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Study on the Mechanisms of Banxia Xiexin Decoction in Treating Diabetic Gastroparesis Based on Network Pharmacology
This study is designated to reveal the molecular mechanisms of BXD in treating DGP by adopting a creative approach known as network pharmacology to explore the active ingredients and therapeutic targets of BXD. In our study, 730 differentially expressed genes of DGP were obtained, and 30 potential targets of BXD against DGP were screened out (including ADRB2, DRD1, FOS, MMP9, FOSL1, FOSL2, JUN, MAP2, DRD2, MYC, F3, CDKN1A, IL6, NFKBIA, ICAM1, CCL2, SELE, DUOX2, MGAM, THBD, SERPINE1, ALOX5, CXCL11, CXCL2, CXCL10, RUNX2, CD40LG, C1QB, MCL1, and ADCYAP1). Based on the findings, BXD contains 60 compounds with therapeutic effec...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 9, 2020 Category: Bioinformatics Source Type: research

Comprehensive Analysis of Long Non-coding RNA-Associated Competing Endogenous RNA Network in Duchenne Muscular Dystrophy
In conclusion, our latest bioinformatic analysis demonstrated that lncRNA is likely involved in DMD. This work highlights the importance of lncRNA and provides new insights for exploring the molecular mechanism of DMD.Graphic abstractThe created ceRNA network contained 6 lncRNA nodes, 69 mRNA nodes, 27 miRNA nodes and 102 edges, while four hub lncRNAs (XIST,AL132709,LINC00310,ALDH1L1-AS2) were uncovered. Remarkably, KEGG analysis indicated that targeted mRNAs in the network were mainly enriched in “microRNAs in cancer” and “proteoglycans in cancer”. Our study may offer novel perspectives on the pathogenesis of DMD ...
Source: Interdisciplinary Sciences, Computational Life Sciences - September 1, 2020 Category: Bioinformatics Source Type: research

Review of Artificial Intelligence Applications and Algorithms for Brain Organoid Research
AbstractThe human brain organoid is a miniature three-dimensional tissue culture that can simulate the structure and function of the brain in an in vitro culture environment. Although we consider that human brain organoids could be used to understand brain development and diseases, experimental models of human brain organoids are so highly variable that we apply artificial intelligence (AI) techniques to investigate the development mechanism of the human brain. Therefore, this study briefly reviewed commonly used AI applications for human brain organoid-magnetic resonance imaging, electroencephalography, and gene editing t...
Source: Interdisciplinary Sciences, Computational Life Sciences - August 23, 2020 Category: Bioinformatics Source Type: research

Fully Automatic Arteriovenous Segmentation in Retinal Images via Topology-Aware Generative Adversarial Networks
AbstractRetinal image contains rich information on the blood vessel and is highly related to vascular diseases. Fully automatic and accurate identification of arteries and veins from the complex background of retinal images is essential for analyzing eye-relevant diseases, and monitoring progressive eye diseases. However, popular methods, including deep learning-based models, performed unsatisfactorily in preserving the connectivity of both the arteries and veins. The results were shown to be disconnected or overlapped by the twos and thus manual calibration was needed to refine the results. To tackle the problem, this pap...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 27, 2020 Category: Bioinformatics Source Type: research

Shiny-DEG: A Web Application to Analyze and Visualize Differentially Expressed Genes in RNA-seq
AbstractRNA-seq analysis has become one of the most widely used methods for biological and medical experiments, aiming to identify differentially expressed genes at a large scale. However, due to lack of programming skills and statistical background, it is difficult for biologists including faculty and students to fully understand what the RNA-seq results are and how to interpret them. In recent years, even though, there are several programs or websites that assist researchers to analyze and visualize NGS results, they have several limitations. Therefore, Shiny-DEG, a web application that facilitates the exploration and vi...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 13, 2020 Category: Bioinformatics Source Type: research

Impact of IL28 Genotypes and Modeling the Interactions of HCV Core Protein on Treatment of Hepatitis C
ConclusionGenerally, mutations in all core CVR regions in all patients showed a relationship between such substitutions and higher liver enzymes that can result in advanced liver disease progression in HCV infected patients. Furthermore, immunoinformatics analysis determined the possible immunodominant regions to be considered in HCV vaccine designs. Furthermore, no association between SVR and IL28B polymorphism was shown. In silico analysis determined modification sites, structures, B-cell epitopes of core protein and interactions with several interactors can lead to persistent  HCV infection in the cell and the progress...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 11, 2020 Category: Bioinformatics Source Type: research

Efficient System Wide Metabolic Pathway Comparisons in Multiple Microbes Using Genome to KEGG Orthology (G2KO) Pipeline Tool
AbstractComparison of system-wide metabolic pathways among microbes provides valuable insights of organisms ’ metabolic capabilities that can further assist in rationally screening organisms in silico for various applications. In this work, we present a much needed, efficient and user-friendly Genome to KEGG Orthology (G2KO) pipeline tool that facilitates efficient comparison of system wide metabolic ne tworks of multiple organisms simultaneously. The optimized strategy primarily involves automatic retrieval of the KEGG Orthology (KO) identifiers of user defined organisms from the KEGG database followed by overlaying and...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 5, 2020 Category: Bioinformatics Source Type: research

Phylogenetic Analysis and Structural Perspectives of RNA-Dependent RNA-Polymerase Inhibition from SARs-CoV-2 with Natural Products
AbstractMost recently, an outbreak of severe pneumonia caused by the infection of SARS-CoV-2, a novel coronavirus first identified in Wuhan, China, imposes serious threats to public health. Upon infecting host cells, coronaviruses assemble a multi-subunit RNA-synthesis complex of viral non-structural proteins (nsp) responsible for the replication and transcription of the viral genome. Therefore, the role and inhibition of nsp12 are indispensable. A cryo-EM structure of RdRp from SARs-CoV-2 was used to identify novel drugs from Northern South African medicinal compounds database (NANPDB) by using computational virtual scree...
Source: Interdisciplinary Sciences, Computational Life Sciences - July 2, 2020 Category: Bioinformatics Source Type: research

AC-Caps: Attention Based Capsule Network for Predicting RBP Binding Sites of LncRNA
AbstractLong non-coding RNA(lncRNA) is one of the non-coding RNAs longer than 200 nucleotides and it has no protein encoding function. LncRNA plays a key role in many biological processes. Studying the RNA-binding protein (RBP) binding sites on the lncRNA chain helps to reveal epigenetic and post-transcriptional mechanisms, to explore the physiological and pathological processes of cancer, and to discover new therapeutic breakthroughs. To improve the recognition rate of RBP binding sites and reduce the experimental time and cost, many calculation methods based on domain knowledge to predict RBP binding sites have emerged. ...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 21, 2020 Category: Bioinformatics Source Type: research

Optimized Attribute Selection Using Artificial Plant (AP) Algorithm with ESVM Classifier (AP-ESVM) and Improved Singular Value Decomposition (ISVD)-Based Dimensionality Reduction for Large Micro-array Biological Data
AbstractIn the tremendous field of the bioinformatics look into, enormous volume of genetic information has been produced. Higher throughput gadgets are made accessible at lower cost made the age of Big data. In a time of developing information multifaceted nature and volume and the approach of huge information, feature selection has a key task to carry out in decreasing high dimensionality in AI issues. Dealing with such huge data has turned out to be incredibly testing strategy for choosing the exact features in enormous medical databases. Large clinical data frequently comprise of an enormous number of identifiers of th...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 11, 2020 Category: Bioinformatics Source Type: research

ProtPCV: A Fixed Dimensional Numerical Representation of Protein Sequence to Significantly Reduce Sequence Search Time
AbstractProtein sequence is a wealth of experimental information which is yet to be exploited to extract information on protein homologues. Consequently, it is observed from publications that dynamic programming, heuristics and HMM profile-based alignment techniques along with the alignment free techniques do not directly utilize ordered profile of physicochemical properties of a protein to identify its homologue. Also, it is found that these works lack crucial bench-marking or validation in absence of which their incorporation in search engines may appears to be questionable. In this direction this research approach offer...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 9, 2020 Category: Bioinformatics Source Type: research

GAD: A Python Script for Dividing Genome Annotation Files into Feature-Based Files
AbstractNowadays, the manipulation and analysis of genomic data stored in publicly accessible repositories have become a daily task in genomics and bioinformatics laboratories. Due to the enormous advancement in the field of genome sequencing and the emergence of many projects, bioinformaticians have pushed for the creation of a variety of programs and pipelines that will automatically analyze such big data, in particular the pipelines of gene annotation. Dealing with annotation files using easy and simple programs is very important, particularly for non-developers, enhancing the genomic data analysis acceleration. One of ...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 9, 2020 Category: Bioinformatics Source Type: research

Next-Generation Sequencing Data Analysis on Pool-Seq and Low-Coverage Retinoblastoma Data
This study provides a guideline for performing NGS data analysis pipeline on pool-seq and low-coverage sequencing data in conjunction. To get more conclusive outcomes of these two strategies, we recommend using cancer data having higher mutation rates and larger pools. (Source: Interdisciplinary Sciences, Computational Life Sciences)
Source: Interdisciplinary Sciences, Computational Life Sciences - June 8, 2020 Category: Bioinformatics Source Type: research

Retinal Image Analysis for Ocular Disease Prediction Using Rule Mining Algorithms
AbstractMedical image processing is now gaining a significant momentum in clinical situation to undertake diagnosis of different anatomical defects. However, with regard to eye diseases, there is no such well-defined image processing technique in medical image analysis. The scope of this study is to automate computer analysis of ocular disease-related retinal images, which may ease the job of ophthalmologists to rule out the diseased condition. In this present work, eye images are subjected for developing a reliable tool for processing the eye retinal fundus images. The primary objective is to effectively probe retinal ima...
Source: Interdisciplinary Sciences, Computational Life Sciences - June 7, 2020 Category: Bioinformatics Source Type: research

Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov
AbstractA novel coronavirus, called 2019-nCoV, was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. Although there are some drugs to treat 2019-nCoV, there is no proper scientific evidence about its activity on the virus. It is of high significance to develop a drug that can combat the virus effectively to save valuable human lives. It usually takes a much longer time to develop a drug using traditional methods. For 2019-nCoV, it is now better to rely on some alternative methods such as deep learning to develop drugs that can combat such a disease effectively...
Source: Interdisciplinary Sciences, Computational Life Sciences - May 31, 2020 Category: Bioinformatics Source Type: research