Yazar "MÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü" için PubMed İndeksli Yayınlar Koleksiyonu listeleme
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ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments
Choi, Meena; Eren-Doğu, Zeynep Filiz; Colangelo, Christopher; Cottrell, John; Hoopmann, Michael R.; Kapp, Eugene A.; Vitek, Olga (Amer Chemical Soc, 2017)Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography tandem mass spectrometry (LC-MS/MS) experiments requires a series of computational steps that identify and quantify ... -
Comparison of protein expression profile of limb regeneration between neotenic and metamorphic axolotl
Sibai, Mustafa; Altuntas, Ebru; Süzek, Barış Ethem; Sahin, Betul; Parlayan, Cuneyd; Ozturk, Gurkan; Demircan, Turan (Academic Press Inc Elsevier Science, 2020)The axolotl (Ambystoma mexicanum) salamander, a urodele amphibian, has an exceptional regenerative capacity to fully restore an amputated limb throughout the life-long lasting neoteny. By contrast, when axolotls are ... -
A correlation coefficient-based feature selection approach for virus-host protein-protein interaction prediction
İbrahim, Ahmed Hassan; Karabulut, Onur Can; Karpuzcu, Betül Asiye; Türk, Erdem; Süzek, Barış Ethem (Plos, 2023)Prediction of virus-host protein-protein interactions (PPI) is a broad research area where various machine-learning-based classifiers are developed. Transforming biological data into machine-usable features is a preliminary ... -
DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing
Türk, Erdem; Ayaz, Akif; Yüksek, Ayhan; Süzek, Barış Ethem (PMC, 2023)The discovery of low-coverage (i.e. uncovered) regions containing clinically significant variants, especially when they are related to the patient's clinical phenotype, is critical for whole-exome sequencing (WES) based ... -
In Silico Analysis of a Highly Mutated Gene in Cancer Provides Insight into Abnormal mRNA Splicing: Splicing Factor 3B Subunit 1(K700E) Mutant
Samy, Asmaa; Süzek, Barış Ethem; Özdemir, Mehmet Kemal; Şensoy, Özge (Mdpi, 2020)Cancer is the second leading cause of death worldwide. The etiology of the disease has remained elusive, but mutations causing aberrant RNA splicing have been considered one of the significant factors in various cancer ... -
In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases
McGarvey, Peter B.; Süzek, Barış Ethem; Baraniuk, James N.; Rao, Shruti; Conkright, Brian; Lababidi, Samir; Madhavan, Subha (Bmc, 2014)Background: Near universal administration of vaccines mandates intense pharmacovigilance for vaccine safety and a stringently low tolerance for adverse events. Reports of autoimmune diseases (AID) following vaccination ... -
Machine Learning Methods for Virus–Host Protein–Protein Interaction Prediction
Karpuzcu, Betül Asiye; Türk, Erdem; İbrahim, Ahmad Hassan; Karabulut, Onur Can; Süzek, Barış Ethem (Humana Press Inc., 2023)The attachment of a virion to a respective cellular receptor on the host organism occurring through the virus–host protein–protein interactions (PPIs) is a decisive step for viral pathogenicity and infectivity. Therefore, ... -
ML-AdVInfect: A Machine-Learning Based Adenoviral Infection Predictor
Karabulut, Onur Can; Karpuzcu, Betül Asiye; Türk, Erdem; Ibrahim, Ahmad Hassan; Süzek, Barış Ethem (Frontiers, 2021)Adenoviruses (AdVs) constitute a diverse family with many pathogenic types that infect a broad range of hosts. Understanding the pathogenesis of adenoviral infections is not only clinically relevant but also important to ... -
Plasma Concentrations and Cancer-Associated Mutations in Cell-Free Circulating DNA of Treatment-Naive Follicular Lymphoma for Improved Non-Invasive Diagnosis and Prognosis
Hatipoğlu, Tevfik; Esmeray Sönmez, Esra; Hu, Xiaozhou; Yuan, Hongling; Önal-Süzek, Tuğba (Frontiers Media SA, 2022)Follicular lymphoma (FL) is the second most frequent non-Hodgkin lymphoma accounting for 10-20% of all lymphomas in western countries. As a clinically heterogeneous cancer, FL occasionally undergoes histological transformation ... -
Preclinical Molecular Signatures of Spinal Cord Functional Restoration: Optimizing the Metamorphic Axolotl (Ambystoma mexicanum) Model in Regenerative Medicine
Demircan, Turan; Hacibektasogu, Harbiye; Sibai, Mustafa; Fescioglu, Ece Cana; Altuntaş, Ebru; Ozturk, Gurkan; Süzek, Barış Ethem (Mary Ann Liebert, Inc, 2020)Regenerative medicine offers hope for patients with diseases of the central and peripheral nervous system. Urodele amphibians such as axolotl display an exceptional regenerative capacity and are considered as essential ... -
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
Süzek, Barış Ethem; Wang, Yuqi; Huang, Hongzhan; McGarvey, Peter B.; Wu, Cathy H. (Oxford Univ Press, 2015)Motivation: UniRef databases provide full-scale clustering of UniProtKB sequences and are utilized for a broad range of applications, particularly similarity-based functional annotation. Non-redundancy and intra-cluster ...