Current Bioinformatics - Volume 16, Issue 4, 2021

Bioactive peptides (BPs) are peptides with hormonal or pharmacological properties. They play a key role in growth, metabolism, disease, aging and death by affecting digestion, endocrine, cardiovascular, immune and nervous systems. They show the potential therapeutic effects on blood pressure-lowering (ACE inhibitory), anticancer, antithrombotic, antibacterial, anti-inflammatory, antioxidant, antiobesity, anti-genotoxic Read More

Background: Batch effects are usually introduced in gene expression data, which can dramatically reduce the accuracy of statistical inference in the genomic analysis since samples in different batches cannot be directly comparable. Objective: To accurately measure biological variability and obtain correct statistical inference, we considered to correct/remove the batch effects for merging the samples from different batches i Read More

Background: A large number of studies have shown that susceptibility to diseases may be related to some Single Nucleotide Polymorphisms (SNPs). Therefore, the location of SNPs associated with diseases in genes can help us understand the genetic mechanism of disease, intervene in risk SNPs and prevent some genetic diseases. Methods: Based on Graph Signal Processing (GSP) theory, a novel method is proposed to locate the Read More

Background: MicroRNA is a type of non-coding RNA molecule whose length is about 22 nucleotides. The growing evidence shows that microRNA makes critical regulations in the development of complex diseases, such as cancers, and cardiovascular diseases. Predicting potential microRNA-disease associations can provide a new perspective to achieve a better scheme of disease diagnosis and prognosis. However, there is a Read More

Background: Antimicrobial peptides (AMPs) can defend the hosts against various pathogens and are found in almost every life form from microorganisms to humans. As the rapid increase of drug-resistant strains in recent years is presenting a serious challenge to healthcare, antimicrobial peptides (AMPs) can revolutionize the antimicrobial development against the drugresistant microbes. Objective: The object Read More

Background: Piwi-interacting RNAs (piRNAs) are an amazing class of small noncoding RNAs (sncRNAs) known for its promising role in germline and somatic cells. Myriad functional studies have been performed to unveil the true potential of this class of ncRNAs; however, global features encoded in their sequence and structure have not been explored. Objectives: We aim to identify the sequence and structural level characteristic f Read More

Background: Circular RNAs (circRNAs) are a newly discovered type of non-coding RNA, which have been demonstrated to act as microRNA (miRNA) “sponges” to modulate gene expression. Emerging evidence has confirmed that circRNAs take part in many biological processes in a variety of malignant tumors, including gliomas, suggesting that they could serve as biomarkers or therapeutic targets for tumors. The purpose of t Read More

Background: Research has shown that essential proteins play important roles in the development and survival of organisms. Because of the high costs of traditional biological experiments, several computational prediction methods based on known protein-protein interactions (PPIs) have been recently proposed to detect essential proteins. Objective: Here, a novel prediction model called IoMCD is proposed to identify essential p Read More

Background: Predicting the protein-ATP binding sites is a highly unbalanced binary classification problem, and higher precision prediction through the machine learning methods is of great significance to the researches on proteins’ functions and the design of drugs. Objective: Most existing researches typically select 17aa as the length of window by experience, and extract features by the Position-specific Scoring Matrix (PSS Read More

Background: Colorectal cancer (CRC) is the third most common cancer among women and men in the USA, and recent studies have shown an increasing incidence in less developed regions, including Sub-Saharan Africa (SSA). We developed a hybrid (DNA mutation and RNA expression) signature and assessed its predictive properties for the mutation status and survival of CRC patients. Methods: Publicly-available microar Read More

Background: Essential proteins play a crucial role in most of the living organisms. The computer-based task of predicting essential proteins is important for target protein identification, disease treatment and suitable drug development. Objective: Traditionally, many experimental and centrality measures have been proposed by researchers to predict protein essentiality. Methods: The prediction accuracy, sensitivity, an Read More

Background: Coronary artery disease (CAD) is an important cause of mortality and morbidity globally. Objective: The early prediction of the CAD would be valuable in identifying individuals at risk, and in focusing resources on its prevention. In this paper, we aimed to establish a diagnostic model to predict CAD by using three approaches of ANN (pattern recognition-ANN, LVQ-ANN, and competitive ANN). Methods: One prom Read More

Background: Primary tracheal adenoid cystic carcinoma is a rare, slow-growing pulmonary malignancy. Due to the low incidence, clinicians are unable to diagnose and treat such disease, which is prone to cause misdiagnosis or missed diagnosis, consequently leading to delayed treatment. Case Presentation: Here, we reported a case of a 72-year-old woman who was diagnosed as primary bronchial adenoid cystic carcinom Read More