Kurum Yazarı "Bakir-Gungor, Burcu" WoS İndeksli Yayınlar Koleksiyonu İçin Listeleme
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Active Subnetwork GA: A Two Stage Genetic Algorithm Approach to Active Subnetwork Search
Ozisik, Ozan; Bakir-Gungor, Burcu; Diri, Banu; Sezerman, Osman Ugur (BENTHAM SCIENCE PUBL LTDEXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES, 2017)Background: A group of interconnected genes in a protein-protein interaction network that contains most of the disease associated genes is called an active subnetwork. Active subnetwork search is an NP-hard problem. In the ... -
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 ... -
Blockchain-based Fog Computing Applications in Healthcare
Adanur, Beyhan; Bakir-Gungor, Burcu; Soran, Ahmet (IEEE, 2020)— Son zamanlarda blokzincir teknolojisinin sağlık alanında kullanımı artmıştır. Blokzincir teknolojisinin sağlık alanına getirdiği birçok yenilik olmasına rağmen, halen çözülmeyi bekleyen problemleri mevcuttur. Bu ... -
Developing a label propagation approach for cancer subtype classification problem
Guner, Pinar; Bakir-Gungor, Burcu; Coskun, Mustafa (TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEYATATURK BULVARI NO 221, KAVAKLIDERE, ANKARA 00000, TURKEY, 2022)Cancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, ... -
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 ... -
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 ... -
microBiomeGSM: the identification of taxonomic biomarkers from metagenomic data using grouping, scoring and modeling (G-S-M) approach
Bakir-Gungor, Burcu; Temiz, Mustafa; Jabeer, Amhar; Wu, Di; Yousef, Malik (FRONTIERS MEDIA SA, 2023)Numerous biological environments have been characterized with the advent of metagenomic sequencing using next generation sequencing which lays out the relative abundance values of microbial taxa. Modeling the human microbiome ... -
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 ... -
Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions
Bakir-Gungor, Burcu; Moreno-Indias, Isabel; Lahti, Leo; Nedyalkova, Miroslava; Elbere, Ilze; Roshchupkin, Gennady; Adilovic, Muhamed; Aydemir, Onder; Santa Pau, Enrique Carrillo-de; D'Elia, Domenica; Desai, Mahesh S.; Falquet, Laurent; Gundogdu, Aycan; Hron, Karel; Klammsteiner, Thomas; Lopes, Marta B.; Marcos-Zambrano, Laura Judith; Marques, Claudia; Mason, Michael; May, Patrick; Pasic, Lejla; Pio, Gianvito; Pongor, Sandor; Promponas, Vasilis J.; Przymus, Piotr; Saez-Rodriguez, Julio; ampri, Alexia; Shigdel, Rajesh; Stres, Blaz; Suharoschi, Ramona; Truu, Jaak; Truica, Ciprian-Octavian; Vilne, Baiba; Vlachakis, Dimitrios; Yilmaz, Ercument; Zeller, Georg; Zomer, Aldert L.; Gomez-Cabrero, David; Claesson, Marcus J. (FRONTIERS MEDIA SAAVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE CH-1015, SWITZERLAND, 2021)The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many ... -
SYNE1 related cerebellar ataxia presents with variable phenotypes in a consanguineous family from Turkey
Yucesan, E.; Iseri, Sibel A. Ugur; Bilgic, B.; Gormez, Z.; Gungor, B. Bakir; Sarac, A.; Ozdemir, O.; Sagiroglu, M.; Gurvit, H.; Hanagasi, H.; Ozbek, U. (SPRINGER-VERLAG ITALIA SRLVIA DECEMBRIO, 28, MILAN 20137, ITALY, 2017)SYNE1 related autosomal recessive cerebellar ataxia type 1 (ARCA1) is a late-onset cerebellar ataxia with slow progression originally demonstrated in French-Canadian populations of Quebec, Canada. Nevertheless, recent ... -
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 ... -
A Top-Down Approach for Finding Affected Pathway Subnetworks in Type 2 Diabetes
Unlu Yazici, Miray; Bakir-Gungor, Burcu (IEEE, 2020)Diyabet (Diabetes Mellitus, DM), insülin üreten pankreas beta hücrelerindeki fonksiyon bozukluğu, insülin direnci veya insülinin işlevselliğinin bozulması ile meydana gelen bir tür metabolik bozukluktur. Diyabet vakalarının ... -
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 ...