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Identification and validation of a previously missed mutational signature in colorectal cancer Kazachkova, Mariya; Otlu Sarıtaş, Burçak; Díaz-Gay, Marcos; Abbasi, Ammal; Moody, Sarah; Jiang, Zichen; Perdomo, Sandra; Wedge, David. C.; Brennan, Paul; Stratton, Michael. R.; Alexandrov, Ludmil. B. (2026-12-01) Mutational signature analysis has enhanced our understanding of mutagenic processes. In a recent study, we analyzed 802 microsatellite-stable colorectal cancers (CRC) and identified a de novo signature, SBS_D, which was de...
Exploring the genetic landscape of COVID-19 susceptibility and severity among patients in Türkiye Er, Ahmet Gorkem; Çakır, Yavuzhan; Er, Berrin; Burduroğlu, Hüseyin Cahit; Çakmak, Mehmet; ÖZIŞIK, LALE; DURUSU TANRIÖVER, MİNE; Topeli, Arzu; Aydın Son, Yeşim; Ünal, Serhat (2026-12-01) Background: One of the most challenging factors for clinicians in managing COVID-19 has been differences in the clinical course. To investigate the parameters associated with severe disease in detail, along with examining ...
SALGINTR: development and early evaluation of a low-cost cloud-based digital participatory surveillance system for influenza-like Illness among physicians in Türkiye — a proof of concept ÖNTAŞ, ERAY; Güçlü, Hasan; Aydın Son, Yeşim (2026-12-01) Background: Participatory surveillance complements sentinel influenza monitoring in high-income settings, yet no such platform has targeted physicians as both participants and clinical sentinels. We established SALGINTR, a...
Implicit security requirements classification with large language models using the OWASP application security verification standard: a shift-left approach Gür, Yusuf; Taşkaya Temizel, Tuğba; Günel Kılıç, Banu (2026-09-01) Cybersecurity threats require early integration of security, starting from the requirements analysis phase of the Software Development Life Cycle (SDLC). However, security requirements in Software Requirements Specificatio...
A process-centric mapping of non-technical debt instances to ISO/IEC 5338 in AI-enabled projects Kapiyasheva, Diana; Özcan Top, Özden; Taşkaya Temizel, Tuğba (2026-09-01) Non-Technical Debt (NTD), arising mainly from organizational, cultural, and people-related inefficiencies, significantly compromises the quality and sustainability of AI-enabled software systems. While a growing ecosystem ...
SOT-GLP: Sparse optimal transport guided local-global prompt learning Kizaroglu, Deniz; Kucuktas, Ulku Tuncer; Cakmakyurdu, Emre; Temizel, Alptekin (2026-09-01) Few-shot adaptation of vision-language models (VLMs) like CLIP typically relies on learning textual prompts matched to global image embeddings. Recent works extend this paradigm by incorporating local image-text alignment ...
Valorisation of Composted Spent Coffee Grounds as a Sustainable Peat Substitute to Enhance Growth and Visual Quality of <i>Dieffenbachia amoena</i> Özdemir, Serkan; Ozer, Hasan; Eren, Beytullah; Ozdemir, Saim (2026-09-01) This study explores the reutilisation of spent coffee grounds (SCG) in the horticultural sector as an eco-functional additive to develop innovative growing media that enhance the propagation of stem cuttings. Raw SCG under...
Synthesizing longitudinal ulcerative colitis progression via disentangled latent diffusion Dundar, Umut; Temizel, Alptekin (2026-08-01)
A robust machine learning framework for predicting the higher heating value of poultry litter using proximate analysis Eren, Beytullah; Uzun, Suleyman; Özdemir, Serkan (2026-08-01) Accurate estimation of the higher heating value (HHV) of poultry litter is critical for its valorization as a renewable energy feedstock. However, the heterogeneity of poultry litter and data scarcity pose challenges for p...
Variational Autoencoders for P-wave detection on strong motion earthquake spectrograms Ispak, Turkan Simge; Tileylioglu, Salih; Akagündüz, Erdem (2026-08-01) Accurate P-wave detection is critical for earthquake early warning, yet strong-motion records pose challenges due to high noise levels, limited labeled data, and complex waveform characteristics. This study reframes P-wave...
Prior therapy defines mutation profiles in childhood cancer at relapse Layeghifard, Mehdi; et. al. (2026-07-22) Children with cancer develop many short- and long-term side-effects of treatment1, but the amount of DNA damage associated with chemotherapy exposure is unclear2. Here we used mutational signatures to measure this damage u...
An ICAP-informed rubric for analyzing students' questions to generative AI: engagement patterns and dynamics exploration Ding, Lu; Rodenberg, Rachel; Er, Erkan; Nguyen, Ha; Yoon, Meehyun (2026-07-22) As generative AI (genAI) tools such as ChatGPT become increasingly integrated into education, understanding how students use them to support learning is essential. This study examines undergraduate students' questioning st...
Design Reuse Via Automated Requirements-Driven Retrieval: A Framework for Electronic Hardware Uyar, Ekrem Bilgehan; Gokce, Cemil; Gursoy, Ali Ergin; Taşkaya Temizel, Tuğba (2026-07-01) Design reuse accelerates hardware development by improving efficiency, reducing costs, and shortening time-to-market. However, retrieving reusable circuit blocks directly from natural-language requirements remains challeng...
Insightful problem solving and social learning in children's tool making: Exploring the role of napping, night sleep, age, and gender Gönül, Gökhan; Karabulut, Anıl; Hohenberger, Annette (2026-07-01) Insight and innovation are two crucial components of our problem-solving capacity to create novel tools. In this study, we explored the possible contribution of task break (napping or wakeful), age (3-to-5-year-olds), gend...
Optimal Transport and Graph Neural Networks for Cross-Session Mental Workload Classification Demirezen, Güliz; Brouwer, Anne-Marie; Taşkaya Temizel, Tuğba (2026-06-01) Electroencephalography (EEG) offers a noninvasive, high-temporal-resolution modality for estimating mental workload. However, session-to-session variability limits the generalizability of workload classifiers, and few syst...
An updated meta-analysis of prognostic factors for secondary amputation following surgical repair of lower-extremity vascular trauma in both civilian and military populations Singh, Yash; Kersey, Alexander; Lauria, Alexis; Yet, Barbaros; Tai, Nigel; Rasmussen, Todd; Ratnayake, Amila; Perkins, Zane (2026-06-01) BACKGROUND: Lower-extremity vascular trauma (LEVT) remains a major cause of limb loss. A thorough understanding of prognostic factors associated with secondary amputation is essential for guiding decision-making, patient c...
Non-coding RNAs as biomarkers and therapeutic targets in pancreatic cancer: Clinical implications and translational perspectives Carretero-Fernández, María; Ruíz-Durán, Lucía; Uysal-Onganer, Pinar; Daniel, Neil; Yiannakopoulou, Eugenia; Otlu Sarıtaş, Burçak; García-Verdejo, Francisco José; López-López, José Antonio; Ortega Sánchez, Francisco Gabriel; Bonilla, Marco; Mesa, Francisco; Reyes-Zurita, Fernando; Gutiérrez-Bautista, Juan Francisco; González-Olmedo, Carmen; Fernández-Baldo, Martín A.; Campa, Daniele; Sánchez-Rovira, Pedro; Hughes, David; Cabrera-Serrano, Antonio José; Sainz, Juan (2026-06-01) Pancreatic cancer remains one of the most lethal malignancies, largely due to late diagnosis, marked tumor heterogeneity, and profound resistance to therapy. Beyond recurrent alterations in protein-coding genes, growing ev...
Deep sequence models for predicting average shear wave velocity from strong motion records Yilmaz, Baris; Akagündüz, Erdem; Tileylioglu, Salih (2026-05-01)
Accuracy of Deep Learning Models in Detecting Mandibular Furcation Defects on Panoramic Radiographs Kurumlu, Meric; KARACAOĞLU, FATMA; KALKAN, MÜRÜVVET; ÜLKÜ, İREM; Akagündüz, Erdem; ORHAN, KAAN (2026-05-01) Background/Objectives: Furcation defects pose a significant challenge in the diagnosis and treatment planning of periodontal diseases. Accurate clinical identification of furcation involvement is essential for improving tr...
Investigating the Structural Properties of Linguistic Biases in Multilingual Language Models Mantri, Raghav; Chen, Saun; Wang, Yixuan; Ataman, Duygu (2026-05-01) As large language models (LLMs) scale to cover more languages, their potential to support low-resource settings becomes increasingly promising. However, the mechanisms underlying cross-lingual transfer and the factors that...

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