Browsing by Author "Bakir-Gungor, Burcu"
Now showing items 1-20 of 23
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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 ... -
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 ... -
The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behçet's Disease
Isik, Yunus EMRE; Gormez, Yasin; Aydin, Zafer; Bakir-Gungor, Burcu (Institute of Electrical and Electronics Engineers Inc., 2021)Behçet's Disease (BD) is a multi-system inflammatory disorder in which the etiology remains unclear. The most probable hypothesis is that genetic tendency and environmental factors play roles in the development of BD. In ... -
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 ... -
'Epistatic interactions between autoimmunity and genetic thrombophilia' Reply
Bakir-Gungor, Burcu; Remmers, Elaine F.; Meguro, Akira; Mizuki, Nobuhisa; Kastner, Daniel L.; Gul, Ahmet; Sezerman, Osman Ugur (NATURE PUBLISHING GROUP, MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND, 2015)[Özet Yok] -
Evaluation of Classification Algorithms, Linear Discriminant Analysis and a New Hybrid Feature Selection Methodology for the Diagnosis of Coronary Artery Disease
Kolukisa, Burak; Hacilar, Hilal; Goy, Gokhan; Kus, Mustafa; Bakir-Gungor, Burcu; Aral, Atilla); Gungor, Vehbi Cagri (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2018)According to the World Health Organization (WHO), 31% of the world's total deaths in 2016 (17.9 million) was due to cardiovascular diseases (CVD). With the development of information technologies, it has become possible ... -
HomSI: a homozygous stretch identifier from next-generation sequencing data
Gormez, Zeliha; Bakir-Gungor, Burcu; Sagiroglu, Mahmut Samil (OXFORD UNIV PRESS, GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND, 2014)In consanguineous families, as a result of inheriting the same genomic segments through both parents, the individuals have stretches of their genomes that are homozygous. This situation leads to the prevalence of recessive ... -
The Identification of Discriminative Single Nucleotide Polymorphism Sets for the Classification of Behcet's Disease
Gormez, Yasin; Isik, Yunus Emre; Bakir-Gungor, Burcu (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2018)Behcet's disease is a long-term multisystem inflammatory disorder, characterized by recurrent attacks affecting several organs. As the genotyping individuals get cheaper and easier following the developments in genomic ... -
Identification of possible pathogenic pathways in Behcet's disease using genome-wide association study data from two different populations
Bakir-Gungor, Burcu; Remmers, Elaine F.; Meguro, Akira; Mizuki, Nobuhisa; Kastner, Daniel L.; Gul, Ahmet; Sezerman, Osman U. (NATURE PUBLISHING GROUP, MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND, 2015)Behcet's disease (BD) is a multi-system inflammatory disorder of unknown etiology. Two recent genome-wide association studies (GWASs) of BD confirmed a strong association with the MHC class I region and identified two ... -
Identify Commonly Affected Pathways in Psychiatric Diseases
Bulut, Umit; Bakir-Gungor, Burcu (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2018)Genome-wide association studies (GWAS) are an extraordinary source of information when it comes to revealing the common variations of human complex diseases. Until now, the large amount of data generated from these studies ... -
In-silico Identification of Papillary Thyroid Carcinoma Molecular Mechanisms
Ersoz, Nur Sebnem; Guzel, Yasin; Bakir-Gungor, Burcu (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2019)Representing approximately 70% to 80% of thyroid cancers, papillary thyroid cancer (PTC) is the most common type of thyroid cancers. PTC is seen in all age groups, but it is seen more frequently in women than in men. ... -
In-Silico Methods to Identify Common MicroRNAs and Pathways of Neuromuscular Diseases
Yazici, Miray Unlu; Menges, Evrim Aksu; Ulum, Yeliz Z. Akkaya; Hayta, Burcu Balci; Bakir-Gungor, Burcu (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2019)Neuromuscular disorders (NMD) are a heterogeneous group of diseases characterized by the loss of function of the peripheral nerves and muscles. However, there are no effective and widespread therapeutic approaches to prevent ... -
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 ... -
Machine Learning Analysis of Inflammatory Bowel Disease-Associated Metagenomics Dataset
Hacilar, Hilal; Nalbantoglu, O. Ufuk; Bakir-Gungor, Burcu (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2018)There is an ongoing interplay between humans and our microbial communities. The microorganisms living in our gut produce energy from our food, strengthen our immune system, break down foreign products, and release metabolites ... -
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 ... -
Multi fragment melting analysis system (MFMAS) for one-step identification of lactobacilli
Kesmen, Zulal; Kilic, Ozge; Gormez, Yasin; Celik, Mete; Bakir-Gungor, Burcu (ELSEVIER, RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS, 2020)The accurate identification of lactobacilli is essential for the effective management of industrial practices associated with lactobacilli strains, such as the production of fermented foods or probiotic supplements. For ... -
PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data
Bakir-Gungor, Burcu; Egemen, Ece; Sezerman, Osman Ugur (OXFORD UNIV PRESS, GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND, 2014)Genome-wide association studies (GWAS) have revolutionized the search for the variants underlying human complex diseases. However, in a typical GWAS, only a minority of the single-nucleotide polymorphisms (SNPs) with the ... -
Performance Evaluations of Active Subnetwork Search Methods in Protein-Protein Interaction Networks
Gunter, Pinar; Bakir-Gungor, Burcu (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 01.01.2019)Protein-protein interaction networks are mathematical representations of the physical contacts between proteins in the cell. A group of interconnected proteins in a protein-protein interaction network that contains most ... -
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 Ltd, 2021)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 ... -
The relationship between PAPP-A levels, maternal characteristics, gestational diabetes and other biochemical markers of the aneuploidy screening
Uzut, Ommu Gulsum; Celebiler, Hande Kaymakcalan; Harkonen, Juho; Bakir-Gungor, Burcu (IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA, 2018)First trimester aneuploidy screening is routinely used in pregnancy follow-ups. In this screening, free /l-hCG and pregnancy-associated plasma protein A (PAPP-A) levels in the blood of the pregnant woman arc measured. The ...
