Research News

Ph.D. Thesis
Alperen Taciroğlu, Variant Impact Prediction in The Obscurin and Trio Protein Families Through Evolutionary Conservation and Structural Analysis

A common evolutionary origin of the Obscurin and Trio protein families was identified through phylogenetic analyses, indicating ancient domain shuffling events across vertebrate lineages. Building on these findings, the novel variant effect predictor TrioNsight was developed for TrioN-like DH domains. The predictor, which integrates structural, evolutionary and physicochemical features, achieved high accuracy in distinguishing pathogenic variants (MCC: 0.906; 1.0 indicates perfect prediction). This work bridges fundamental evolutionary biology and clinical application, offering both mechanistic insights into protein family evolution and a practical tool for the interpretation of disease-associated variants in functionally critical domains.

Date: 30.05.2025 / 10:00 Place: A-212

M.S. Thesis
Cansu Demir Kartbol, Constructing a Forecasting Model for Decreasing Demand Deviation Effects of Products

 

In this thesis, a forecasting model has been developed for cooling and freezing products of a home appliance company. Economic fluctuations, global events, and market competition increase demand variability, complicating supply chain management. In this context, various clustering techniques have been utilized to improve product and country groupings, aiming to enhance forecasting accuracy and optimize supply chain strategies. Additionally, external factors such as the impact of Covid-19, economic indicators, and stock levels have been incorporated into the forecasting model.

Date: 26.05.2025 / 10:30 Place: B-116

Ph.D. Thesis
Samet Albayrak, Testing The Effects of tVNS Neuromodulation of Food Reward Cycle via Gut-Brain Signals with EEG

Flavor perception and gut-brain signaling influence eating behavior. The vagus nerve (VN) may become desensitized to high-calorie foods, promoting overeating, a process potentially reversible through VN stimulation. This study examined whether transcutaneous VNS (tVNS) modulates brain responses to food using EEG during chocolate milkshake consumption. Key findings: (1) Spontaneous eyeblink rates (a dopamine proxy) increased after food intake, suggesting dopaminergic engagement. (2) Event-related potentials (ERPs) time-locked to swallowing were only observed with food stimuli, validating the sip-and-swallow protocol for flavor research. (3) No significant tVNS effects were found on resting-state oscillations or ERPs, but the method captured food-specific neural responses. These results support the protocol’s utility for future gut-brain studies.

Date: 14.04.2025 / 14:00 Place: A-212

M.S. Thesis
Tina Afshar Ghochani, Defining Culture and People Related Processes in Advanced Data Analytics Projects

This thesis explores the critical role of people and culture-related capabilities in the success of Advanced Data Analytics (ADA) projects, addressing a gap in current literature that predominantly focuses on technical aspects. By conducting a systematic literature review and semi-structured interviews, the study identifies and categorizes these capabilities, integrating them into structured processes tailored from the People Capability Maturity Model (Curtis et al., 2009). The research contributes actionable frameworks and practices to enhance workforce readiness, collaboration, and organizational culture, enabling businesses to align ADA initiatives with strategic goals and achieve sustainable success.

Date: 10.01.2025 / 13:30 Place: A-212

M.S. Thesis
Hüseyin Hilmi Kılınç, A Robust Approach for Predicting Mutation Effects on Transcription Factor Binding: Insights from Mutational Signatures in 560 Breast Cancer Samples

Somatic mutations in non-coding regions can disrupt transcription factor (TF)-DNA interactions, affecting gene regulation and contributing to cancer. This thesis introduces an in silico pipeline to assess the impact of these mutations on TF binding affinities. Using k-mer-based linear regression models trained on ChIP-seq and PBM data for 403 TFs, we analyzed somatic mutations in 560 breast cancer samples. Predicted TF binding changes were classified as gain or loss of function and linked to oncogene and tumor suppressor dysregulation using enhancer-target gene maps. Signature-specific and statistical analyses highlight distinct patterns, providing insights into the regulatory role of mutations in cancer.

Date: 07.01.2025 / 10:00 Place: A-212