A5019572869- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- Molecular Biology Techniques and Applications
- Microbial Community Ecology and Physiology
- RNA and protein synthesis mechanisms
- Connexins and lens biology
- Innovative Microfluidic and Catalytic Techniques Innovation
- Neuroscience and Neuropharmacology Research
- Topic Modeling
- Cancer Genomics and Diagnostics
- Natural Language Processing Techniques
- Genomics and Chromatin Dynamics
- S100 Proteins and Annexins
- Gene expression and cancer classification
- RNA regulation and disease
- Environmental DNA in Biodiversity Studies
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
Weill Cornell Medicine
2018-2024
New York Genome Center
2024
Cornell University
2018-2024
MIND Research Institute
2018-2024
Center for Neuro-Oncology
2021-2024
Columbia University
2024
Tri-Institutional PhD Program in Chemical Biology
2022-2023
The Ohio State University
2016
Abstract Splicing varies across brain regions, but the single-cell resolution of regional variation is unclear. We present a investigation differential isoform expression (DIE) between regions using long-read sequencing in mouse hippocampus and prefrontal cortex 45 cell types at postnatal day 7 ( www.isoformAtlas.com ). Isoform tests for DIE show better performance than exon tests. detect hundreds events traceable to types, often corresponding functionally distinct protein isoforms. Mostly,...
Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex incompletely solved problems. Here we present IsoQuant-a computational tool using intron graphs that accurately reconstructs transcripts both with without reference genome annotation. For novel transcript discovery, IsoQuant reduces the false-positive rate fivefold 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively. also improves performance Pacific...
Abstract Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder study of isoforms. Here we present isoform (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold naive sequencing. We applied adult human frontal cortex found that exons associated...
Abstract RNA isoforms influence cell identity and function. However, a comprehensive brain isoform map was lacking. We analyze single-cell across regions, subtypes, developmental time points species. For 72% of genes, full-length expression varies along one or more axes. Splicing, transcription start polyadenylation sites vary strongly between types, protein architecture associate with disease-linked variation. Additionally, neurotransmitter transport synapse turnover genes harbor cell-type...
Long-read transcriptomics require understanding error sources inherent to technologies. Current approaches cannot compare methods for an individual RNA molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and long-read sequencing sequence cDNA copies representing molecule on both Pacific Biosciences (PacBio) Oxford Nanopore Technologies (ONT). We these pairs in terms of content isoform patterns. Although read show high similarity, find differences...
Abstract Summary RNA isoforms contribute to the diverse functionality of proteins they encode within cell. Visualizing how isoform expression differs across cell types and brain regions can inform our understanding disease gain or loss caused by alternative splicing with potential negative impacts. However, extent which this occurs in specific is largely unknown. This kind information that ScisorWiz plots provide an informative easily communicable manner. affords its user opportunity...
RNA isoforms influence cell identity and function. Until recently, technological limitations prevented a genome-wide appraisal of isoform on in various parts the brain. Using enhanced long-read single-cell sequencing, we comprehensively analyze multiple mouse brain regions, subtypes, developmental timepoints from postnatal day 14 (P14) to adult (P56). For 75% genes, full-length expression varies along one or more axes phenotypic origin, underscoring pervasiveness regulation across scales. As...
Abstract Multimodal measurements have become widespread in genomics, however measuring open chromatin accessibility and splicing simultaneously frozen brain tissues remains unconquered. Hence, we devised Single-Cell-ISOform-RNA sequencing coupled with the Assay-for-Transposase-Accessible-Chromatin (ScISOr-ATAC). We utilized ScISOr-ATAC to assess whether alterations convergently affect same cell types or divergently different ones. applied three major conditions: comparing (i) Rhesus macaque...
Abstract 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 genomic sequence predict exon inclusion in neurons and glia as measured by long-read single-cell data human hippocampus frontal cortex. We found that alternative is harder compared both regions. Comparing glia, position of alternatively spliced exons differ more...
Abstract Long reads are reshaping RNA biology. However, determining alternative isoforms from long-read data is a complex and incompletely solved problem even when the reference genome known. Here we present IsoQuant - reference-based tool that accurately discovers novel transcripts with at least 3-fold lower false positive rate 1.8-fold increase in F1-score compared to other tools for Oxford Nanopore data. also increases performance Pacific Biosciences
Abstract Barcoding strategies are fundamental to droplet-based single-cell sequencing, and understanding the biases caveats between approaches is essential. Here, we comprehensively evaluated both short long reads of cDNA obtained through two marketed from 10x Genomics, “3’ assay” “5’ assay”, which attach barcodes at different ends mRNA molecule. Although barcode detection, cell-type identification, gene expression profile similar in assays, 5’ assay captured more exonic molecules fewer...
Abstract Alternative RNA splicing varies across brain regions, but the single-cell resolution of such regional variation is unknown. Here we present first investigation differential isoform expression (DIE) between by performing single cell long-read transcriptome sequencing in mouse hippocampus and prefrontal cortex 45 types at postnatal day 7 ( www.isoformAtlas.com ). Using tests for brain-region specific DIE, which outperform exon-based tests, detect hundreds DIE events traceable to...
RNA isoforms contribute to the diverse functionality of proteins they encode within cell. Visualizing how isoform expression differs across cell types and brain regions can inform our understanding disease gain or loss caused by alternative splicing with potential negative impacts. However, extent which this occurs in specific is largely unknown. This kind information that ScisorWiz plots provide an informative easily communicable manner. affords its user opportunity visualize genes any...
Abstract Full-length isoform sequencing has advanced our knowledge of biology 1–11 . However, apart from applying full-length to very few single cells 12,13 , been limited bulk tissue, cell lines, or sorted cells. Single splicing events have described for <=200 with great statistical success 14,15 but these methods do not describe mRNAs. short-read 3’ allowed identification many sub-types 16–23 isoforms types profiled. Using new method single-cell-isoform-RNA-sequencing (ScISOr-Seq) we...
Abstract Single-nuclei RNA-Seq is being widely employed to investigate cell types, especially of human brain and other frozen samples. In contrast single-cell approaches, however, the majority single-nuclei RNA counts originate from partially processed leading intronic cDNAs, thus hindering investigation complete isoforms. Here, using microfluidics, PCR-based artifact removal, target enrichment, long-read sequencing, we developed isoform RNA-sequencing (‘SnISOr-Seq’), applied it analysis...