WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Conference Object Understanding the Role of FAM120A Gene in a Neurodevelopmental Disorder(Springernature, 2024) Sezer, Abdullah; Pucak, Damla; Cevik, Sebiha; Kaplan, Oktay I.Conference Object Is the Homozygous Mutation Pattern Reminding Uniparental Disomy on DHCR7 Gene Responsible for Smith-Lemli (SLO) Syndrome(Springernature, 2024) Kosem, Zeyneb Berrin; Sunar, Ilknur; Demircioglu, Ayse Sena; Akarsu, Rukiye; Gencay, Ismail; Akalin, IbrahimConference Object Is the Homozygous Mutation Pattern Reminding Uniparental Disomy on DHCR7 Gene Responsible for Smith-Lemli-Opitz (SLO) Syndrome(Springernature, 2024) Kosem, Zeyneb Berrin; Sunar, Ilknur; Demircioglu, Ayse Sena; Akarsu, Rukiye; Gencay, Ismail; Akalin, IbrahimArticle Citation - WoS: 3Citation - Scopus: 3Inequality in Access to Urban Amenities(Springernature, 2025-07-12) Michelangeli, Alessandra; Osth, John; Toger, Marina; Turk, UmutThis paper provides an overview of urban inequality in the Stockholm Metropolitan Area analyzing the spatial distribution of amenities and their accessibility. Inequality in urban amenities is measured by a multidimensional index at a fine geographical scale and it can be decomposed into the sum of inequality indices computed on the marginal distributions of amenities across locations plus a residual term accounting for their joint distribution. Our research leverages a unique dataset that combines income data for approximately 90,000 geocoded individuals residing in the metropolitan area with information from the OpenStreetMap platform, enabling us to examine the distribution of both natural and urban design-related amenities. Furthermore, we integrate data from online platforms to analyze the housing market. Our findings reveal moderate levels of inequality in amenities within the Stockholm Metropolitan Area, with social segregation emerging as the primary driver of this inequality.Conference Object ConVarT: A New Search Engine for Orthologous Variants for Functional Inference of Human Genetic Variants(Springernature, 2022) Pir, Mustafa S.; Bilgin, Halil I.; Sayici, Ahmet; Coskun, Fatih; Torun, Furkan M.; Zhao, Pei; Kaplan, Oktay I.Conference Object Citation - WoS: 1CC2D1A as a Novel Ciliopathy Gene(Springernature, 2020) Sakin, I.; Tuncel, G.; Sag, S. Ozemri; Kaplan, O. I.; Khokha, M. K.; Ergoren, M. C.; Temel, S. G.Article Citation - WoS: 16Citation - Scopus: 11An Empirical Study of Sentiment Analysis Utilizing Machine Learning and Deep Learning Algorithms(Springernature, 2023-12-09) Erkantarci, Betul; Bakal, GokhanAmong text-mining studies, one of the most studied topics is the text classification task applied in various domains, including medicine, social media, and academia. As a sub-problem in text classification, sentiment analysis has been widely investigated to classify often opinion-based textual elements. Specifically, user reviews and experiential feedback for products or services have been employed as fundamental data sources for sentiment analysis efforts. As a result of rapidly emerging technological advancements, social media platforms such as Twitter, Facebook, and Reddit, have become central opinion-sharing mediums since the early 2000s. In this sense, we build various machine-learning models to solve the sentiment analysis problem on the Reddit comments dataset in this work. The experimental models we constructed achieve F1 scores within intervals of 73-76%. Consequently, we present comparative performance scores obtained by traditional machine learning and deep learning models and discuss the results.Article Citation - WoS: 1Citation - Scopus: 1A Homozygous Frameshift Variant in the CILK1 Gene Causes Cranioectodermal Dysplasia(Springernature, 2025-07-04) Sezer, Abdullah; Oner, Sukru S.; Saat, Hanife; Turan, Merve G.; Gungor, Tulin; Cevik, Sebiha; Kaplan, Oktay I.Cranioectodermal dysplasia (CED) is a ciliopathy characterized by skeletal and ectodermal abnormalities, renal failure, and liver fibrosis. Pathogenic variants in genes that encode the intraflagellar transport (IFT) complex components, particularly IFT-A, are responsible for approximately two-thirds of the CED cases. However, the cause of the remaining cases remains unknown. Ciliogenesis-associated kinase 1 (CILK1) is a highly conserved ciliary serine/threonine kinase with an N-terminal catalytic domain responsible for kinase activity and a C-terminal non-catalytic domain that interacts with the IFT-B complex. Biallelic variants in the catalytic domain are associated with lethal skeletal dysplasia, endocrine cerebroosteodysplasia, and short-rib polydactyly syndrome. No human disease has been linked to biallelic variants in the non-catalytic domain. We present a homozygous frameshift variant in the CILK1 gene that affects the distal part of the non-catalytic domain, causing CED in five patients from two pedigrees. All the patients survived into childhood and had disproportionately short stature, skeletal abnormalities, ectodermal dysplasia, renal issues, and liver complications. Functional data from patient-derived cells and the C. elegans model indicate that the variant reduces cilia number, increases cilia length, and disrupts the localization of IFT components. In contrast, the ciliary localization of CILK1 bearing the variant itself remains unaffected. Notably, we rescued the majority of these abnormalities by reintroducing CILK1 into patient-derived cells. Finally, our study describes CILK1 as a novel causal gene and the first non-IFT protein-encoding gene in the etiology of CED, thus expanding the known genotypic, mechanistic, and phenotypic spectrum of CED.Article Citation - WoS: 1Citation - Scopus: 1A Comprehensive MicroRNA-seq Transcriptomic Analysis of Tay-Sachs Disease Mice Revealed Distinct miRNA Profiles in Neuroglial Cells(Springernature, 2025-08-09) Kaya, Beyza; Orhan, Mehmet Emin; Yanbul, Selman; Demirci, Muserref Duygu Sacar; Demir, Secil Akyildiz; Seyrantepe, VolkanTay-Sachs disease (TSD) is a rare lysosomal storage disorder marked by the progressive buildup of GM2 in the central nervous system (CNS). This condition arises from mutations in the HEXA gene, which encodes the alpha subunit of the enzyme beta-hexosaminidase A. A newly developed mouse model for early-onset TSD (Hexa-/-Neu3-/-) exhibited signs of neurodegeneration and neuroinflammation, evidenced by elevated levels of pro-inflammatory cytokines and chemokines, as well as significant astrogliosis and microgliosis. Identifying disease-specific MicroRNAs (miRNAs) may aid the development of targeted therapies. Although previous small-scale studies have investigated miRNA expression in some regions of GM2 gangliosidosis mouse models, thorough profiling of miRNAs in this innovative TSD model remains to be done. In this study, we employed next-generation sequencing to analyze the complete miRNA profile of neuroglial cells from Hexa-/-Neu3-/- mice. By comparing KEGG and Reactome pathways associated with neurodegeneration, neuroinflammation, and sphingolipid metabolism in Hexa-/-Neu3-/- neuroglial cells, we discovered new MicroRNAs and their targets related to the pathophysiology of GM2 gangliosidosis. For the first time, our findings showed that miR-708-5p, miR-672-5p, miR-204-5p, miR-335-5p, and miR-296-3p were upregulated, while miR-10 b-5p, miR-615-3p, miR-196a-5p, miR-214-5p, and miR-199a-5p were downregulated in Hexa-/-Neu3-/- neuroglial cells in comparison to age-matched wild-type (WT). These specific changes in miRNA expression deepen our understanding of the disease's neuropathological characteristics in Hexa-/-Neu3-/- mice. Our study suggests that miRNA-based therapeutic strategies may improve clinical outcomes for TSD patients.