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Recent Submissions

Teaching Agile in an Agile Way: A Case from the First Iteration in a University Özkan, Necmettin; Özcan Top, Özden; Bal, Şevval; Gök, Mehmet Şahin (2022-12-29) In parallel with the increasing demands for Agile in industry and academia, many lecturers have started teaching Agile Software Development in varying programs. As one of them, in this study, we exhibit our selective cours...
Determinative Factors of Cloud Computing Adoption in Government Organizations Koç, Burcu; Şener, Umut; Eren, Pekin Erhan (2022-12-29)
Tailoring Choices Made in Scrum Projects: A Systematic Literature Review Özkan, Özgün; Özcan Top, Özden (2022-11-11) Among various Agile Software Development (ASD) methods, Scrum is one of the most widely adopted ones. The Scrum Guide gives a clear description of the Scrum practices, artifacts, and roles. However, due to various project ...
Evaluation of Effects of Different Base Calling Models on Single Nucleotide Variant Calling Using Lowcoverage Long Read Sequencing Karakurt, Hamza Umut; Pekcan, Hasan Ali; Kahraman, Ayşe; Çınar, Esra; Akgün, Bilçağ (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Long-read sequencing technologies such as Oxford Nanopore Technologies (ONT) enabled researchers to sequence long reads fast and cost effectively. ONT sequencing uses nanopores integrated to semiconductor surfaces and sequ...
PROT-ON: Structure-Based Detection of Critical Mutations in Redesigning Protein-Protein Interfaces Koşaca, Mehdi; Yılmazbilek, İrem; Karaca , Ezgi (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Deformation of protein-protein interactions (PPIs) causes several diseases. Many therapeutic agents have been developed by time-consuming experimental techniques. On the other hand, computational methods have been used to ...
Drug Repositioning Approach Based on Network Neighborhood Metrics and Transcriptome Data Cüvitoğlu, Ali; Işık, Zerrin (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Development of new drugs is a complex and very expensive process. Drug repositioning (DR) explores new treatment area to approved drugs. DR provides lower cost, shorter time and risk-free investment compared to traditional...
Investigating conversion from mild cognitive impairment to alzheimer's disease using latent space manipulation Ayvaz, Deniz Sezin; Baytaş, İnci M. (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Alzheimer’s disease, a progressive neurologic disorder, is the most common cause of dementia, affecting millions worldwide. Mild Cognitive Impairment (MCI) is considered an intermediate stage before Alzheimer's. Early pred...
Computational design of a genetically encoded iron biosensor Berksöz, Melike; Atılgan, Canan (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Genetically encoded fluorescent biosensors (GEFB) proved to be reliable tracers for many metabolites and cellular processes. In the simplest case, a fluorescent protein (FP) is genetically fused to a sensing protein which ...
Network Based NLP Approach to Reveal Disease Comorbidities. COVID Case Study Taylan , Emre; Pir, Pinar (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) SARS-CoV-2 virus, which caused the pandemic COVID-19 , infects the host cells via ACE2 receptor protein binding to spike proteins. Viral binding also alters the vascular effects of the ACE/ACE2 ratio, which results in a nu...
Structural and docking analysis of a spirulina platensis DPP-IV inhibitory peptide Bakar , Bahar; Kaplan Türköz , Burcu (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Diabetes is a very common chronic disease defined by high blood glucose levels [1]. Dipeptidyl peptidase IV (DPP-IV) enzyme causes the degredation of glucose-dependent insulin releasing polypeptide (GIP) and glucagon like ...
Detection of Possible Significant Metabolites by Comparison of Metabolic Simulation Profiles of Healthy and Breast Cancer Tissues Akkuzu Özyeşer, Selin; Bülbül, Abdullah Alper; Başaran, Gül; Sezerman, Osman Uğur (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Breast cancer is the most frequent malignancy in women worldwide and is curable in ~70–80% of patients with early- stage, non- metastatic disease. In Breast cancer there are pathways related to Luminal A breast cancer, Lum...
Criteria for the Evaluation of Workflow Management Systems for Scientific Data Analysis Dilan Kiran, Aleyna; Ay, Mehmet Can; Alllmer, Jens (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Many scientific endeavors, such as molecular biology, have become dependent on largescale data and its analysis. For example, precision medicine depends on molecular measurements and data analysis on a per-patient basis. D...
Bioinformatic prediction and coexpression network identifies repurposed novel drugs for papillary thyroid cancer Temiz, Kubra (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Thyroid cancer is a type of cancer that affects the endocrine system and has a high malignancy. Papillary thyroid cancer, the most common subtype of thyroid cancer, also has well-differentiated features. Early diagnosed an...
Investigation Of The Structure Of Celecoxib Molecule And Its Interaction With Cox-2 By Quantum Mechanical Methods Using Model Systems Kıran, Aleyna Dilan; Selçuki , Cenk (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Non-steroidal anti-inflammatory drugs (NSAID) inhibit the eventual conversion of COXs to metabolites of arachidonic acid, including prostaglandins, prostacyclin, and thromboxanes, in the immune response after injury or inf...
Disease Centric Large Scale De Novo Design of Drug Candidate Molecules with Graph Generative Deep Adversarial Networks Ünlü, Atabey; Çevrim, Elif; Sarıgün, Ahmet; Ataş, Heval; Koyaş, Altay; Çelikbilek, Hayriye; Kahraman, Deniz Cansen; Olğaç, Abdurrahman; Rifaioğlu, Ahmet Süreyya; Doğan, Tunca (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. It is especially challenging to develop new drug-based treatments for complex diseases, such as various canc...
Background Orta Doğu Teknik Üniversitesi , Enformatik Enstitüsü (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) Glucose-6-phosphate dehydrogenase (G6PD, E.C. 1.1.1.49) is a ubiquitous enzyme that has a housekeeping role in all cells. This enzyme catalyzes the first step in the pentose phosphate pathway (PPP) converting glucose 6-pho...
Ancient Upper Mesopotamia, 10,000 years ago: first genomic impressions Altınışık, N. Ezgi; Kazancı, Duygu Deniz; Aydoğan, Ayça; Gemici, Hasan Can; Erdal, Ömür Dilek; Sarıaltun, Savaş; Vural, Kıvılcım Başak; Koptekin, Dilek; Gürün, Kanat; Sağlıcan, Ekin; Koruyucu, Meliha Melis; Karamurat, Cansu; Özkan, Mustafa; Kılınç, Gülşah Merve; Götherström, Anders; Atakuman, Çiğdem; Erdal, Yılmaz Selim; Özer, Füsun; Özdoğan, Aslı Erim; et.al. (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) We present partial ancient genomes from 13 individuals from the Pre-Pottery Neolithic period of Çayönü Tepesi in present-day Diyarbakır, Turkey. The sample coversa 1,000 year range, between approximately 10,500-9,500 years...
Reproducible and scalable data analysis on high performance computing Akkoyun, Emrah; Kuru, Nurdan; Dereli, Onur; Bircan, Aylin; Taştan, Öznur; Adebali, Ogün (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) We recently presented the PHACT tool ( PHylogeny-Aware Computation of Tolerance) for assessing amino acid substitutions that achieved superior predictive performance compared to widely adapted tools [1]. PHACT scores alter...
Assessment of machine-learning- versus experimental structural models of sex-specific isoforms of linker histone H1 Uça, Merve; Dimitrov, Stefan; Kale, Seyit (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) The nucleosome is the repeating unit of chromatin and it is composed of an octamer histone core that holds together around 145 base pairs of DNA in a disc-shaped configuration. In higher eukaryotes, an additional histone, ...
Probing the structural impacts of arg388 replacements in pkp2 protein complex: spesific case in arvc Kutlu, Aslı; Şahin, Şuara; Özkan, Mehmet Emre; Ulukaya, Engin (Orta Doğu Teknik Üniversitesi Enformatik Enstitüsü; 2022-10) In this study, we aimed to probe the roles of missense variants in PKP2 protein structures in ARVC-related clinics. Within the structure of PKP2 protein, there were many missense var-iants, whose associations with ARVC we...

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