Current Bioinformatics - Volume 17, Issue 10, 2022

Background: Technical advances and cost reduction have allowed for the worldwide popularity of array platforms. Otherwise called “molecular karyotyping”, it yields a large amount of CNV data, which is useless without interpretation. Objective: This study aims to review existing CNV interpretation software and algorithms to reveal their possibilities and limitations. Results: Open and user-friendly CNV interpretation soft Read More

Single-cell RNA-sequencing (scRNA-seq) is a rapidly growing field in transcriptomics, which generates a tremendous amount of gene expression data at the single-cell level. Improved statistical approaches and tools are required to extract informative knowledge from such data. Gene network modeling and analysis is one such approach for downstream analysis of scRNA-seq data. Therefore, newer and innovative methods hav Read More

Background: Nowadays, non-small cell lung cancer (NSCLC) is a common and highly fatal malignancy worldwide. Therefore, identifying the potential prognostic markers and therapeutic targets is urgent for patients. Objective: This study aimed at finding hub targets associated with NSCLC using multiple databases. Methods: Differentially expressed genes (DEGs) from Genome Expression Omnibus (GEO) cohorts were Read More

Background: Molecular alterations have been recognized as valuable diagnostic biomarkers for papillary thyroid carcinoma (PTC). Objectives: This study aimed to identify immune-related gene signatures associated with PTC progression using a computational pipeline and to develop an expression-based panel for rapid PTC risk classification. Methods: RNA-seq data and clinical information for PTC samples were download Read More

Background: Shizi Sanhua Decoction, a traditional Chinese medicine (TCM) prescription, shows a treatment advantage on male oligospermia. While due to the complexity of the compatibility (multiple herbs composition), the underlying mechanism remains to be deciphered. Methods: Herbs-ingredients-target genes were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform ( Read More

Background: There are correlations between the multiple types of data stored in the tensor space. The matrix formed by the data in the high-dimensional space is of low rank. Therefore, the potential association between genes and cancers can be explored in low-rank space. Tensor robust principal component analysis (TRPCA) is used to extract information by obtaining coefficient tensors with low-rank representation. In pra Read More