Current Bioinformatics - Volume 16, Issue 9, 2021

There has been an exponential rise in the field of bioinformatics in the last decade. The specialists of this field need to be well versed in computing, statistics, and mathematics, along with expertise in biological sciences. This review is an attempt to understand the existing skill gaps in the education of bioinformatics globally and to give the policy developers some indicators while designing the curriculum of the bioinformati Read More

Background: Intrinsically disordered proteins lack a well-defined three-dimensional structure under physiological conditions. They have performed multiple functions in life activities and are closely related to many human diseases. The identification of the disordered region of intrinsically disordered proteins is important to protein function annotation. Objective: To accurately identify the disordered regions in intrinsically dis Read More

Background: Human brain development is a series of complex processes exhibiting profound changes from gestation to adulthood. Objective: We aimed to construct dynamic developmental networks for each anatomical structure of the human brain based on omics’ levels in order to gain a new systematical brain map on the molecular level. Methods: We performed the brain development analyses by constructing dynamical Read More

Aim: In exploiting cancer initialization and progression, a great challenge is to identify the driver genes. Background: With advances in Next-Generation Sequencing (NGS) technologies, the identification of specific oncogenic genes has emerged through integrating multi-omics data. Although the existing computational models have identified many common driver genes, they rely on individual regulatory mechanisms Read More

Background: The effect of quercetin on blood glucose levels has been widely studied. However, the mechanism of hypoglycemic effect of quercetin remains unclear. Objective: To elucidate hypoglycemic effect of quercetin, microarray data of GSE38067 dataset have been used to screen Differential Hub Genes (DHGs) by differential expression analysis, weighted gene co-expression network analysis and protein-protein inte Read More

Background: Essential proteins play an important role in the process of life, which can be identified by experimental methods and computational approaches. Experimental approaches to identify essential proteins are of high accuracy but with the limitation of time and resource-consuming. Objective: Herein, we present a computational model (PEPRF) to identify essential proteins based on machine learning. Methods: Differe Read More

Background: CRISPR/Cas9, a new generation of targeted gene editing technology with low cost and simple operation has been widely employed in the field of gene editing. The erroneous cutting of off-target sites in CRISPR/Cas9 is called off-target effect, which is also the biggest complication that CRISPR/Cas9 confronts in practical application. To be specific, the off-target effects could lead to unexpected gene editing results. T Read More

Background: Long non-coding RNAs (lncRNAs) are nonprotein-coding transcripts of more than 200 nucleotides in length. In recent years, studies have shown that long non-coding RNAs (lncRNA) play a vital role in various biological processes, complex disease diagnosis, prognosis, and treatment. Objective: Analysis of known lncRNA-disease associations and prediction of potential lncRNA-disease associations are necess Read More

Background: Mammalian genes are regulated at the transcriptional and posttranscriptional levels. These mechanisms may involve the direct promotion or inhibition of transcription via a regulator or post-transcriptional regulation through factors such as micro (mi)RNAs. Objective: Construct gene regulation relationships modulated by causality inference-based miRNA- (transition factor)-(target gene) networks and a Read More

Objectives: Gastrointestinal (GI) cancer is the most common and lethal malignant tumor, while limited research and biomarkers are available to stratify patients who are likely to benefit from immunotherapy in GI cancers. During early diagnosis and prognosis of GI cancers, searching for shared potential biomarkers and differences among stages is an urgent and challenging task. The staging RNA expression data correspo Read More

Background: Identification of protein phenotypic annotations is an essential and challenging problem in modern genetics. Such problem is related to some serious diseases, including cancers, HIV and so on. The factors of genotype and environment increase the difficulties in determining the phenotype of proteins. The experiment methods to achieve such a goal are always timeconsuming and expensive. Objective: The aim of Read More