Hagen Tilgner

The paper develops a humanized neuroimmune model to study tauopathy and identifies microglial and lncRNA mechanisms that protect neurons.

This study identifies cGAS as a key mediator of TDP-43 pathology in ALS and shows that its inhibition reduces RNA splicing defects and neurodegeneration.

The paper introduces a spatial long-read sequencing method to study developmental splicing and polyadenylation changes in cortical layers and cell types, finding layer-specific and age-related regulatory patterns.

The paper identifies a NRCAM proteoform with skipped microexons as a targetable surface antigen in pHGG and demonstrates its utility in immunotherapy.

The paper develops a high-resolution spatial long-read sequencing method and software to analyze isoform variability in brain cell types, revealing both region-specific and cell-type-specific patterns.

This study compares germ cell development between chicken and zebra finch using single-cell RNA sequencing, revealing distinct early germ cell types in zebra finch that are absent in chicken.

The paper uses Iso-Seq to discover novel isoform variants in human retinal cells at single-cell resolution, identifying thousands of new transcripts and differential splicing patterns.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper predicts cell-type-specific exon inclusion in human brain cells using RBP binding sites and genomic sequence, revealing more complex splicing mechanisms in neurons than glia.

The paper introduces ScISOr-ATAC to measure splicing and chromatin accessibility in frozen brain tissues, finding convergent and divergent patterns in different cell types and conditions.

cloudrnaSPAdes assembles full-length isoforms from barcoded RNA-seq linked-read data, accurately handling high isoform diversity in simulated and real human data.

The paper analyzes single-cell long-read mRNA isoform regulation across mouse brain regions, cell types, and development, finding pervasive isoform variability and cell-type specific splicing patterns.

This study compares 10x Genomics 3' and 5' assays using short and long reads, finding differences in exonic/intronic capture and transcript completeness.

The paper provides a guide to the BRAIN Initiative Cell Census Network (BICCN) data ecosystem, its tools, and resources for analyzing brain cell types across species.

ScisorWiz visualizes differential isoform expression in single-cell long-read data, highlighting alternative exons and SNVs across cell types and brain regions.

The paper compares error patterns in long-read transcriptomics using Pacific Biosciences and Oxford Nanopore by analyzing cDNA copies of individual RNA molecules.

The paper introduces SnISOr-Seq, a method for single-nuclei isoform RNA sequencing, and finds distinct combination patterns of transcript elements in human brain cell types.

This study uses patient-derived cerebral organoids to identify molecular and cellular mechanisms of Schizophrenia, revealing altered neuronal programming factors and growth factors like BRN2 and PTN.

The paper identifies brain-region specific splicing patterns at single-cell and spatial resolution in postnatal mice, revealing cell-type specific and region-specific isoform expression.

The paper identifies novel non-coding RNAs in human brain tissue associated with neuropsychiatric traits using targeted RNA capture and long-read sequencing.

The paper introduces ScISOr-Seq, a method combining single-cell full-length cDNA amplification with short-read and long-read sequencing to identify isoforms in cerebellar cell types across thousands of cells.