The accurate quantification of tumor-infiltrating immune cells turns crucial to uncover their role in tumor immune escape, to determine patient prognosis and to predict response to immune checkpoint blockade. Current state-of-the-art methods that qua...
Unsupervised methods, such as clustering methods, are essential to the analysis of single-cell genomic data. The most current clustering methods are designed for one data type only, such as single-cell RNA sequencing (scRNA-seq), single-cell ATAC seq...
Disease-gene association through genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms that correlate with specific diseases needs statistical analysis of associations. Considering the ...
A promoter is a region in the DNA sequence that defines where the transcription of a gene by RNA polymerase initiates, which is typically located proximal to the transcription start site (TSS). How to correctly identify the gene TSS and the core prom...
Origins of replication sites (ORIs), which refers to the initiative locations of genomic DNA replication, play essential roles in DNA replication process. Detection of ORIs' distribution in genome scale is one of key steps to in-depth understanding t...
Although great progress has been made in prognostic outcome prediction, small sample size remains a challenge in obtaining accurate and robust classifiers. We proposed the Rescaled linear square Regression based Least Squares Learning (RRLSL), a join...
Angiosarcomas are soft-tissue sarcomas that form malignant vascular tissues. Angiosarcomas are very rare, and due to their aggressive behavior and high metastatic propensity, they have poor clinical outcomes. Hemangiosarcomas commonly occur in domest...
MOTIVATION: DNA methylation is a biological process impacting the gene functions without changing the underlying DNA sequence. The DNA methylation machinery usually attaches methyl groups to some specific cytosine residues, which modify the chromatin...
Despite impressive improvement in the next-generation sequencing technology, reliable detection of indels is still a difficult endeavour. Recognition of true indels is of prime importance in many applications, such as personalized health care, diseas...
Exon skipping using antisense oligonucleotides (ASOs) has recently proven to be a powerful tool for mRNA splicing modulation. Several exon-skipping ASOs have been approved to treat genetic diseases worldwide. However, a significant challenge is the d...