PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7645

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Citation - WoS: 2
Computational Mirnomics - Integrative Approaches
(Informationsmanagement in der Biotechnologie e.V. (IMBio e.V.), 2017) Hofestaedt, Ralf; Schreiber, Falk; Sommer, Bjoern; Allmer, Jens
With this special issue on Computational miRNomics, we would like to start a new generation of publications in the Journal of Integrative Bioinformatics (JIB). From 2017 onwards, JIB will be published by De Gruyter which is one of the largest Open Access publishers in Germany with a long history. Established in 1918 with roots reaching even further back, the JIB editorial board decided that De Gruyter is the perfect partner to increase the level of professionalism for our publication processing and journal development.
Citation - WoS: 1
Creation of Mutants by Using Centrality Criteria in Social Network Analysis
(PeerJ Inc., 2020) Takan, Savaş
Mutation testing is a method widely used to evaluate the effectiveness of the test suite in hardware and software tests or to design new software tests. In mutation testing, the original model is systematically mutated using certain error assumptions. Mutation testing is based on well-defined mutation operators that imitate typical programming errors or which form highly successful test suites. The success of test suites is determined by the rate of killing mutants created through mutation operators. Because of the high number of mutants in mutation testing, the calculation cost increases in the testing of finite state machines (FSM). Under the assumption that each mutant is of equal value, random selection can be a practical method of mutant reduction. However, in this study, it was assumed that each mutant did not have an equal value. Starting from this point of view, a new mutant reduction method was proposed by using the centrality criteria in social network analysis. It was assumed that the central regions selected within this frame were the regions from where test cases pass the most. To evaluate the proposed method, besides the feature of detecting all failures related to the model, the widely-used W method was chosen. Random and proposed mutant reduction methods were compared with respect to their success by using test suites. As a result of the evaluations, it was discovered that mutants selected via the proposed reduction technique revealed a higher performance. Furthermore, it was observed that the proposed method reduced the cost of mutation testing.
Citation - WoS: 13
Citation - Scopus: 18
Database Covering the Prayer Movements Which Were Not Available Previously
(Nature Publishing Group, 2023-05-12) Mihçin, Şenay; Şahin, Ahmet Mert; Yılmaz, Mehmet; Alpkaya, Alican Tuncay; Tuna, Merve; Akdeniz, Sevinç; Can, Nuray Korkmaz; Tosun, Aliye; Şahin, Serap
Lower body implants are designed according to the boundary conditions of gait data and tested against. However, due to diversity in cultural backgrounds, religious rituals might cause different ranges of motion and different loading patterns. Especially in the Eastern part of the world, diverse Activities of Daily Living (ADL) consist of salat, yoga rituals, and different style sitting postures. A database covering these diverse activities of the Eastern world is non-existent. This study focuses on data collection protocol and the creation of an online database of previously excluded ADL activities, targeting 200 healthy subjects via Qualisys and IMU motion capture systems, and force plates, from West and Middle East Asian populations with a special focus on the lower body joints. The current version of the database covers 50 volunteers for 13 different activities. The tasks are defined and listed in a table to create a database to search based on age, gender, BMI, type of activity, and motion capture system. The collected data is to be used for designing implants to allow these sorts of activities to be performed.
Citation - WoS: 1
Citation - Scopus: 1
Dnmso; an Ontology for Representing De Novo Sequencing Results From Tandem-Ms Data
(PeerJ Inc., 2020) Takan, Savaş; Allmer, Jens
For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.
Citation - WoS: 24
Citation - Scopus: 23
The Effect of Age, Menopausal State, and Breast Density on 18f-Fdg Uptake in Normal Glandular Breast Tissue
(Society of Nuclear Medicine and Molecular Imaging, 2010-03) Mavi, Ayşe; Çermik, Tevfik F.; Urhan, Muammer; Püskülcü, Halis; Basu, Sandip; Cucchiara, Andrew J.; Yu, Jian Q.; Alavi, Abass
Theoretically, the degree of 18F-FDG uptake in the glandular tissues of the normal breast can affect the detection of breast cancer. The aim of this prospective study was to investigate relationships among age, menopausal state, and breast density and determine whether they affect 18F-FDG uptake in normal glandular breast tissue. Methods: Among 250 newly diagnosed breast cancer patients, 149 patients (mean age ± SD, 50.9 ± 9.70 y; range, 32-77 y) were analyzed because they had normal contralateral breasts confirmed by MRI, mammography, and 18F-FDG PET examinations. PET images were acquired 60 ± 2 min after the administration of 18F-FDG (5.2 MBq/kg of body weight). The maximum and average standardized uptake value (SUVmax and SUVavg, respectively) of 18F-FDG were calculated in the normal breast. Patients were divided into groups according to qualitative breast density and menopausal state. Descriptive statistics and 2-factorial analysis of covariance were used to assess the effects of qualitative breast density, menopausal state, and age on SUVmax and SUVavg. Pearson χ2 was used to test the relationship between menopausal state and qualitative breast density. Results: The average age of patients with nondense breasts was significantly higher than that of patients with dense breasts (P < 0.01). Also, breast density related to menopausal state (P < 0.05). Dense breasts had an average SUVmax of 1.243 and mean SUVavg of 0.694, whereas nondense breasts had a mean SUVmax of 0.997 and mean SUVavg of 0.592. Analysis of covariance indicated that density and the linear effect of age were significant with regard to both SUVmax and SUVavg. After removing the linear effect of age, menopausal state had no effect on SUVmax and SUVavg. Conclusion: 18F-FDG uptake significantly decreases as age increases and breast density decreases. Age and qualitative breast density are independent factors and significantly affect 18F-FDG uptake for both SUVmax and SUVavg. Menopausal state had no effect on SUVmax and SUVavg. Copyright © 2010 by the Society of Nuclear Medicine, Inc.
Citation - WoS: 72
Citation - Scopus: 75
The Effects of Estrogen, Progesterone, and C-Erbb Receptor States on 18f-Fdg Uptake of Primary Breast Cancer Lesions
(Society of Nuclear Medicine and Molecular Imaging, 2007-08) Mavi, Ayşe; Çermik, Tevfik F.; Urhan, Muammer; Püskülcü, Halis; Basu, Sandip; Yu, Jian Q.; Zhuang, Hongming; Czerniecki, Brian; Alavi, Abass
The purpose of this prospective study was to investigate whether correlations exist between 18F-FDG uptake of primary breast cancer lesions and predictive and prognostic factors such as estrogen receptor (ER), progesterone receptor (PR), and C-erbB-2 receptor (C-erbB-2R) states. Methods: Before undergoing partial or total mastectomy, 213 patients with newly diagnosed breast cancer underwent 18F-FDG PET (5.2 MBq/kg of body weight). The maximum standardized uptake value (SUV) of the primary lesion was measured in each patient. Standard immunohistochemistry was performed on a surgical specimen of the cancer lesion to characterize the receptor state of the tumor cells. Pearson χ2 tests were performed on the cross-tables of different receptor states to test any association that may exist among ER, PR, and C-erbB-2R. Maximum SUV measurements for different receptor states were compared using factorial ANOVA in a completely random design. Results: After exclusion of certain lesions, 118 lesions were analyzed for this study. The mean maximum SUVs of ER-positive and ER-negative lesions were 3.03 ± 0.26 and 5.64 ± 0.75, whereas those of PR were 3.24 ± 0.29 and 4.89 ± 0.67, respectively, and those of C-erbB-2R were 4.64 ± 0.70 and 3.70 ± 0.35, respectively, χ2 tests for ER and PR showed that if one is positive then the other tends to be positive as well (χ2 = 71.054, P < 0.01). For ER and C-erbB-2R states, if ER is positive, C-erbB-2R will more likely be negative (χ2 = 13.026, P < 0.01). No relationship was detected between PR and C-erbB-2R states (χ2 = 3.695, P > 0.05). ANOVAs showed that PR state alone (F = 0.095, P > 0.05) and C-erbB-2R state alone (F = 0.097, P > 0.05) had no effect on 18F-FDG uptake but ER state alone had an effect (F = 9.126, P < 0.01). ER and PR being together had no additional effect on 18F-FDG uptake. Our study also demonstrated that interactions exist between ER and C-erbB-2R state and between PR and C-erbB-2R state. Conclusion: SUV measurements may provide valuable information about the state of ER, PR, and C-erbB-2R and the associated glucose metabolism as measured by 18F-FDG uptake of the primary breast cancer lesions. Such an association may be of importance to treatment planning and outcome in these patients.
Citation - WoS: 5
Citation - Scopus: 9
Efficient Privacy-Preserving Whole-Genome Variant Queries
(Oxford University Press, 2022-04) Akgün, Mete; Pfeifer, Nico; Kohlbacher, Oliver
Motivation: Diagnosis and treatment decisions on genomic data have become widespread as the cost of genome sequencing decreases gradually. In this context, disease-gene association studies are of great importance. However, genomic data are very sensitive when compared to other data types and contains information about individuals and their relatives. Many studies have shown that this information can be obtained from the query-response pairs on genomic databases. In this work, we propose a method that uses secure multi-party computation to query genomic databases in a privacy-protected manner. The proposed solution privately outsources genomic data from arbitrarily many sources to the two non-colluding proxies and allows genomic databases to be safely stored in semi-honest cloud environments. It provides data privacy, query privacy and output privacy by using XOR-based sharing and unlike previous solutions, it allows queries to run efficiently on hundreds of thousands of genomic data. Results: We measure the performance of our solution with parameters similar to real-world applications. It is possible to query a genomic database with 3 000 000 variants with five genomic query predicates under 400 ms. Querying 1 048 576 genomes, each containing 1 000 000 variants, for the presence of five different query variants can be achieved approximately in 6 min with a small amount of dedicated hardware and connectivity. These execution times are in the right range to enable real-world applications in medical research and healthcare. Unlike previous studies, it is possible to query multiple databases with response times fast enough for practical application. To the best of our knowledge, this is the first solution that provides this performance for querying large-scale genomic data.
Citation - WoS: 49
Citation - Scopus: 56
Evaluation of an Artificial Intelligence System for Diagnosing Scaphoid Fracture on Direct Radiography
(Springer Verlag, 2020) Özkaya, Emre; Topal, Fatih Esad; Bulut, Tuğrul; Gürsoy, Merve; Özuysal, Mustafa; Karakaya, Zeynep
Purpose The aim of this study is to determine the diagnostic performance of artificial intelligence with the use of convolutional neural networks (CNN) for detecting scaphoid fractures on anteroposterior wrist radiographs. The performance of the deep learning algorithm was also compared with that of the emergency department (ED) physician and two orthopaedic specialists (less experienced and experienced in the hand surgery). Methods A total 390 patients with AP wrist radiographs were included in the study. The presence/absence of the fracture on radiographs was confirmed via CT. The diagnostic performance of the CNN, ED physician and two orthopaedic specialists (less experienced and experienced) as measured by AUC, sensitivity, specificity, F-Score and Youden index, to detect scaphoid fractures was evaluated and compared between the groups. Results The CNN had 76% sensitivity and 92% specificity, 0.840 AUC, 0.680 Youden index and 0.826Fscore values in identifying scaphoid fractures. The experienced orthopaedic specialist had the best diagnostic performance according to AUC. While CNN's performance was similar to a less experienced orthopaedic specialist, it was better than the ED physician. Conclusion The deep learning algorithm has the potential to be used for diagnosing scaphoid fractures on radiographs. Artificial intelligence can be useful for scaphoid fracture diagnosis particularly in the absence of an experienced orthopedist or hand surgeon.
Citation - WoS: 30
Citation - Scopus: 34
Gddom: an Online Tool for Calculation of Dominant Marker Gene Diversity
(Springer Verlag, 2017-04) Abuzayed, Mazen; El-Dabba, Nourhan; Frary, Anne; Doğanlar, Sami
Gene diversity (GD), also called polymorphism information content, is a commonly used measure of molecular marker polymorphism. Calculation of GD for dominant markers such as AFLP, RAPD, and multilocus SSRs is valuable for researchers. To meet this need, we developed a free online computer program, GDdom, which provides easy, quick, and accurate calculation of dominant marker GD with a commonly used formula. Results are presented in tabular form for quick interpretation. © 2016, Springer Science+Business Media New York.
Citation - WoS: 4
Citation - Scopus: 4
Integrative Biological Network Analysis To Identify Shared Genes in Metabolic Disorders
(Institute of Electrical and Electronics Engineers, 2022) Tenekeci, Samet; Işık, Zerrin
Identification of common molecular mechanisms in interrelated diseases is essential for better prognoses and targeted therapies. However, complexity of metabolic pathways makes it difficult to discover common disease genes underlying metabolic disorders; and it requires more sophisticated bioinformatics models that combine different types of biological data and computational methods. Accordingly, we built an integrative network analysis model to identify shared disease genes in metabolic syndrome (MS), type 2 diabetes (T2D), and coronary artery disease (CAD). We constructed weighted gene co-expression networks by combining gene expression, protein-protein interaction, and gene ontology data from multiple sources. For 90 different configurations of disease networks, we detected the significant modules by using MCL, SPICi, and Linkcomm graph clustering algorithms. We also performed a comparative evaluation on disease modules to determine the best method providing the highest biological validity. By overlapping the disease modules, we identified 22 shared genes for MS-CAD and T2D-CAD. Moreover, 19 out of these genes were directly or indirectly associated with relevant diseases in the previous medical studies. This study does not only demonstrate the performance of different biological data sources and computational methods in disease-gene discovery, but also offers potential insights into common genetic mechanisms of the metabolic disorders.
Citation - WoS: 290
Citation - Scopus: 391
Introduction To Machine Learning
(Humana Press, 2014) Baştanlar, Yalın; Özuysal, Mustafa
The machine learning field, which can be briefly defined as enabling computers make successful predictions using past experiences, has exhibited an impressive development recently with the help of the rapid increase in the storage capacity and processing power of computers. Together with many other disciplines, machine learning methods have been widely employed in bioinformatics. The difficulties and cost of biological analyses have led to the development of sophisticated machine learning approaches for this application area. In this chapter, we first review the fundamental concepts of machine learning such as feature assessment, unsupervised versus supervised learning and types of classification. Then, we point out the main issues of designing machine learning experiments and their performance evaluation. Finally, we introduce some supervised learning methods.
Citation - WoS: 7
Citation - Scopus: 5
A Machine Learning Approach for Microrna Precursor Prediction in Retro-Transcribing Virus Genomes
(Informationsmanagement in der Biotechnologie e.V. (IMBio e.V.), 2016) Saçar Demirci, Müşerref Duygu; Toprak, Mustafa; Allmer, Jens
Identification of microRNA (miRNA) precursors has seen increased efforts in recent years. The difficulty in experimental detection of pre-miRNAs increased the usage of computational approaches. Most of these approaches rely on machine learning especially classification. In order to achieve successful classification, many parameters need to be considered such as data quality, choice of classifier settings, and feature selection. For the latter one, we developed a distributed genetic algorithm on HTCondor to perform feature selection. Moreover, we employed two widely used classification algorithms libSVM and random forest with different settings to analyze the influence on the overall classification performance. In this study we analyzed 5 human retro virus genomes; Human endogenous retrovirus K113, Hepatitis B virus (strain ayw), Human T lymphotropic virus 1, Human T lymphotropic virus 2, Human immunodeficiency virus 2, and Human immunodeficiency virus 1. We then predicted pre-miRNAs by using the information from known virus and human pre-miRNAs. Our results indicate that these viruses produce novel unknown miRNA precursors which warrant further experimental validation.
Citation - WoS: 16
Citation - Scopus: 19
Pixelated Colorimetric Nucleic Acid Assay
(Elsevier, 2020) Aydın, Hakan Berk; Cheema, Jamal Ahmed; Arnmanath, Gopal; Toklucu, Cihan; Yücel, Müge; Özenler, Sezer; Yıldız, Ümit Hakan
Conjugated polyelectrolytes (CPEs) have been widely used as reporters in colorimetric assays targeting nucleic acids. CPEs provide naked eye detection possibility by their superior optical properties however, as concentration of target analytes decrease, trace amounts of nucleic acid typically yield colorimetric responses that are not readily perceivable by naked eye. Herein, we report a pixelated analysis approach for correlating colorimetric responses of CPE with nucleic acid concentrations down to 1 nM, in plasma samples, utilizing a smart phone with an algorithm that can perform analytical testing and data processing. The detection strategy employed relies on conformational transitions between single stranded nucleic acid-cationic CPE duplexes and double stranded nucleic acid-CPE triplexes that yield distinct colorimetric responses for enabling naked eye detection of nucleic acids. Cationic poly[N,N,N-triethyl-3-((4-methylthiophen-3-yl)oxy)propan-1-aminium bromide] is utilized as the CPE reporter deposited on a polyvinylidene fluoride (PVDF) membrane for nucleic acid assay. A smart phone application is developed to capture and digitize the colorimetric response of the individual pixels of the digital images of CPE on the PVDF membrane, followed by an analysis using the algorithm. The proposed pixelated approach enables precise quantification of nucleic acid assay concentrations, thereby eliminating the margin of error involved in conventional methodologies adopted for interpretation of colorimetric responses, for instance, RGB analysis. The obtained results illustrate that a ubiquitous smart phone could be utilized for point of care colorimetric nucleic acids assays in complex matrices without requiring sophisticated software or instrumentation.
Citation - WoS: 17
Citation - Scopus: 19
Pro-Metastatic Functions of Notch Signaling Is Mediated by Cyr61 in Breast Cells
(Elsevier, 2020) Küçükköse, Cansu; Efe, Eda; Günyüz, Zehra Elif; Fıratlıgil, Burcu; Doğan, Hülya; Yalçın Özuysal, Özden; İlhan, Mustafa
Metastasis is the main cause of cancer related deaths, and unfolding the molecular mechanisms underlying metastatic progression is critical for the development of novel therapeutic approaches. Notch is one of the key signaling pathways involved in breast tumorigenesis and metastasis. Notch activation induces pro-metastatic processes such as migration, invasion and epithelial to mesenchymal transition (EMT). However, molecular mediators working downstream of Notch in these processes are not fully elucidated. CYR61 is a secreted protein implicated in metastasis, and its inhibition by a monoclonal antibody suppresses metastasis in xenograft breast tumors, indicating the clinical importance of CYR61 targeting. Here, we aimed to investigate whether CYR61 works downstream of Notch in inducing pro-metastatic phenotypes in breast cells. We showed that CYR61 expression is positively regulated by Notch activity in breast cells. Notch1-induced migration, invasion and anchorage independent growth of a normal breast cell line, MCF10A, were abrogated by CYR61 silencing. Furthermore, upregulation of core EMT markers upon Notch1-activation was impaired in the absence of CYR61. However, reduced migration and invasion of highly metastatic cell line, MDA MB 231, cells upon Notch inhibition was not dependent on CYR61 downregulation. In conclusion, we showed that in normal breast cell line MCF10A, CYR61 is a mediator of Notch1-induced pro-metastatic phenotypes partly via induction of EMT. Our results imply CYR61 as a prominent therapeutic candidate for a subpopulation of breast tumors with high Notch activity.

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