:49 PM
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...
www.biorxiv.org/content/10.1...