Natan Belchikov
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View article: A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain
A single-cell, long-read, isoform-resolved case-control study of FTD reveals cell-type-specific and broad splicing dysregulation in human brain Open
View article: 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
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 Open
View article: Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state
Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease state Open
Measuring splicing and chromatin accessibility simultaneously in frozen tissues remains challenging. Here we combined single-cell isoform RNA sequencing and assay for transposase accessible chromatin (ScISOr–ATAC) to interrogate the correl…
View article: 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
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 Open
Genome-wide single-cell and spatial long-read approaches have gained traction, but mostly lack single-cell resolution - and yield limited read lengths. Here, we introduce spatial ISOform sequencing (Spl-ISO-Seq), which reveals exons and po…
View article: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics Open
RNA isoform diversity, produced via alternative splicing, and alternative usage of transcription start and poly(A) sites, results in varied transcripts being derived from the same gene. Distinct isoforms can play important biological roles…
View article: Predicting cell-type-specific exon inclusion in the human brain reveals more complex splicing mechanisms in neurons than glia
Predicting cell-type-specific exon inclusion in the human brain reveals more complex splicing mechanisms in neurons than glia Open
Alternative splicing contributes to molecular diversity across brain cell types. RNA-binding proteins (RBPs) regulate splicing, but the genome-wide mechanisms remain poorly understood. Here, we used RBP binding sites and/or the genomic seq…
View article: ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer’s Disease
ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer’s Disease Open
Multimodal measurements have become widespread in genomics, however measuring open chromatin accessibility and splicing simultaneously in frozen brain tissues remains unconquered. Hence, we devised Single-Cell-ISOform-RNA sequencing couple…
View article: Ariadne: synthetic long read deconvolution using assembly graphs
Ariadne: synthetic long read deconvolution using assembly graphs Open
View article: Comparing 10x Genomics single-cell 3’ and 5’ assay in short-and long-read sequencing
Comparing 10x Genomics single-cell 3’ and 5’ assay in short-and long-read sequencing Open
Barcoding strategies are fundamental to droplet-based single-cell sequencing, and understanding the biases and caveats between approaches is essential. Here, we comprehensively evaluated both short and long reads of the cDNA obtained throu…
View article: Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue
Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue Open
View article: Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types
Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types Open
Single-nuclei RNA-Seq is being widely employed to investigate cell types, especially of human brain and other frozen samples. In contrast to single-cell approaches, however, the majority of single-nuclei RNA counts originate from partially…
View article: Ariadne: Synthetic Long Read Deconvolution Using Assembly Graphs
Ariadne: Synthetic Long Read Deconvolution Using Assembly Graphs Open
Synthetic Long Read (SLR) sequencing techniques such as UST’s TELL-Seq, and Loop Genomics’ LoopSeq combine 3 ′ barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of ba…