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
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Dr. Öğr. Üyesi
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07. Core Program
01. Kadir Has University
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07. Core Program
01. Kadir Has University
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11
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9
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21
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1.73
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1.91
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6
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2
| Journal | Count |
|---|---|
| ACS Omega | 1 |
| Genes & Genomics | 1 |
| Güvenlik Bilimleri Dergisi | 1 |
| PLOS Computational Biology | 1 |
| Proteins: Structure, Function, and Bioinformatics | 1 |
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11 results
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Now showing 1 - 10 of 11
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 pH-Driven β2AR Dynamics Reveal Loop-Mediated Allosteric Communication(Amer Chemical Soc, 2026) Sogunmez Erdogan, Nuray; Akten, E. DemetMembrane protein structure and dynamics are highly sensitive to environmental conditions, including changes in pH that can alter the protonation states of ionizable residues and, in turn, influence local electrostatics and stability. Constant-pH molecular dynamics (CpHMD) provides a framework to explore such effects by allowing dynamic proton exchange during simulations. Here, we applied CpHMD at pH:6.5, 7.0, and 8.0, alongside conventional MD, to examine how pH variations may influence the local conformational behaviors of the beta 2-adrenergic receptor (beta 2AR). During the 1.2-mu s-long total simulation, loop regions rich in titratable residues, particularly ICL3 and ECL2, showed the strongest responses to protonation changes. CpHMD trajectories suggested a pH-dependent redistribution of loop flexibility and hydrogen-bonding patterns, producing a see-saw-like effect, while fixed-protonation Control runs showed more constrained behavior. Across all simulations, the key GPCR microswitches, such as the ionic lock, the Y-Y gate, the NPxxY and PIF motifs, and the Trp286-Phe290 toggle pair, stayed within the ranges expected for an inactive receptor. This suggests that pH changes mainly influence local loop motions in the inactive receptor without pushing it toward activation-like states. Finally, mutual information analysis on both C alpha atoms and dihedral angles revealed altered communication between the extracellular and intracellular loops under different pH environments. While limited in time scale, these results provide a computational perspective on how protonation dynamics can modulate the GPCR behavior and highlight the value of incorporating pH effects in molecular-level investigations.Article Transcriptomic Identification and Developmental Mapping of Nrg3b Expression in Zebrafish(2025) Erdogan, Nuray Sogunmez; Tarahomi, ElhamBackground/aim: Neuregulin 3 (NRG3) is an epidermal growth factor-like ligand that is involved in neuronal circuit formation in mammals. However, the expression profile of its zebrafish ortholog, nrg3b, remains poorly defined. The transcriptomic analyses of zebrafish sco-spondin mutants, which display alterations in their neurodevelopmental pathways, have indicated potential dysregulation of Nrg3b. Guided by these insights, this study aimed to characterize the temporal and spatial expression patterns of nrg3b in vivo in embryonic and adult zebrafish. Materials and methods: Publicly available RNA-seq data from heterozygous and maternal-zygotic zebrafish sco-spondin mutants at 5, 15, and 30 days postfertilization (dpf) were analyzed to evaluate differential expression, coexpression network positioning, and functional enrichment. Temporal expression of nrg3b was validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) in embryos at 1, 3, and 5 dpf. Spatial nrg3b localization at 5 dpf was validated by whole-mount in situ hybridization (WISH), alongside neuronal subtype specificity using GABAergic and glutamatergic markers. Adult brain expression was further evaluated via ISH on telencephalon sections. Results: Developmental stage was the main driver of early transcriptomic variation, with minor genotype-specific differences detected at 5 dpf. Network analysis positioned nrg3b as a hub gene within a neuronal function associated module. RT-qPCR showed a significant increase in nrg3b expression on days 3 and 5 compared to day 1. WISH revealed strong nrg3b expression in anterior brain regions and the spinal cord at 5 dpf, with greater overlap observed with the glutamatergic marker compared to the GABAergic one. In adults, ISH suggested the expression of nrg3b in telencephalic nuclei, particularly in dorsomedial and ventral regions. Conclusion: nrg3b exhibits stage-dependent upregulation and preferential enrichment in excitatory neuronal regions during development, with sustained expression in adult telencephalon. These findings suggest a potential role for Nrg3b in synaptic organization and provide a foundation for future studies on the Nrg3b–ErbB4 signaling axis in zebrafish neurodevelopment.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 Citation - WoS: 9Citation - 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.Article Citation - WoS: 1Citation - Scopus: 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 Deniz Güvenliğinde Siber Güvenlik ve Gizlilik: Teoriler, Zorluklar, Vaka Çalışmaları ve Gelecek Beklentileri(2025) Erdoğan, Alperen; Erdogan, Nuray SogunmezDenizcilik alanı küresel ticaret, ulaşım ve güvenlikte önemli bir rol oynamaktadır. Ancak dijital teknolojilerin denizcilik operasyonlarına giderek daha fazla entegre olmasıyla birlikte siber güvenlik ve gizlilik önemli endişeler olarak ortaya çıkmıştır. Bu araştırma makalesi, denizcilik alanında siber güvenlik ve gizliliğin altında yatan teorileri incelemekte, temel zorlukları belirlemekte ve bu sorunların ele alınmasına yönelik gelecekteki beklentileri tartışmaktadır. Nitel araştırma metodolojisi kullanılarak mevcut literatür, vaka çalışmaları ve teknolojik gelişmeler analiz edilerek denizcilikte siber güvenliğin güncel durumu hakkında fikir edinilmiştir. Bilimsel veri tabanları (Web of Science, Scopus, EBSCO, Google Scholar, DOAJ ve TR Dizin), kitaplar, raporlar ve bültenler başlıca araştırma alanları olmuştur. “Siber güvenlik”, “siber”, “güvenlik”, “denizcilik güvenliği”, “deniz bilimleri güvenliği” ve “gizlilik” gibi konular, başlıklar, özetler ve anahtar kelimeler analiz edilmiştir. En çok okunan, indirilen ve atıfta bulunulan dokümanlar ve makaleler araştırılmış, analiz edilmiş ve incelenmiştir. Bu makalede vaka çalışmaları da gözlemlenmiş ve çalışmaya dahil edilmiştir. Bulgularımız; riskleri azaltmaya, güvenli ve özel denizcilik operasyonlarını sağlamak için gerçek çerçevelere, uluslararası işbirliklerine ve gelişmiş teknolojilere olan ihtiyacı vurgulamaktadır.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: 7Citation - Scopus: 8Distinctive 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.
