Söğünmez Erdoğan, Nuray
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Sogunmez Erdogan,Nuray
NURAY SÖĞÜNMEZ ERDOĞAN
S., Nuray
Sogunmez Erdogan,N.
Sogunmez Erdogan, Nuray
Nuray Söğünmez Erdoğan
N. Söğünmez Erdoğan
Nuray, Sogunmez Erdogan
SÖĞÜNMEZ ERDOĞAN, NURAY
Söğünmez Erdoğan, N.
S.,Nuray
Söğünmez Erdoğan, Nuray
Söğünmez Erdoğan,N.
Nuray SÖĞÜNMEZ ERDOĞAN
Söğünmez Erdoğan, NURAY
SÖĞÜNMEZ ERDOĞAN, Nuray
Söğünmez, Nuray
Soğünmez, Nuray
Erdoğan, Nuray Söğünmez
NURAY SÖĞÜNMEZ ERDOĞAN
S., Nuray
Sogunmez Erdogan,N.
Sogunmez Erdogan, Nuray
Nuray Söğünmez Erdoğan
N. Söğünmez Erdoğan
Nuray, Sogunmez Erdogan
SÖĞÜNMEZ ERDOĞAN, NURAY
Söğünmez Erdoğan, N.
S.,Nuray
Söğünmez Erdoğan, Nuray
Söğünmez Erdoğan,N.
Nuray SÖĞÜNMEZ ERDOĞAN
Söğünmez Erdoğan, NURAY
SÖĞÜNMEZ ERDOĞAN, Nuray
Söğünmez, Nuray
Soğünmez, Nuray
Erdoğan, Nuray Söğünmez
Job Title
Dr. Öğr. Üyesi
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Core Program
07. Core Program
01. Kadir Has University
Core Program
07. Core Program
01. Kadir Has University
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5
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8
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6
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17
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19
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2
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2.13
Scopus Citations per Publication
2.38
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| Journal | Count |
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| Genes & Genomics | 1 |
| PLOS Computational Biology | 1 |
| Proteins: Structure, Function, and Bioinformatics | 1 |
| Scientific Reports | 1 |
| The FEBS Journal | 1 |
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8 results
Scholarly Output Search Results
Now showing 1 - 8 of 8
Article Multi-Omics Profiling Uncovers LINC00486-Associated LncRNA Regulation in Human Traumatic Brain Injury(Genetics Society of Korea, 2025) Al-Rubaye, T.; Isa, Z.; Erenkol, D.; Tarahomi, E.; Erdogan, N.S.Background : Traumatic brain injury (TBI) induces broad molecular changes in the human brain, altering gene expression in diverse neural and glial cells. While the transcriptional effects of TBI on protein-coding genes are well characterized, the roles of long noncoding RNAs (lncRNAs), key regulators of gene expression and chromatin, remain largely unknown. Objective : Our objective was to identify lncRNAs altered in TBI and explore their potential regulatory functions. Methods : We applied an integrative multi-omics approach combining single-nucleus RNA sequencing (snRNA-seq), isoform-level transcriptomics, transposable element (TE) annotation, and RNA-binding protein (RBP) interaction analyses. Public snRNA-seq datasets from cortical tissues of 12 TBI patients and 5 controls were analyzed to resolve injury-driven transcriptional signatures. We have performed differential expression analysis on 12,801 human lncRNAs, examined isoform-specific expression with TE content, and explored RBP–lncRNA interactions using CLIP-seq data. Results : Cell-type diversity decreased in TBI, and reactive and progenitor-like states were expanded. We identified 190 upregulated lncRNAs, mainly in glial cells. Among these, LINC00486 emerged as a brain-enriched lncRNA consistently increased after TBI. Isoform analysis showed its dominant brain isoform contains LINEs and LTRs, linking it to regulatory networks associated with endogenous retroelement activation. Functional enrichment connected LINC00486 to neurodevelopment, serotonin metabolism, and neuroinflammatory pathways. CLIP-seq data confirmed its interactions with stress-responsive RBPs such as AGO2 and TARDBP. Conclusions : Our multi-omics analysis identifies LINC00486 as a potential regulator of transcriptional plasticity in TBI. Its TE content and RBP interactions suggest a role in lncRNA-mediated regulatory networks during injury, highlighting possible therapeutic targets in neurotrauma. © 2025 Elsevier B.V., All rights reserved.Article Citation - WoS: 8Citation - Scopus: 10Hb-Egf Promotes Progenitor Cell Proliferation and Sensory Neuron Regeneration in the Zebrafish Olfactory Epithelium(Wiley, 2024) Sireci, Siran; Kocagoz, Yigit; Alkiraz, Aysu Sevval; Guler, Kardelen; Dokuzluoglu, Zeynep; Balcioglu, Ecem; Fuss, Stefan HerbertMaintenance and regeneration of the zebrafish olfactory epithelium (OE) are supported by two distinct progenitor cell populations that occupy spatially discrete stem cell niches and respond to different tissue conditions. Globose basal cells (GBCs) reside at the inner and peripheral margins of the sensory OE and are constitutively active to replace sporadically dying olfactory sensory neurons (OSNs). In contrast, horizontal basal cells (HBCs) are uniformly distributed across the sensory tissue and are selectively activated by acute injury conditions. Here we show that expression of the heparin-binding epidermal growth factor-like growth factor (HB-EGF) is strongly and transiently upregulated in response to OE injury and signals through the EGF receptor (EGFR), which is expressed by HBCs. Exogenous stimulation of the OE with recombinant HB-EGF promotes HBC expansion and OSN neurogenesis in a pattern that resembles the tissue response to injury. In contrast, pharmacological inhibition of HB-EGF membrane shedding, HB-EGF availability, and EGFR signaling strongly attenuate or delay injury-induced HBC activity and OSN restoration without affecting maintenance neurogenesis by GBCs. Thus, HB-EGF/EGFR signaling appears to be a critical component of the signaling network that controls HBC activity and, consequently, repair neurogenesis in the zebrafish OE.Master Thesis ScRNA-seq Alt Kümeleri Kullanılarak Uzamsal Transkriptomik Verilerin Seyrek Dekonvolüsyonu ile Hücre Tipi Heterojenitesının Ortaya Konması(2025) Rinch, Wardah Afzal; Erdoğan, Nuray SöğünmezHücrelerin doğal ortamlarındaki uzamsal organizasyonu, mimarilerini, karşılıklı etkileşimlerini ve işlevlerini anlamak açısından çok önemlidir ve bu da Uzamsal Transkriptomik (ST) yönteminin ortaya koymayı hedeflediği bir konudur. Ancak günümüz teknolojisi, tüm genom kapsayıcılığına sahip tek hücre çözünürlüğünde uzamsal organizasyonun belirlenmesinde yetersiz kalmaktadır. Bu hedef, kısmen tek hücreli RNA dizileme (scRNA-seq) yöntemiyle sağlansa da, bu süreçte uzamsal bilgi kaybı yaşanmaktadır. Bu nedenle, hem uzamsal hem de yüksek çözünürlüklü hücresel verilerin elde edilebilmesi için ST ve scRNA-seq veri kümeleri birlikte kullanılarak çözümlenme (dekonvolüsyon) işlemi gibi hesaplamalı yöntemlerden yararlanılmaktadır. scRNA-seq aracılığıyla ST'nin çözümlenmesi umut vadetse de, hala aşılması gereken bazı engeller bulunmaktadır. Parti (batch) arası etkiler teknik varyansa yol açarken, dikkate alınması gereken biyolojik varyanslar da mevcuttur. Çoğu dekonvolüsyon yöntemi, hedef verideki tüm referans hücre türlerini tahmin etmeye çalışırken, hücresel heterojenite gibi biyolojik ayrıntıları ve nadir ya da geçiş halindeki alt popülasyonları göz ardı ederek, gerçek hücre türü lokalizasyonlarının tahmin gücünü sınırlandırmaktadır. Bu zorlukları aşmak için, hücre türü alt kümelendirmesini içeren Uzamsal Transkriptomik çözümlenmesini geliştiren WISpR-DeFine (İyi Çözünürlüklü Dekonvolüsyon için Ağırlıklı Seyrek Regresyon) adlı yeni teknik geliştirdik. WISpR-DeFine, anlık tek hücre referans verilerinde mevcut olan hücre tipi heterojenliğini hesaba katarak daha hassas ve ayrıntılı dekonvolüsyona olanak tanır. Toplam 4 veri setinde (2 hasta, 1 sağlıklı ve SeqFISH+) karşılaştırmalı olarak incelendiğinde, WISpR'ye kıyasla tahmin üstünlüğü göstermiştir. Ayrıca, yaygın olarak kullanılan toplu etki düzeltme araçlarını karşılaştırarak toplu etki zorluğunu ele aldık ve LIGER'i en doğru model olarak belirledik.Doctoral Thesis Identification of Distinct Communication Networks in Human ?2 Adrenergic Receptor Via Molecular Dynamics Simulation(Kadir Has Üniversitesi, 2020) Erdoğan, Nuray SöğünmezG-protein-bağlı reseptörler (GPCR), hücre dışı ligand bağlanma işlemini hücre içi tepkilere dönüştürerek çok çeşitli insan fizyolojik fonksiyonlarına aracılık eden ve yedi transmembran (TM) yapısından oluşan proteinlerdir. Karşılıklı sinyal aktarımı, ancak iki uzak bölge arasında allosterik iletişimle oluşur. Hem inaktif hem de aktif kristal yapıların mevcut olduğu bir arketipik GPCR olan insan β2-adrenerjik reseptörüne (β2AR) odaklandık. β2AR 'ın farklı konformasyonlarının yörüngelerini oluşturmak için moleküler dinamik (MD) simülasyonları gerçekleştirildi. Burada, β2AR'a ait orijinal inaktif durum (Faz I), çok inaktif durum (Faz II), ara durum ve G-proteine bağlı aktif durumun yörüngelerini kullanarak potansiyel iletişim ağlarını araştırdık. Bu nedenle, bu tezde nedenselliğe bağlı potansiyel allosterik etkileşim ve bilgi aktarımını ortaya çıkarmak için proteindeki Cα dalgalanmaları ve omurga/yan zincir dihedral açı rotasyonları üzerinde hem korelasyon hem de entropi bazlı olasılıksal yaklaşımlar kullanılmıştır. Serbest ICL3 içeren yapılarda bilgi akışı yönü hücre içinden hücre dışına doğru iken, ICL3'ün hareketinin kısıtlandığı yapılarda bu akış yönünün tam tersine olduğu görüldü. Ayrıca, esnek alanlarda lokalize olmuş amino asitler genellikle polar özelliklere sahip olup iletişime büyük katkıda bulunmuşlardır. aktif-Gp için bağımsız iki çalışma, ICL3'ün z-yönünde hareketi ile birbirinden ayrılmış ve burada G proteini etkisinden dolayı iletişim ve polarite gücünün azaldığı saptanmıştır. Son olarak, mutlak Cα dalgalanma değerleri ve sterik engeller farklı dihedral açılarının oluşmasına neden olabildiğinden, Cα dalgalanmaları ve dihedral açıların ortak hareketi gözlemlenmemiştir. Bu nedenle de dihedral verilerde çoğunlukla ilmik alanlarının ortaya çıktığı görüntülenmiştir. Bu sonuçlar β2AR 'daki allosterik iletişimi açıklamak için yapı temelli bir mekanizma sağlamakta ve dahası rasyonel ilaç tasarımı ve protein mühendisliği gibi uygulamalar için bir temel oluşturmaktadır.Article Notum1a Inhibition Promotes Neurogenesis in the Adult Zebrafish Brain(Nature Portfolio, 2025) Kocagoz, Yigit; Erdogan, Nuray Sogunmez; Ozdinc, Sevval; Ipekgil, Dogac; Katkat, Esra; Ozhan, GunesNotum is a carboxylesterase enzyme that modulates extracellular signaling by hydrolyzing palmitoleoyl residues from proteins, thereby influencing key pathways involved in cell differentiation, survival, and proliferation. While notum1 expression has been identified in the brain, its role in adult neurogenesis remains poorly understood. Using the adult zebrafish brain as a model system, we demonstrate that the notum1a homolog is broadly expressed across various brain cell types but is absent in undifferentiated radial glial cells. Pharmacological inhibition of Notum activity with the small molecule inhibitor ABC99 stimulates activation of radial glial cells, leading to increased neurogenesis. A BrdU pulse-chase assay confirms that ABC99-induced proliferation enhances the production of mature neurons. Despite Notum's established role in Wnt signaling, transcriptional analysis following ABC99 treatment reveals no sustained impact on Wnt pathway targets, suggesting that Notum may regulate neurogenesis through alternative mechanisms. Our findings highlight notum1a as a potential modulator of neural progenitor cell dynamics in the adult brain and suggest that targeting Notum could represent a novel therapeutic strategy for neurodegenerative conditions characterized by impaired neurogenesis.Article Citation - WoS: 1Sparse Deconvolution of Cell Type Medleys in Spatial Transcriptomics(Public Library Science, 2025) Erdogan, Nuray Sogunmez; Eroglu, DenizMapping cell distributions across spatial locations with whole-genome coverage is essential for understanding cellular responses and signaling However, current deconvolution models aim to estimate the proportions of distinct cell types in each spatial transcriptomics spot by integrating reference single-cell data. These models often assume strong overlap between the reference and spatial datasets, neglecting biology-grounded constraints such as sparsity and cell-type variations, as well as technical sparsity. As a result, these methods rely on over-permissive algorithms that ignore given constraints leading to inaccurate predictions, particularly in heterogeneous or unmatched datasets. We introduce Weight-Induced Sparse Regression (WISpR), a machine learning algorithm that integrates spot-specific hyperparameters and sparsity-driven modeling. Unlike conventional approaches that neglect biology-grounded constraints, WISpR accurately predicts cell-type distributions while preserving biological coherence, i.e., spatially and functionally consistent cell-type localization, even in unmatched datasets. Benchmarking against five alternative methods across ten datasets, WISpR consistently outperformed competitors and predicted cellular landscapes in both normal and cancerous tissues. By leveraging sparse cell-type arrangements, WISpR provides biologically informed, high-resolution cellular maps. Its ability to decode tissue organization in both healthy and diseased states highlights WISpR's practical utility for spatial transcriptomics, particularly in challenging settings involving noise, sparsity, or reference mismatches.Article Citation - WoS: 6Citation - Scopus: 7Distinctive Communication Networks in Inactive States of Beta(2)-Adrenergic Receptor: Mutual Information and Entropy Transfer Analysis(Wiley, 2020) Soğünmez, Nuray; Akten, Ebru DemetMutual information and entropy transfer analysis employed on two inactive states of human beta-2 adrenergic receptor (beta(2)-AR) unraveled distinct communication pathways. Previously, a so-called "highly" inactive state of the receptor was observed during 1.5 microsecond long molecular dynamics simulation where the largest intracellular loop (ICL3) was swiftly packed onto the G-protein binding cavity, becoming entirely inaccessible. Mutual information quantifying the degree of correspondence between backbone-C(alpha)fluctuations was mostly shared between intra- and extra-cellular loop regions in the original inactive state, but shifted to entirely different regions in this latest inactive state. Interestingly, the largest amount of mutual information was always shared among the mobile regions. Irrespective of the conformational state, polar residues always contributed more to mutual information than hydrophobic residues, and also the number of polar-polar residue pairs shared the highest degree of mutual information compared to those incorporating hydrophobic residues. Entropy transfer, quantifying the correspondence between backbone-C(alpha)fluctuations at different timesteps, revealed a distinctive pathway directed from the extracellular site toward intracellular portions in this recently exposed inactive state for which the direction of information flow was the reverse of that observed in the original inactive state where the mobile ICL3 and its intracellular surroundings drove the future fluctuations of extracellular regions.Article Citation - WoS: 2Citation - Scopus: 2Intrinsic Dynamics and Causality in Correlated Motions Unraveled in Two Distinct Inactive States of Human Beta(2)-Adrenergic Receptor(Amer Chemical Soc, 2019) Söğünmez, Nuray; Akten, Ebru DemetThe alternative inactive state of the human beta(2)-adrenergic receptor originally exposed in molecular dynamics simulations was investigated using various analysis tools to evaluate causality between correlated residue-pair fluctuations and suggest allosteric communication pathways. A major conformational shift observed in the third intracellular loop (ICL3) displayed a novel inactive state featuring an inaccessible G protein binding site blocked by ICL3 and an expanded orthosteric ligand binding site. Residue-based mean square fluctuation and stiffness calculations revealed a significant mobility decrease in ICL3 which induced a mobility increase in the remaining loop regions. This indicates conformational entropy loss in one mobile region being compensated by residual intermolecular motions in other mobile regions. Moreover the extent motions decreased and correlations that once existed between transmembrane helices shifted toward regions with increased mobility. Conditional time-delayed cross-correlation analysis identified distinct driver follower relationship profiles. Prior to its packing freely moving ICL3 was markedly driven by transmembrane helix-8 whereas once packed ICL3 controlled future fluctuations of nearby helices. Moreover two transmembrane helices (H5 and H6) started to control future fluctuations of a remote site the extracellular loop ECL2. This clearly suggests that allosteric coupling between extra- and intracellular parts intensified in agreement with the receptor's well recognized feature which is the inverse proportionality between activity and the degree of coupling.
