Immune cell heterogeneity due to the differential expression of RNA splicing variants still remains unexplored. This is mainly because single-cell imaging technologies of splicing variants with...
Read More »FreePSI – an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome
Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for ...
Read More »Network embedding-based representation learning for single cell RNA-seq data
Single cell RNA-seq (scRNA-seq) techniques can reveal valuable insights of cell-to-cell heterogeneities. Projection of high-dimensional data into a low-dimensional subspace is a powerful strategy in general for mining such big data. However, scRNA-seq suffers from higher noise and lower coverage ...
Read More »Improved transcript discovery from partially observed short reads caused by missing information
The automated transcript discovery and quantification of high-throughput RNA sequencing (RNA-seq) data are important tasks of next-generation sequencing (NGS) research. However, these tasks are challenging due to the uncertainties that arise in the inference of complete splicing isoform variants from ...
Read More »Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites
Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome-wide binding sites of RNA-binding protein (RBP) with high resolution. Tsinghua University researchers apply a soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs that specifically bind the ...
Read More »Splicing-based RNA tagging (SRT) – a new method for tissue-specific RNA-seq of transgenic worms
Current approaches to profiling tissue-specific gene expression in C. elegans require delicate manipulation and are difficult under certain conditions, e.g. from dauer or aging worms. Researchers at Tsinghua University have developed an easy and robust method for tissue-specific RNA-seq by ...
Read More »Sinova – Systematic Reconstruction of Molecular Cascades Using Single-Cell RNA-Seq
The growth plate (GP) comprising sequentially differentiated cell layers is a critical structure for bone elongation and regeneration. Although several key regulators in GP development have been identified using genetic perturbation, systematic understanding is still limited. Here, researchers from Tsinghua ...
Read More »mRIN – direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data
The volume of RNA-Seq data sets in public repositories has been expanding exponentially, providing unprecedented opportunities to study gene expression regulation. Because degraded RNA samples, such as those collected from post-mortem tissues, can result in distinct expression profiles with potential ...
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