[HTML][HTML] Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single macrophages infected with Candida albicans
… spliced in) of previously annotated splicing events and identified differential isoform usage
between single-infected macrophages using BRIE 29 (… Our analysis of single cells revealed …
between single-infected macrophages using BRIE 29 (… Our analysis of single cells revealed …
Single-cell analysis of the transcriptome and epigenome
… for single-cell alternative splicing analysis. Moreover, recently introduced SMART-seq3
method, with improved sensitivity and UMI incorporation promises to accelerate discovery of …
method, with improved sensitivity and UMI incorporation promises to accelerate discovery of …
An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data
H Matsumoto, T Hayashi, H Ozaki… - NAR Genomics and …, 2020 - academic.oup.com
… to quantify the transcriptomes of individual cells, infer cell types and investigate differential
expression among cell types… , and we can now discover such cell type-specific splicing events. …
expression among cell types… , and we can now discover such cell type-specific splicing events. …
[HTML][HTML] Exploring the complexity of cortical development using single-cell transcriptomics
… splicing, non-coding transcripts, and nascent RNAs. Importantly, all of these comprehensive
single-cell genomics analysis … the comprehensive understanding of cellular subpopulations. …
single-cell genomics analysis … the comprehensive understanding of cellular subpopulations. …
Single-cell genomics and regulatory networks for 388 human brains
… levels, from gene expression in individual cells to complex brain circuits between cells (1–3).
At every level, they manifest themselves differently depending on the cell type in question. …
At every level, they manifest themselves differently depending on the cell type in question. …
Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis
… To investigate whether specific OL populations are targeted in MS, we isolated single cells
… Alternatively spliced cassette exons were identified with BRIE 0.1.3 in the cell type clusters …
… Alternatively spliced cassette exons were identified with BRIE 0.1.3 in the cell type clusters …
[HTML][HTML] Rapid and sensitive single-cell RNA sequencing with SHERRY2
L Di, B Liu, Y Lyu, S Zhao, Y Pang, C Zhang, J Wang… - BMC biology, 2022 - Springer
… The frequency of exon usage in each cell was calculated by BRIE (v2.0.5) [50]. For each …
read should detect junctions involved in this exon splicing events. A pairwise comparison of …
read should detect junctions involved in this exon splicing events. A pairwise comparison of …
dSreg: a Bayesian model to integrate changes in splicing and RNA-binding protein activity
… We analyzed the data also with MISO, BRIE and DARTS. Both BRIE and DARTS use prior
information to improve detection of splicing changes (Huang and Sanguinetti, 2017; Katz et al.…
information to improve detection of splicing changes (Huang and Sanguinetti, 2017; Katz et al.…
Statistical Methods for Single‐Cell RNA‐Sequencing
TS Andrews, V Yu. Kiselev… - Handbook of Statistical …, 2019 - Wiley Online Library
… often each splice junction is used. Splice junction usage is quantified by the percent splicing
… The prior allows BRIE to overcome some of the issues related to dropouts and it serves as a …
… The prior allows BRIE to overcome some of the issues related to dropouts and it serves as a …
Self-supervised deep learning of gene–gene interactions for improved gene expression recovery
… indicators of underlying biology processes, presenting discriminative signatures of the
cells. A genomic data analysis framework that is capable of leveraging the underlying gene–gene …
cells. A genomic data analysis framework that is capable of leveraging the underlying gene–gene …