Yazar "Yousef, Malik" için WoS İndeksli Yayınlar Koleksiyonu listeleme
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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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
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 ... -
Review of feature selection approaches based on grouping of features
Kuzudisli, Cihan; Bakir-Gungor, Burcu; Bulut, Nurten; Qaqish, Bahjat; Yousef, Malik (PeerJ Inc., 2023)With the rapid development in technology, large amounts of high-dimensional data have been generated. This high dimensionality including redundancy and irrelevancy poses a great challenge in data analysis and decision ... -
TextNetTopics Pro, a topic model-based text classification for short text by integration of semantic and document-topic distribution information
Voskergian, Daniel; Bakir-Gungor, Burcu; Yousef, Malik (FRONTIERS MEDIA SA, 2023)With the exponential growth in the daily publication of scientific articles, automatic classification and categorization can assist in assigning articles to a predefined category. Article titles are concise descriptions ... -
A toolbox of machine learning software to support microbiome analysis
Marcos-Zambrano, Laura Judith; López-Molina, Víctor Manuel; Bakir-Gungor, Burcu; Frohme, Marcus; Karaduzovic-Hadziabdic, Kanita; Klammsteiner, Thomas; Ibrahimi, Eliana; Lahti, Leo; Loncar-Turukalo, Tatjana; Dhamo, Xhilda; Simeon, Andrea; Nechyporenko, Alina; Pio, Gianvito; Przymus, Piotr; Sampri, Alexia; Trajkovik, Vladimir; Lacruz-Pleguezuelos, Blanca; Aasmets, Oliver; Araujo, Ricardo; Anagnostopoulos, Ioannis; Aydemir, Önder; Berland, Magali; Calle, M. Luz; Ceci, Michelangelo; Duman, Hatice; Gündoğdu, Aycan; Havulinna, Aki S.; Kaka Bra; Kardokh Hama Najib; Kalluci, Eglantina; Karav, Sercan; Lode, Daniel; Lopes, Marta B.; May, Patrick; Nap, Bram; Nedyalkova, Miroslava; Paciência, Inês; Pasic, Lejla; Pujolassos, Meritxell; Shigdel, Rajesh; Susín, Antonio; Thiele, Ines; Truică, Ciprian-Octavian; Wilmes, Paul; Yilmaz, Ercument; Yousef, Malik; Claesson, Marcus Joakim; Truu, Jaak; Carrillo de Santa Pau, Enrique (Frontiers Media SA, 2023)The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and ...