Browsing by Author "Yousef, Malik"
Now showing items 1-13 of 13
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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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
Recursive Cluster Elimination based Rank Function (SVM-RCE-R) implemented in KNIME
Yousef, Malik; Bakir Gungor, Burcu; Jabeer, Amhar; Goy, Gokhan; Qureshi, Rehman; C Showe, Louise (F1000 Research, 2020)In our earlier study, we proposed a novel feature selection approach, Recursive Cluster Elimination with Support Vector Machines (SVM-RCE) and implemented this approach in Matlab. Interest in this approach has grown over ... -
SVM-RCE-R-OPT: Optimization of Scoring Function for SVM-RCE-R
Yousef, Malik; Jabeer, Amhar; Bakir-Gungor, Burcu (SPRINGER INTERNATIONAL PUBLISHING AGGEWERBESTRASSE 11, CHAM, CH-6330, SWITZERLAND, 2021)Gene expression data classification provides a challenge in classification due to it having high dimensionality and a relatively small sample size. Different feature selection approaches have been used to overcome this ...
