Current Bioinformatics - Volume 16, Issue 10, 2021

Background: Verifying interactions between drugs and targets is key to discover new drugs. Many computational methods have been developed to predict drug-target interactions and performed successfully, but challenges still exist in the field. Objective: We have made an attempt to develop a machine learning method to predict drug-target affinity, which can determine the strength of the binding relationship between drug and Read More

Aims: The aim of this article was to find functional (or disease-relevant) modules using gene expression data. Background: Biotechnological developments are leading to a rapid increase in the volume of transcriptome data and thus driving the growth of interactome data. This has made it possible to perform transcriptomic analysis by integrating interactome data. Considering that genes do not exist nor operate in isolatio Read More

Background: m6A methylation is a ubiquitous post-transcriptional modification that exists in mammals. MeRIP-seq technology makes the acquisition of m6A data in the whole transcriptome under different conditions realizable. The specific regulation of the enzyme will present comethylation module on m6A methylation level data. Thus, mining the co-methylation module from which can help to unveil the mechanism of m6A Read More

Background: Malignant Mesothelioma (MM) is a rare but aggressive tumor that arises in the lungs. Commonly, costly imaging and laboratory resources, i.e. (X-rays imaging, Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET) scans, biopsies, and blood tests) have already been utilized for the diagnosis of MM. Even though these diagnostic measures are expensive and unavailable in distant areas, so Read More

Background: The number of human genetic variants deposited into publicly available databases has been increasing exponentially. Among these variants, non-synonymous single nucleotide polymorphisms (nsSNPs), also known as single Amino Acid Polymorphisms (SAPs), have been demonstrated to be strongly correlated with phenotypic variations of traits/diseases. Objective: However, the detailed mechanisms gove Read More

Background: Hepatocellular Carcinoma (HCC) is one of the most common malignant tumors. Due to the insidious onset and poor prognosis, most patients have reached the advanced stage at the time of diagnosis. Objective: Studies have shown that Dynamic Network Biomarkers (DNB) can effectively identify the critical state of complex diseases such as HCC from normal state to disease state. Therefore, it is very important Read More

Background: The analysis of DNA nucleotide sequence similarity among different species is crucial in identifying their functional, structural or evolutionary relationships. The number of bioinformatics tools designed to perform the similarity analysis of nucleotide sequences has been growing rapidly. According to the current literature, alignment-free methods have not been performed on repetitive nucleotide sequenc Read More

Background: The open and accessible regions of the chromosome are more likely to be bound by transcription factors which are important for nuclear processes and biological functions. Studying the change of chromosome flexibility can help to discover and analyze disease markers and improve the efficiency of clinical diagnosis. Current methods for predicting chromosome flexibility based on Hi-C data include the Flexibil Read More

Background: SARS-Cov-2 is a newly emerged coronavirus and causes a severe type of pneumonia in the host organism. So, it is an urgent need to find some inhibitors against SARS-Cov-2. Therefore, drug repurposing study is an effective strategy for treating pneumonia to find the inhibitors of SARS-Cov-2 proteins. Methods: For this purpose, a library of 2500 verified drug chemical compounds was generated and the compounds Read More

Background: Through the in-depth study of the thermophilic protein heat resistance principle, it is of great significance for people to deeply understand the folding, structure, function, and the evolution of proteins, and the directed design and modification of protein molecules in protein processing. Objective: Aiming at the problem of low accuracy and low efficiency of thermophilic protein prediction, a thermophilic protei Read More

Background: Endometrial carcinoma (EC) is one of the most common malignancies in women worldwide. For EC patients discovered at an early stage, the prognosis is good. However, the advanced EC patients (stage III-IV) have very poor prognoses. The competitive endogenous RNAs (ceRNA) regulatory network in EC remains unclear, and the relationship between hub RNAs and important clinical characters (clinical sta Read More