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Scholars/Hagen Tilgner, PhD/Co-authored with mentees

Co-authored publications with mentees

Hagen Tilgner, PhD · 20 publications across 5 mentees

PhD mentee

Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.
Nature methods · 2026
HTHagen TilgnerCFCareen FoordLMLieke Michielsen YMYelizaveta Mochalova TKTaewoo Kim+5 more →
PMID: 42697995PMCID: PMC13545012DOI
With Careen Foord · Neuroscience (PhD) · Class of 2025
Real-time Targeted Enrichment in Single-cell Long-read Sequencing.
Genomics, proteomics & bioinformatics · 2026
HTHagen TilgnerNBNatan BelchikovJHJustine HsuWHWen Hu
PMID: 42384931DOI
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.
Genome biology · 2026
HTHagen TilgnerNBNatan BelchikovLMLieke MichielsenJHJustine Hsu
PMID: 41764538PMCID: PMC13059442DOI
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain.
Cell reports · 2025
HTHagen TilgnerNBNatan BelchikovWHWen HuLFLi FanAJAnoushka Joglekar+8 more →
PMID: 40913764PMCID: PMC12558363DOI5 citations
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain.
Cell reports · 2025
HTHagen TilgnerCFCareen FoordNBNatan BelchikovWHWen HuLFLi Fan+8 more →
PMID: 40913764PMCID: PMC12558363DOI5 citations
With Careen Foord · Neuroscience (PhD) · Class of 2025
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.
Nature communications · 2025
HTHagen TilgnerNBNatan BelchikovCFCareen FoordWHWen HuLMLieke Michielsen+6 more →
PMID: 40883294PMCID: PMC12397408DOI16 citations
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
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.
Nature communications · 2025
HTHagen TilgnerCFCareen FoordWHWen HuLMLieke MichielsenBEBrian Evans+6 more →
PMID: 40883294PMCID: PMC12397408DOI16 citations
With Careen Foord · Neuroscience (PhD) · Class of 2025
Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.
Nature biotechnology · 2025
HTHagen TilgnerNBNatan BelchikovWHWen HuCFCareen FoordJHJustine Hsu+9 more →
PMID: 40696189PMCID: PMC12425497DOI10 citations
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state.
Nature biotechnology · 2025
HTHagen TilgnerCFCareen FoordWHWen HuJHJustine HsuLFLi Fan+9 more →
PMID: 40696189PMCID: PMC12425497DOI10 citations
With Careen Foord · Neuroscience (PhD) · Class of 2025
Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types.
bioRxiv : the preprint server for biology · 2025
HTHagen TilgnerCFCareen FoordLMLieke MichielsenWHWen HuJJJulien Jarroux+2 more →
PMID: 40667010PMCID: PMC12262416DOI
With Careen Foord · Neuroscience (PhD) · Class of 2025
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.
bioRxiv : the preprint server for biology · 2025
HTHagen TilgnerNBNatan BelchikovCFCareen FoordWHWen HuLMLieke Michielsen+6 more →
PMID: 40661641PMCID: PMC12259066DOI
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
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.
bioRxiv : the preprint server for biology · 2025
HTHagen TilgnerCFCareen FoordWHWen HuLMLieke MichielsenBEBrian Evans+6 more →
PMID: 40661641PMCID: PMC12259066DOI
With Careen Foord · Neuroscience (PhD) · Class of 2025
Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics.
Genome research · 2024
HTHagen TilgnerNBNatan BelchikovJHJustine HsuJJJulien JarrouxWHWen Hu
PMID: 39567235PMCID: PMC11610585DOI19 citations
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's Disease.
bioRxiv : the preprint server for biology · 2024
HTHagen TilgnerNBNatan BelchikovWHWen HuCFCareen FoordJHJustine Hsu+9 more →
PMID: 38464236PMCID: PMC10925193DOI
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's Disease.
bioRxiv : the preprint server for biology · 2024
HTHagen TilgnerCFCareen FoordWHWen HuJHJustine HsuLFLi Fan+9 more →
PMID: 38464236PMCID: PMC10925193DOI
With Careen Foord · Neuroscience (PhD) · Class of 2025
From words to complete phrases: insight into single-cell isoforms using short and long reads.
Transcription · 2023
HTHagen TilgnerCFCareen FoordJJJulien Jarroux
PMID: 37314295PMCID: PMC10807471DOI10 citations
With Careen Foord · Neuroscience (PhD) · Class of 2025
The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing.
Nature methods · 2023
HTHagen TilgnerNBNatan BelchikovCFCareen FoordJHJustine HsuJJJulien Jarroux+3 more →
PMID: 36635536DOI26 citations
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing.
Nature methods · 2023
HTHagen TilgnerCFCareen FoordJHJustine HsuJJJulien JarrouxWHWen Hu+3 more →
PMID: 36635536DOI26 citations
With Careen Foord · Neuroscience (PhD) · Class of 2025
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.
Nature biotechnology · 2022
HTHagen TilgnerNBNatan BelchikovSASimon A HardwickWHWen HuAJAnoushka Joglekar+8 more →
PMID: 35256815PMCID: PMC9287170DOI93 citations
With Natan Belchikov · Physiology, Biophysics & Systems Biology (PhD) · Class of 2026
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.
Nature biotechnology · 2022
HTHagen TilgnerCFCareen FoordSASimon A HardwickWHWen HuAJAnoushka Joglekar+8 more →
PMID: 35256815PMCID: PMC9287170DOI93 citations
With Careen Foord · Neuroscience (PhD) · Class of 2025

Postdoc mentee

Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.
Nature methods · 2026
HTHagen Tilgner LMLieke MichielsenCFCareen FoordYMYelizaveta Mochalova TKTaewoo Kim+5 more →
PMID: 42697995PMCID: PMC13545012DOI
With Lieke Michielsen · Postdoc mentee
Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.
Nature methods · 2026
HTHagen Tilgner YMYelizaveta Mochalova LMLieke MichielsenCFCareen FoordTKTaewoo Kim+5 more →
PMID: 42697995PMCID: PMC13545012DOI
With Yelizaveta Mochalova · Postdoc mentee
Decoding exon inclusion in the human brain reveals more divergent splicing mechanisms in neurons than glia.
Genome biology · 2026
HTHagen Tilgner LMLieke MichielsenJHJustine HsuNBNatan Belchikov
PMID: 41764538PMCID: PMC13059442DOI
With Lieke Michielsen · Postdoc mentee
A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain.
Cell reports · 2025
HTHagen TilgnerAJAnoushka JoglekarNBNatan BelchikovWHWen HuLFLi Fan+8 more →
PMID: 40913764PMCID: PMC12558363DOI5 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022
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.
Nature communications · 2025
HTHagen Tilgner LMLieke MichielsenCFCareen FoordWHWen HuBEBrian Evans+6 more →
PMID: 40883294PMCID: PMC12397408DOI16 citations
With Lieke Michielsen · Postdoc mentee
Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types.
bioRxiv : the preprint server for biology · 2025
HTHagen Tilgner LMLieke MichielsenCFCareen FoordWHWen HuJJJulien Jarroux+2 more →
PMID: 40667010PMCID: PMC12262416DOI
With Lieke Michielsen · Postdoc mentee
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.
bioRxiv : the preprint server for biology · 2025
HTHagen Tilgner LMLieke MichielsenCFCareen FoordWHWen HuBEBrian Evans+6 more →
PMID: 40661641PMCID: PMC12259066DOI
With Lieke Michielsen · Postdoc mentee
The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing.
Nature methods · 2023
HTHagen TilgnerAJAnoushka JoglekarCFCareen FoordJHJustine HsuJJJulien Jarroux+3 more →
PMID: 36635536DOI26 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022
Accurate isoform discovery with IsoQuant using long reads.
Nature biotechnology · 2023
HTHagen TilgnerAJAnoushka JoglekarJJJulien Jarroux
PMID: 36593406PMCID: PMC10344776DOI160 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022
ScisorWiz: visualizing differential isoform expression in single-cell long-read data.
Bioinformatics (Oxford, England) · 2022
HTHagen TilgnerAJAnoushka JoglekarZPZhi-Lin Pan
PMID: 35604081PMCID: PMC9237735DOI18 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022
Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.
Genome research · 2022
HTHagen TilgnerAJAnoushka Joglekar
PMID: 35301264PMCID: PMC8997348DOI32 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue.
Nature biotechnology · 2022
HTHagen TilgnerAJAnoushka JoglekarSASimon A HardwickWHWen HuLFLi Fan+8 more →
PMID: 35256815PMCID: PMC9287170DOI93 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.
Nature communications · 2021
HTHagen TilgnerAJAnoushka JoglekarSLSusan LinAKAnna Katharina SchluscheJMJordan Marrocco+4 more →
PMID: 33469025PMCID: PMC7815907DOI161 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022
Getting the Entire Message: Progress in Isoform Sequencing.
Frontiers in genetics · 2019
HTHagen TilgnerAJAnoushka JoglekarSASimon A Hardwick
PMID: 31475029PMCID: PMC6706457DOI36 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse.
Neuron · 2019
HTHagen TilgnerAJAnoushka JoglekarRJRyan J FarrellHMHuaiyu MiGAGhazaleh Ashrafi+3 more →
PMID: 31171447PMCID: PMC6764089DOI705 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022
Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells.
Nature biotechnology · 2018
HTHagen TilgnerAJAnoushka JoglekarTFTaylor FloydWLWenjie Luo MEMargaret Elizabeth Ross
PMID: 30320766DOI267 citations
With Anoushka Joglekar · Tri-I Program in Computational Biology & Medicine · Class of 2022