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- Volume 16, Issue 6, 2021
Current Bioinformatics - Volume 16, Issue 6, 2021
Volume 16, Issue 6, 2021
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Bioinformatics Tools and Databases for Genomics-assisted Breeding and Population Genetics of Plants: A Review
Authors: Supriya B. Aglawe, Amit Kumar Verma and Atul Kumar UpadhyayGenomics is the study of the complete genetic material of an organism. It would not be an exaggeration to say that we are at the peak of the genomics era as with the advent of high-throughput sequencing technologies we have an enormous amount of genomic data coming every day. Genomics assisted breeding (GAB) is becoming increasingly popular in the field of crop improvement. GAB utilizes available genomics inf Read More
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Intelligent Techniques Analysis for Glycosylation Site Prediction
Authors: Alhasan Alkuhlani, Walaa Gad, Mohamed Roushdy and Abdel-Badeeh M. SalemBackground: Glycosylation is one of the most common post-translation modifications (PTMs) in organism cells. It plays important roles in several biological processes including cell-cell interaction, protein folding, antigen recognition, and immune response. In addition, glycosylation is associated with many human diseases such as cancer, diabetes and coronaviruses. The experimental techniques for identifying glycosyl Read More
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Chemical Genetic Validation of GWAS-derived Disease Loci
Authors: Yuan Quan and Hong-Yu ZhangBackground: Genome-wide association studies (GWAS) have opened the door to unprecedented large-scale identification of susceptibility loci for human diseases and traits. However, it is still a great challenge to validate these loci and elucidate how these sequence variants give rise to the genetic and phenotypic changes. Because many drug targets are genetic disease genes and the general drug mode of action (MoA, ago Read More
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Predicting Interactions Between Pathogen and Human Proteins Based on the Relation Between Sequence Length and Amino Acid Composition
Authors: Saud Alguwaizani, Shulei Ren, De-Shuang Huang and Kyungsook HanAim: Both bacterial infection and viral infection involve a large number of protein-protein interactions (PPIs) between a pathogen and its target host. Background: So far, many computational methods have focused on predicting PPIs within the same species rather than PPIs across different species. Methods: From the extensive analysis of PPIs between Yersinia pestis bacteria and humans, we recently discovered an interestin Read More
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Prediction of Microbe-drug Associations Based on Chemical Structures and the KATZ Measure
Authors: Lingzhi Zhu, Guihua Duan, Cheng Yan and Jianxin WangBackground: Microbial communities have important influences on our health and disease. Identifying potential human microbe-drug associations will be greatly advantageous to explore complex mechanisms of microbes in drug discovery, combinations and repositioning. Until now, the complex mechanism of microbe-drug associations remains unknown. Objective: Computational models play an important role in discove Read More
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Effective Classification of Melting Curve in Real-time PCR Based on Dynamic Filter-based Convolutional Neural Network
Authors: Di Gai, Xuanjing Shen and Haipeng ChenBackground: The effective classification of the melting curve is conducive to measure the specificity of the amplified products and the influence of invalid data on subsequent experiments is excluded. Objective: In this paper, a convolutional neural network (CNN) classification model based on dynamic filter is proposed, which can categorize the number of peaks in the melting curve image and distinguish the pollution data repr Read More
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A Network Pharmacology Approach to Explore the Underlying Mechanism of Tufuling Qiwei Tangsan in Treating Psoriasis
Authors: Xiaolei Ma, Yinan Lu, Yang Lu and Zhili PeiBackground: Tufuling Qiwei Tangsan (TQTS) is a commonly used Mongolian medicine preparation against psoriasis in China. However, its mechanism of action and molecular targets for the treatment of psoriasis is still unclear. Network pharmacology can reveal the synergistic mechanism of drugs at the molecular, target, and pathway levels and is suitable for the complex study of traditional Chinese medicine f Read More
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Development of a Gene Expression Panel, for the Prediction of Protein Abundances in Cancer Cell Lines
Authors: Gunhee Lee, Yeun-Jun Chung and Minho LeeBackground: Due to the ease of quantifying mRNA expression in comparison with that of protein abundances, many studies have utilized it to infer protein product quantification. However, the mRNA expression values for a gene and its protein products are not known to have a strong relationship, because of the complex mechanisms required to regulate the amounts of protein levels, from translation to post-translatio Read More
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Development of Machine Learning Based Blood-brain Barrier Permeability Prediction Models Using Physicochemical Properties, MACCS and Substructure Fingerprints
Authors: Deeksha Saxena, Anju Sharma, Mohammed H. Siddiqui and Rajnish KumarBackground: Blood-Brain Barrier (BBB) protects the central nervous system from systemic circulation and maintains the homeostasis of the brain. BBB permeability is one of the essential characteristics of drugs acting on the central nervous system to indicate if the drug could reach the brain or not. The available laboratory methods for the prediction of BBB permeability are accurate but expensive and time-consuming. Theref Read More
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Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework
Authors: Fee F. Ahmed, Mst. Shamima Khatun, Md. Parvez Mosharaf and Md. N. H. MollahBackground: Protein-protein interactions (PPI) play a vital role in a wide range of biological processes starting from cell-cell interactions to developmental control in all organisms. However, experimental identification of PPI is often laborious, time-consuming and costly compared to computational prediction. There are several computational prediction models in the literature based on complete training samples, but Read More
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Genome-wide Characterization Deciphers Distinct Properties of Aquaporins in Six Phytophthora Species
Background: Aquaporins, also known as major intrinsic proteins (MIPs), facilitate the membrane diffusion of water and some other small solutes. The roles of MIPs in plant physiological processes are established and now their roles in plant-pathogen interactions are getting more attention. Objective: To investigate the evolution, diversity, and structural insights of Phytophthora MIPs (PhyMIPs) and to compare them to those i Read More
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Volumes & issues
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Volume 20 (2025)
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Volume 19 (2024)
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Volume 18 (2023)
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Volume 17 (2022)
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Volume 16 (2021)
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Volume 15 (2020)
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Volume 14 (2019)
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Volume 13 (2018)
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Volume 12 (2017)
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Volume 11 (2016)
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Volume 10 (2015)
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Volume 9 (2014)
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Volume 8 (2013)
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Volume 7 (2012)
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Volume 6 (2011)
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Volume 5 (2010)
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Volume 4 (2009)
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Volume 3 (2008)
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Volume 2 (2007)
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Volume 1 (2006)
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