Current Bioinformatics - Volume 17, Issue 7, 2022

Background: Single-cell technologies provide unprecedented opportunities to study heterogeneity of molecular mechanisms. In particular, single-cell RNA-sequence data have been successfully used to infer gene regulatory networks with stochastic expressions. However, there are still substantial challenges in measuring the relationships between genes and selecting the important genetic regulations. Objective: This pro Read More

Background: In biology, the translation of genetic information to its corresponding protein sequences is carried out using the Universal Genetic Code. Out of all the possible combinations of 20 amino acids, proteins are formed by the possible combinations that occur naturally. This leaves a large number of unknown combinations of protein sequences that include the Never Born Proteins. A Never Born Protein is a theoretical Read More

Background: Inferring feature importance is both a promise and challenge in bioinformatics and computational biology. While multiple biological computation methods exist to identify decisive factors of single cell subpopulation, there is a need for a comprehensive toolkit that presents an intuitive and custom view of the feature importance. Objective: We developed a Feature-scML, a scalable and friendly toolkit that allows Read More

Objectives: Ganoderic acid Me [GA-Me], a major bioactive triterpene extracted from Ganoderma lucidum, is often used to treat immune system diseases caused by viral infections. Although triterpenes have been widely employed in traditional medicine, the comprehensive mechanisms by which GA-Me acts against viral infections have not been reported. Sendai virus [SeV]-infected host cells have been widely employed as a Read More

Background: CENPA is a rare histone variant that regulates various active centromeres and neocentromeres via diverse signal pathways. However, the expression of CENPA correlated with the prognosis of patients in human pan-cancer is still largely underexplored. Objective: To find the role of CENPA in the prognosis and immunotherapy of cancer patients. Methods: In this study, multiple bioinformatic methods, including the ON Read More

Background: A promoter is a DNA regulatory region typically found upstream of a gene that plays a significant role in gene transcription regulation. Due to their function in transcription initiation, sigma (σ) promoter sequences in bacterial genomes are important. σ70 is among the most notable sigma factors. Therefore, the precise recognition of the σ70 promoter is essential in bioinformatics. Objective: Several methods for pred Read More

Background: Breast cancer is one cancer that develops from breast tissue and one of the major reasons of deaths in of women all over the world. The tumor-infiltrating lymphocytes in tumor immune microenvironment are correlated with the prognosis in breast cancer patients, and play an important role in the occurrence and development of breast cancer. Methods: In this study, by integrating the immune gene expression Read More

Background: RNA-dependent RNA polymerase (RdRp) contributes to the transcription cycle of the SARS-CoV-2 virus with the possible assistance of nsp-7-8 cofactors. Objective: The study aims to investigate the viral protective effects of complementary drugs in computational approaches that use viral proteins. Methods: For the in silico studies, the identified compounds were subjected to molecular docking with RdRp protein fol Read More

Background: As an essential positively charged RNA modification, N7-methylguanosine (m7G) has been reported to be associated with multiple diseases including cancers. While transcriptomewide m7G sites have been identified by high-throughput sequencing approaches, the disease-associated m7G sites are still largely unknown. Therefore, computational methods are urgently needed to predict potential m7G-disease Read More