Yazar "0000-0002-2272-6270" için PubMed İndeksli Yayınlar Koleksiyonu listeleme
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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 ... -
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 ... -
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 ... -
Topological feature generation for link prediction in biological networks
Temiz, Mustafa; Bakir-Gungor, Burcu; Sahan, Pinar Guner; Coskun, Mustafa (PEERJ INC, 2023)Graph or network embedding is a powerful method for extracting missing or potential information from interactions between nodes in biological networks. Graph embedding methods learn representations of nodes and interactions ...