Joachim Luginbühl

TP53 and RB1 are predictive genetic biomarkers for sensitivity to cytarabine in gliomas

The paper identifies TP53 and RB1 wild-type status as predictors of cytarabine sensitivity in gliomas using CRISPRi screening and machine learning analysis.

Antisense oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

The paper performs knockdown of 200 lncRNAs in human iPS cells, identifies 36 with growth inhibition, and finds molecular phenotypes in 29.3% of cases, with higher agreement in molecular than cell growth phenotypes across cell types.

Recombination of repeat elements generates somatic complexity in human genomes.

The paper investigates somatic recombination of Alu and L1 repeat elements in human genomes, finding tissue-specific patterns and links to neurodegenerative diseases.

Comparative analysis of human brain organoids of brainstem and midbrain at single-cell resolution

This study compares single-cell transcriptomes of human brainstem and midbrain organoids, identifying unique cell types and similarities with fetal midbrain data.

Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids

The paper uses single-cell RNA-sequencing to identify multiple neuronal cell types in human midbrain organoids, including dopaminergic, GABAergic, and glutamatergic neurons.

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

RADICL-seq maps genome-wide RNA-chromatin interactions in intact nuclei, revealing general and cell type-specific patterns of transcript occupancy and the role of transcription in chromatin structure.

Brainstem organoids from human pluripotent stem cells contain neural crest population

This study develops human brainstem organoids containing neural crest cells and various neuron types, validated by single-cell RNA sequencing, proteomics, and electrophysiology.

Decoding neuronal diversity by single-cell Convert-seq

This study introduces Convert-seq, a method combining scRNA-seq and ectopic gene expression to identify gene regulatory networks during cell reprogramming.

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

C1 CAGE detects transcription start sites and enhancer activity in lung cancer cells, revealing subpopulations with distinct responses to TGF-β and enhancer RNA dynamics.