Machine Learning in Bioinformatics, Computational Biology and Biomedical Text Classification

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 6502

Special Issue Editor


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Guest Editor
Department of Information Systems, Zefat Academic College, Zefat 1320611, Israel
Interests: bioinformatics; text mining; biological domain knowledge based feature selection on gene expression data; microRNA; one-class
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Special Issue Information

Dear Colleagues,

The "big data challenge" currently facing biomedical sciences is that of determining how to analyze the large quantities of raw biological data, including genomic sequences, proteomic and metabolic measurements and transcriptomic and metagenomic profiles. Thus, the application of machine learning (ML) is becoming an important element in meeting the challenge of analysis and integration of different data types. ML is also becoming increasingly important for mining information in biomedical literature and electronic documents where text mining and classification are becoming more important.

In this Special Issue, we envision providing a primer for the application of machine learning to a wide variety of different data sets to demonstrate its utility in addressing these growing computational challenges. We invite your contributions (original research articles, reviews, or shorter perspective articles) on all aspects related to the theme of “Machine Learning in Bioinformatics, Computational Biology and Biomedical Text Classification”. Articles with sound methodology and scientific practice are particularly welcome. Relevant topics include, but are not limited to, the following:

  • Machine learning;
  • Feature selection;
  • Computational biology;
  • Biomedical text classification;
  • Integrative analysis of biomedical data;
  • Machine learning in bioinformatics integrated with biological domain knowledge;
  • Integrative analysis of multi-omics;
  • Deep learning approaches;
  • Genomics;
  • Proteomics;
  • Systems biology;
  • Gene expression analysis;
  • Machine learning for biomedical data analysis;
  • Computational modeling and data integration;
  • Biomedical text mining and ontologies;
  • Next-generation sequencing data analysis;
  • Drug discovery;
  • Single-cell sequencing data analysis;
  • Microbiome and metagenomics;
  • Machine learning and deep learning in image analysis.

Prof. Dr. Malik Yousef
Guest Editor

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Keywords

  • Bioinformatics
  • Machine learning
  • Computational biology
  • Text classification
  • Genomics
  • Biomedical text mining
  • Integrative analysis of biomedical big data
  • Electronic medical records

Published Papers (2 papers)

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Research

27 pages, 3594 KiB  
Article
Prediction of Linear Cationic Antimicrobial Peptides Active against Gram-Negative and Gram-Positive Bacteria Based on Machine Learning Models
by Ümmü Gülsüm Söylemez, Malik Yousef, Zülal Kesmen, Mine Erdem Büyükkiraz and Burcu Bakir-Gungor
Appl. Sci. 2022, 12(7), 3631; https://0-doi-org.brum.beds.ac.uk/10.3390/app12073631 - 03 Apr 2022
Cited by 11 | Viewed by 3270
Abstract
Antimicrobial peptides (AMPs) are considered as promising alternatives to conventional antibiotics in order to overcome the growing problems of antibiotic resistance. Computational prediction approaches receive an increasing interest to identify and design the best candidate AMPs prior to the in vitro tests. In [...] Read more.
Antimicrobial peptides (AMPs) are considered as promising alternatives to conventional antibiotics in order to overcome the growing problems of antibiotic resistance. Computational prediction approaches receive an increasing interest to identify and design the best candidate AMPs prior to the in vitro tests. In this study, we focused on the linear cationic peptides with non-hemolytic activity, which are downloaded from the Database of Antimicrobial Activity and Structure of Peptides (DBAASP). Referring to the MIC (Minimum inhibition concentration) values, we have assigned a positive label to a peptide if it shows antimicrobial activity; otherwise, the peptide is labeled as negative. Here, we focused on the peptides showing antimicrobial activity against Gram-negative and against Gram-positive bacteria separately, and we created two datasets accordingly. Ten different physico-chemical properties of the peptides are calculated and used as features in our study. Following data exploration and data preprocessing steps, a variety of classification algorithms are used with 100-fold Monte Carlo Cross-Validation to build models and to predict the antimicrobial activity of the peptides. Among the generated models, Random Forest has resulted in the best performance metrics for both Gram-negative dataset (Accuracy: 0.98, Recall: 0.99, Specificity: 0.97, Precision: 0.97, AUC: 0.99, F1: 0.98) and Gram-positive dataset (Accuracy: 0.95, Recall: 0.95, Specificity: 0.95, Precision: 0.90, AUC: 0.97, F1: 0.92) after outlier elimination is applied. This prediction approach might be useful to evaluate the antibacterial potential of a candidate peptide sequence before moving to the experimental studies. Full article
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20 pages, 8483 KiB  
Article
Bioinformatics Characterization of Candidate Genes Associated with Gene Network and miRNA Regulation in Esophageal Squamous Cell Carcinoma Patients
by Bharathi Muruganantham, Bhagavathi Sundaram Sivamaruthi, Periyanaina Kesika, Subramanian Thangaleela and Chaiyavat Chaiyasut
Appl. Sci. 2022, 12(3), 1083; https://0-doi-org.brum.beds.ac.uk/10.3390/app12031083 - 20 Jan 2022
Viewed by 1896
Abstract
The present study aimed to identify potential therapeutic targets for esophageal squamous cell carcinoma (ESCC). The gene expression profile GSE161533 contained 84 samples, in that 28 tumor tissues and 28 normal tissues encoded as ESCC patients were retrieved from the Gene Expression Omnibus [...] Read more.
The present study aimed to identify potential therapeutic targets for esophageal squamous cell carcinoma (ESCC). The gene expression profile GSE161533 contained 84 samples, in that 28 tumor tissues and 28 normal tissues encoded as ESCC patients were retrieved from the Gene Expression Omnibus database. The obtained data were validated and screened for differentially expressed genes (DEGs) between normal and tumor tissues with the GEO2R tool. Next, the protein–protein network (PPI) was constructed using the (STRING 2.0) and reconstructed with Cytoscape 3.8.2, and the top ten hub genes (HGsT10) were predicted using the Maximal Clique Centrality (MCC) algorithm of the CytoHubba plugin. The identified hub genes were mapped in GSE161533, and their expression was determined and compared with The Cancer Genome Atlas (TCGA.) ESCC patient’s samples. The overall survival rate for HGsT10 wild and mutated types was analyzed with the Gene Expression Profiling Interactive Analysis2 (GEPIA2) server and UCSC Xena database. The functional and pathway enrichment analysis was performed using the WebGestalt database with the reference gene from lumina human ref 8.v3.0 version. The promoter methylation for the HGsT10 was identified using the UALCAN server. Additionally, the miRNA-HGsT10 regulatory network was constructed to identify the top ten hub miRNAs (miRT10). Finally, we identified the top ten novel driving genes from the DEGs of GSE161533 ESCC patient’s sample using a multi-omics approach. It may provide new insights into the diagnosis and treatment for the ESCC affected patients early in the future. Full article
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