Hagen Tilgner

Humanized tauopathy chimeras uncover microglial and lncRNA strategies for neuroprotection

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

cGAS inhibition delays TDP-43-driven ALS Pathogenesis

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.

A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types.

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.

NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas

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

Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types

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.

Iso-Seq enables discovery of novel isoform variants in human retina at single cell resolution

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.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

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.

Predicting cell-type-specific exon inclusion in the human brain reveals more complex splicing mechanisms in neurons than glia

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.

ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's disease.

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: Isoform assembly using bulk barcoded RNA sequencing data

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

Single-cell long-read mRNA isoform regulation is pervasive across mammalian brain regions, cell types, and development

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.

Comparing 10x Genomics single-cell 3' and 5' assay in short-and long-read sequencing

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

The BRAIN Initiative Cell Census Data Ecosystem: A User's Guide

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: Visualizing Differential Isoform Expression in Single-Cell Long-Read Data

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

Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore reveals platform-specific error patterns

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

Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types

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.

BRN2 and PTN unveil multiple neurodevelopmental mechanisms in Schizophrenia patient-derived cerebral organoids

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.

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

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.

Targeted, High-Resolution RNA Sequencing Of Non-Coding Genomic Regions Associated With Neuropsychiatric Functions

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

Single-cell isoform RNA sequencing (ScISOr-Seq) across thousands of cells reveals isoforms of cerebellar cell types.

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.