Browsing by Author "Yousef, Malik"
Now showing items 1-20 of 25
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AMP-GSM: Prediction of Antimicrobial Peptides via a Grouping–Scoring–Modeling Approach
Soylemez, Ummu Gulsum; Yousef, Malik; Bakir-Gungor, Burcu (MDPI, 2023)Due to the increasing resistance of bacteria to antibiotics, scientists began seeking new solutions against this problem. One of the most promising solutions in this field are antimicrobial peptides (AMP). To identify ... -
Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data
Yousef, Malik; Kumar, Abhishek; Bakir-Gungor, Burcu (MDPIST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND, 2021)In the last two decades, there have been massive advancements in high throughput technologies, which resulted in the exponential growth of public repositories of gene expression datasets for various phenotypes. It is ... -
CCPred: Global and population-specific colorectal cancer prediction and metagenomic biomarker identification at different molecular levels using machine learning techniques
Bakir-Gungor, Burcu; Temiz, Mustafa; Inal, Yasin; Cicekyurt, Emre; Yousef, Malik (ELSEVIER, 2024)Colorectal cancer (CRC) ranks as the third most common cancer globally and the second leading cause of cancer-related deaths. Recent research highlights the pivotal role of the gut microbiota in CRC development and ... -
Classification of Breast Cancer Molecular Subtypes with Grouping-Scoring-Modeling Approach that Incorporates Disease-Disease Association Information
Qumsiyeh, Emma; Bakir-Gungor, Burcu; Yousef, Malik (IEEE Xplore, 2024)This study uses modern sequencing technology and large biological databases to investigate the molecular intricacies of complicated diseases like cancer. Using gene expression databases and biomarkers, the research aims ... -
Computational Prediction of Functional MicroRNA-mRNA Interactions
Demirci, Muserref Duygu Sacar; Yousef, Malik; Allmer, Jens (HUMANA PRESS INC, 999 RIVERVIEW DR, STE 208, TOTOWA, NJ 07512-1165 USA, 01.01.2019)Proteins have a strong influence on the phenotype and their aberrant expression leads to diseases. MicroRNAs (miRNAs) are short RNA sequences which posttranscriptionally regulate protein expression. This regulation is ... -
Discovering Potential Taxonomic Biomarkers of Type 2 Diabetes From Human Gut Microbiota via Different Feature Selection Methods
Bakir-Gungor, Burcu; Bulut, Osman; Jabeer, Amhar; Nalbantoglu, O. Ufuk; Yousef, Malik (FRONTIERS MEDIA SAAVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE CH-1015, SWITZERLAND, 2021)Human gut microbiota is a complex community of organisms including trillions of bacteria. While these microorganisms are considered as essential regulators of our immune system, some of them can cause several diseases. In ... -
The Effect of Different Classifiers on Recursive Cluster Elimination in the Analysis of Transcriptomic Data
Bulut, Nurten; Bakir-Gungor, Burcu; Qaqish, Bahjat F.; Yousef, Malik (Institute of Electrical and Electronics Engineers Inc., 2023)Gene expression data with limited sample size and a large number of genes are frequently encountered in genetic studies. In such high-dimensional data, identification of genes that distinguish between disease states is ... -
GeNetOntology: identifying affected gene ontology terms via grouping, scoring, and modeling of gene expression data utilizing biological knowledge-based machine learning
Ersoz, Nur Sebnem; Bakir-Gungor, Burcu; Yousef, Malik (FRONTIERS MEDIA SA, 2023)Introduction: Identifying significant sets of genes that are up/downregulated under specific conditions is vital to understand disease development mechanisms at the molecular level. Along this line, in order to analyze ... -
Identifying Taxonomic Biomarkers of Colorectal Cancer in Human Intestinal Microbiota Using Multiple Feature Selection Methods
Jabeer, Amhar; Kocak, Aysegul; Akkas, Huseyin; Yenisert, Ferhan; Nalbantoglu, Ozkan Ufuk; Yousef, Malik; Bakir Gungor, Burcu (Institute of Electrical and Electronics Engineers Inc., 2022)A variety of bacterial species called gut microbiota work together to maintain a steady intestinal environment. The gastrointestinal tract contains tremendous amount of different species including archaea, bacteria, fungi, ... -
Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods
Bakır Güngör, Burcu; Hacılar, Hilal; Jabeer, Amhar; Nalbantoğlu, Özkan Ufuk; Aran, Oya; Yousef, Malik (PEERJ INC, 2022)The tremendous boost in next generation sequencing and in the “omics” technologies makes it possible to characterize the human gut microbiome—the collective genomes of the microbial community that reside in our gastrointestinal ... -
Integrating Gene Ontology Based Grouping and Ranking into the Machine Learning Algorithm for Gene Expression Data Analysis
Yousef, Malik; Sayici, Ahmet; Bakir-Gungor, Burcu (SPRINGER INTERNATIONAL PUBLISHING AGGEWERBESTRASSE 11, CHAM, CH-6330, SWITZERLAND, 2021)Recent advances in the high throughput technologies resulted in the production of large gene expression data sets for several phenotypes. Via comparing the gene expression levels under different conditions, such as disease ... -
Integrative analyses in omics data: Machine learning perspective
Yazici, Miray Unlu; Bakir-Gungor, Burcu; Yousef, Malik (Deutsche Gesellschaft fur Medizinische Informatik, Biometrie und Epidemiologie e.V., 2023)Developments in the high throughput technologies have enabled the production of an immense amount of knowledge at the multi-omics level. Considering complex diseases which are affected by multi-factors, single omics datasets ... -
Invention of 3Mint for feature grouping and scoring in multi-omics
Yazici, Miray Unlu; Marron, J. S.; Bakir-Gungor, Burcu; Zou, Fei; Yousef, Malik (FRONTIERS MEDIA SA, 2023)Advanced genomic and molecular profiling technologies accelerated the enlightenment of the regulatory mechanisms behind cancer development and progression, and the targeted therapies in patients. Along this line, intense ... -
miRcorrNet: machine learning-based integration of miRNA and mRNA expression profiles, combined with feature grouping and ranking
Yousef, Malik; Goy, Gokhan; Mitra, Ramkrishna; Eischen, Christine M.; Jabeer, Amhar; Bakir-Gungor, Burcu (PEERJ INC341-345 OLD ST, THIRD FLR, LONDON EC1V 9LL, ENGLAND, 2021)A better understanding of disease development and progression mechanisms at the molecular level is critical both for the diagnosis of a disease and for the development of therapeutic approaches. The advancements in high ... -
miRcorrNetPro: Unraveling Algorithmic Insights through Cross-Validation in Multi-Omics Integration for Comprehensive Data Analysis
Yazici, Miray Unlu; Yousef, Malik; Marron J.S.; Bakir-Gungor, Burcu (Institute of Electrical and Electronics Engineers Inc., 2023)High throughput -omics technologies facilitate the investigation of regulatory mechanisms of complex diseases. Along this line, scientists develop promising tools and methods to extend our understanding at the molecular ... -
miRdisNET: Discovering microRNA biomarkers that are associated with diseases utilizing biological knowledge-based machine learning
Jabeer, Amhar; Temiz, Mustafa; Bakir-Gungor, Burcu; Yousef, Malik (Frontiers Media S.A., 2023)During recent years, biological experiments and increasing evidence have shown that microRNAs play an important role in the diagnosis and treatment of human complex diseases. Therefore, to diagnose and treat human complex ... -
miRModuleNet: Detecting miRNA-mRNA Regulatory Modules
Yousef, Malik; Goy, Gokhan; Bakır Güngör, Burcu (RONTIERS MEDIA SAAVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE CH-1015, SWITZERLAND, 2022)Increasing evidence that microRNAs (miRNAs) play a key role in carcinogenesis has revealed the need for elucidating the mechanisms of miRNA regulation and the roles of miRNAs in gene-regulatory networks. A better understanding ... -
Population Specific Classification of Colorectal Cancer with Meta-Analysis of Metagenomic Data
Temiz, Mustafa; Yousef, Malik; Bakir-Gungor, Burcu (Institute of Electrical and Electronics Engineers Inc., 2023)Yeni nesil dizilemedeki ve "-omik" teknolojilerdeki gelişmeler, insan bağırsak mikrobiyomunu karakterize etmeyi mümkün kılmaktadır. Bu mikroorganizmaların bazıları bağışıklık sistemimizin temel düzenleyicileriyken, ... -
Prediction of Linear Cationic Antimicrobial Peptides Active against Gram-Negative and Gram-Positive Bacteria Based on Machine Learning Models
Bakır Güngör, Burcu; Söylemez, Ümmü Gülsüm; Yousef, Malik; Kesmen, Zulal; Büyükkiraz, Mine Erdem (MDPI, 2022)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 ... -
PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach
Yousef, Malik; Ozdemir, Fatma; Jaber, Amhar; Allmer, Jens; Bakir-Gungor, Burcu (BMC, 2023)BackgroundCell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their products do not act alone but within networks. Subsets of these networks ...
