Yesim Aydin Son

Yesim Aydin Son
Middle East Technical University | METU · Department of Health Informatics

MD, PhD

About

64
Publications
16,627
Reads
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1,700
Citations
Introduction
Dr. Yeşim Aydın Son is a medical scientist holding a M.D. and a Ph.D. in Genome Sciences and Technologies. She is a full time faculty of METU Graduate School of Informatics since 2010, and promoted to the Assoc. Prof. position in the Bioinformatics Program in 2017. Main focus of her research is modeling of chronic and complex diseases based on integrated genomic and clinical data. METU-SNP is an analysis tool developed by her group for the prioritization of biologically significant variants through AHP based scoring, build on integrative analysis of genotyping data, biological annotation databases, and variant effect prediction tools. Integrating genomic and phenotypic data for the modelling of Schizophrenia and Alzheimer’s disease are among her ongoing projects. Dr. Aydın Son’s group cont
Additional affiliations
September 2009 - present
Middle East Technical University
Position
  • Chair
August 2002 - August 2006
Oak Ridge National Laboratory
Position
  • Research Assistant
August 2000 - August 2002
University of Tennessee at Knoxville
Position
  • Research Assistant

Publications

Publications (64)
Article
Full-text available
Through Genome Wide Association Studies (GWAS) many Single Nucleotide Polymorphism (SNP)-complex disease relations can be investigated. The output of GWAS can be high in amount and high dimensional, also relations between SNPs, phenotypes and diseases are most likely to be nonlinear. In order to handle high volume-high dimensional data and to be ab...
Article
Full-text available
A novel framework for the automated evaluation of various deep learning-based splice site detectors is presented. The framework eliminates time-consuming development and experimenting activities for different codebases, architectures, and configurations to obtain the best models for a given RNA splice site dataset. RNA splicing is a cellular proces...
Article
Full-text available
Introduction: Despite the significant progress in understanding cancer biology, the deduction of metastasis is still a challenge in the clinic. Transcriptional regulation is one of the critical mechanisms underlying cancer development. Even though mRNA, microRNA, and DNA methylation mechanisms have a crucial impact on the metastatic outcome, there...
Article
Background The complex genetic etiology of the LOAD is still unclear, which restrains the early and/or differential diagnosis of LOAD. Genome‐Wide Association Studies (GWAS) is designed to explore the statistical interactions of variants, but interactions between variants are overseen by the univariate analysis. The machine learning algorithms are...
Article
Background Boron is a prominent part of the human diet and one of the essential trace elements for humans. Dietary boron is mostly transformed into boric acid within the body and has been associated with desirable health outcomes. Non-dietary resources of boron, such as boron-based drugs and occupational exposure, might lead to excessive boron leve...
Chapter
Full-text available
This study provides an overview of genetic testing reimbursement, methodology, and benefit catalogue and explores medical professionals' perspectives and policy recommendations regarding the current status of genetic/genomic testing in Türkiye, along with a broad discussion. Semi-structured interviews are conducted with 13 key-informant medical gen...
Article
Full-text available
Through technological innovations, patient cohorts can be examined from multiple views with high-dimensional, multiscale biomedical data to classify clinical phenotypes and predict outcomes. Here, we aim to present our approach for analyzing multimodal data using unsupervised and supervised sparse linear methods in a COVID-19 patient cohort. This p...
Preprint
Full-text available
Late-Onset Alzheimer Disease (LOAD) is a progressive and complex neurodegenerative disorder in the aging population. LOAD is characterized by cognitive decline, such as deterioration of memory, loss of intellectual abilities, and other cognitive domains depending on traumatic brain injuries. Alzheimer's Disease (AD) presents a complex genetic lands...
Article
Full-text available
Background Non-linear relationships at the genotype level are essential in understanding the genetic interactions of complex disease traits. Genome-wide association Studies (GWAS) have revealed statistical association of the SNPs in many complex diseases. As GWAS results could not thoroughly reveal the genetic background of these disorders, Genome-...
Article
Full-text available
Understanding health-related work loss and creating a comprehensive approach requires the identification of lifestyle behaviour patterns. An essential aspect of this process is the examination of different profiles within the target population to develop effective intervention strategies. This study explored the wellness profiles of information tec...
Preprint
Full-text available
Through technological innovations, patient cohorts can be examined from multiple views with high-dimensional, multiscale biomedical data to classify clinical phenotypes and predict outcomes. Here, we aim to present our approach for analyzing multimodal data using unsupervised and supervised sparse linear methods in a COVID-19 patient cohort. This p...
Article
Full-text available
Since the 1970s and more rigorously since the 1990s, many countries have regulated data protection and privacy laws in order to ensure the safety and privacy of personal data. First, a comparison is made of different acts regarding genetic information that are in force in the EU, the USA, and China. In Turkey, changes were adopted only recently fol...
Article
Advances in genetic/genomic research and translational studies drive the progress on molecular diagnosis, personalised treatment, and monitoring. Healthcare professionals and governments are encouraged to set administrative regulations and implement structured and interoperable representation to utilise the genetic/genomic data, which will support...
Article
Full-text available
Background/aim: The COVID-19 Pandemic originated in Wuhan, China, in December 2019 and became one of the worst global health crises ever. While struggling with the unknown nature of this novel coronavirus, many researchers and groups attempted to project the progress of the pandemic using empirical or mechanistic models, each one having its drawba...
Preprint
Full-text available
With the increasing use of genetic testing and applications of bioinformatics in healthcare, genetic and genomic data needs to be integrated into electronic health systems. We administered a descriptive survey to 174 participants to elicit their views on the privacy and security of mobile health record systems and inclusion of their genetic data in...
Preprint
Full-text available
Background Splicing mechanism in eukaryotic cells, drives the protein diversity. This important mechanism is orchestrated by regulatory factors controlled through various splicing signals. 3’ and 5’ splice sites, and common branch point sequences are known as initiating signals of splicing, and changes in these signals can be the underlying cause o...
Conference Paper
In order to determine the essential design components of a mobile personal health record system (mPHR), which can manage genetic/genomic data along with other healthcare data, we have applied four different sub-studies in the scope of this paper. First of all, we analyzed the popular mobile application markets and evaluated the mobile personal heal...
Chapter
Between November 23 and December 4, 2016, Prof. Dr. Gerhard-Wilhelm Weber visited Japan and Taiwan as a part of his annual travel program of 2016. He gave seminars of various subjects at Konan University (Kobe), Kansai University (Osaka), National Taiwan University of Science and Technology and National Taiwan University (Taipei). The following vid...
Article
Full-text available
Background Multifactor dimensionality reduction (MDR) is a nonparametric approach that can be used to detect relevant interactions between single-nucleotide polymorphisms (SNPs). The aim of this study was to build the best genomic model based on SNP associations and to identify candidate polymorphisms that are the underlying molecular basis of the...
Article
Full-text available
Recently, there has been increasing research to discover genomic biomarkers, haplotypes, and potentially other variables that together contribute to the development of diseases. Single Nucleotide Polymorphisms (SNPs) are the most common form of genomic variations and they can represent an individual’s genetic variability in greatest detail. Genome-...
Article
Full-text available
Recent studies show that RNA-binding proteins (RBPs) and microRNAs (miRNAs) function in coordination with each other to control post-transcriptional regulation (PTR). Despite this, the majority of research to date has focused on the regulatory effect of individual RBPs or miRNAs. Here, we mapped both RBP and miRNA binding sites on human 3′UTRs and...
Article
Full-text available
Salmonella enterica is a bacterial pathogen that usually infects its host through food sources. Translocation of the pathogen proteins into the host cells leads to changes in the signaling mechanism either by activating or inhibiting the host proteins. Given that the bacterial infection modifies the response network of the host, a more coherent vie...
Article
Full-text available
Genome wide association studies (GWAS) determine susceptibility profiles for complex diseases. In this study, GWAS was performed in 26 patients with oligo and rheumatoid factor negative polyarticular juvenile idiopathic artritis (JIA) and their healthy parents by Affymetrix 250K SNP arrays. Biological function and pathway enrichment analysis was do...
Conference Paper
Full-text available
In this study, our main focus was to understand necessities of a Personal Health Records (PHR) System for managing individuals' health and genetic information. Recently the outcomes of Human Genome Project have begun to transform the clinic practice but still there is very limited number of studies in the area of genetic information exchange. Espec...
Article
Full-text available
Objective: As a result of studies of multifactorial conditions, genetic, physiological and environmental factors, the overall heritability of bipolar disorders has been estimated to be up to 70%. In this study, an analysis of genome-wide association study data using data mining algorithms has revealed single-nucleotide polymorphisms that may be the...
Article
Full-text available
Despite the rise in type 2 diabetes prevalence worldwide, we do not have a method for early risk prediction. The predictive ability of genetic models has been found to be little or negligible so far. In this study, we aimed to develop a better early risk prediction method for type 2 diabetes. We used phenotypic and genotypic data from the Nurses' H...
Article
Full-text available
Single Nucleotide Polymorphisms (SNPs) are the most common genomic variations where only a single nucleotide differs between individuals. Individual SNPs and SNP profiles associated with diseases can be utilized as biological markers. But there is a need to determine the SNP subsets and patients' clinical data which is informative for the diagnosis...
Article
Full-text available
The relations between Single Nucleotide Polymorphism (SNP) and complex diseases are likely to be non-linear and require analysis of the high dimensional data. Previous studies in the field mostly focus on genotyping and effects of various phenotypes are not considered. To fill this gap a hybrid feature selection model of support vector machine and...
Article
Full-text available
Background: A personalized medicine approach provides opportunities for predictive and preventive medicine. Using genomic, clinical, environmental, and behavioral data, the tracking and management of individual wellness is possible. A prolific way to carry this personalized approach into routine practices can be accomplished by integrating clinical...
Article
Full-text available
Background: A personalized medicine approach provides opportunities for predictive and preventive medicine. Using genomic, clinical, environmental, and behavioral data, the tracking and management of individual wellness is possible. A prolific way to carry this personalized approach into routine practices can be accomplished by integrating clinical...
Article
Full-text available
Background: Personalized medicine approaches provide opportunities for predictive and preventive medicine. Using genomic, clinical, environmental, and behavioral data, tracking and management of individual wellness is possible. A prolific way to carry this personalized approach into routine practices can be accomplished by integrating clinical int...
Chapter
Full-text available
Today, with the technology-driven developments, healthcare systems and services are being radically transformed to become more effective and efficient. Omics technologies along with mobile sensors and monitoring systems are emerging disruptive technologies, which will provide us the opportunities of a paradigm shifting in medical theory, research a...
Book
Full-text available
"Omics for Personalized Medicine" will give to its prospective readers the insight of both the current developments and the future potential of personalized medicine. The book brings into light how the pharmacogenomics and omics technologies are bringing a revolution in transforming the medicine and the health care sector for the better. Students o...
Conference Paper
In the life sciences, semantic web can support many aspects of bio- and health informatics, with exciting applications appearing in areas ranging from plant genetics to drug discovery. Using semantic technologies with open linked data, provides two kinds of advantages: ability to search multiple datasets through a single framework and ability to se...
Chapter
Full-text available
Pharmacogenomics of today has its origins in the 1950s with pioneering studies of monogenic variations in drug metabolism and pharmacokinetics. With the completion of the Human Genome Project in 2003 and the advances in genomics such as the high-throughput genomics technologies we are now in the postgenomics era. This transition is increasingly mar...
Conference Paper
Full-text available
Background / Purpose: Formalin fixed paraffin embedded (FFPE) tissues are the most available material for routine diagnostics in pathology laboratories worldwide. They can be used for both microscopic examinations and molecular diagnostic assays after microscopy. Molecular assays, such as PCR and high throughput microarrays, have the potential to...
Conference Paper
Full-text available
Background / Purpose: Osteosarcoma (OS) is the primary malignant tumor of bone, with an incidence rate of 19% among all cancer types. The vast majority of patients have pulmonary metastases at diagnosis, and about half develop lung disease later, which leads to poor prognosis and increased death rate. It is therefore essential to investigate mole...
Conference Paper
Full-text available
In synthetic biology, designing a new genetic construct demands in-detail studies of its candidate components individually and in a composition with each other. These costly wet lab experiments require considerable amount of time and usually result in undesired output. In this paper, we propose a method for the extraction of existing or novel synth...
Conference Paper
Full-text available
Genome wide association studies (GWAS) aim to identify genomic variance associated with certain disease conditions. Major bottleneck of standard GWAS approaches are the prioritization and subset selection after the statistically significant SNPs are determined. Our group has recently developed an analysis pipeline, where p-value and combined p valu...
Conference Paper
RNA induced gene silencing complex (RISC) has a role in many cellular processes which includes regulation of gene expression, immune response, cell differentiation and embryonic development. Dicer protein is a key regulator of these processes. Dicer1 specifically has central role in maturation of RISC substrate RNA and RISC assembly in mouse. Here...
Conference Paper
Single Nucleotide Polymorphisms (SNP) is a DNA sequence variation that occurs when a single nucleotide differs between members of a biological species or paired chromosomes in an individual. Studies on SNP data are important for scientists to shed light on identifying genetic variations underlying complex diseases. While recent advances in high-thr...
Article
Full-text available
Recently, there has been increasing research to discover genomic biomarkers, haplotypes, and potentially other variables that together contribute to the development of diseases. Single Nucleotide Polymorphisms (SNPs) are the most common form of genomic variations and they can represent an individual’s genetic variability in greatest detail. Genome-...
Article
Full-text available
After the completion of Human Genome Project in 2003, it is now possible to associate genetic variations in the human genome with common and complex diseases. The current challenge now is to utilize the genomic data efficiently and to develop tools to improve our understanding of etiology of complex diseases. Many of the algorithms needed to deal w...
Article
Full-text available
Selecting a subset of SNPs (Single Nucleotide Polymorphism pronounced snip) that is informative and small enough to conduct association studies and reduce the experimental and analysis overhead has become an important step toward effec-tive disease-gene association studies. In this study, we developed a novel methods for selecting Informative SNP s...
Chapter
In: book of extended abstracts of 8th International Conference on Optimization: Techniques and Applications (ICOTA8), Shanghai, China, December 10-13, 2010, by Prof. Xioaling Sun et al.
Conference Paper
Full-text available
As the field of Synthetic Biology is on the rise, iGEM is growing up very fast and the number of parts in the parts registry is increasing with the addition of more complex parts each day. Finding a part according to desired purposes is becoming more and more difficult. After facing some difficulty while running our algorithms on the parts registry...
Poster
As Synthetic Biology field is on the rise, iGEM also grows up and number of parts in parts registry increase with submission of more complex constructs each year. Our first milestone was to perform more efficient standardization on parts entry due to facing some difficulty while running our algorithms on the parts registry. We also used Software Re...
Presentation
Outline: - Introduction: Biological Background, Problem Statement; - Informative SNP Selection Algorithm; - Experimental Study: Data, Methods; - Results & Conclusion
Article
Full-text available
The Oak Ridge Polycystic Kidney (ORPK) mouse was described nearly 14 years ago as a model for human recessive polycystic kidney disease. The ORPK mouse arose through integration of a transgene into an intron of the Ift88 gene resulting in a hypomorphic allele (Ift88Tg737Rpw). The Ift88Tg737Rpw mutation impairs intraflagellar transport (IFT), a proc...
Article
The mouse agouti protein is transiently expressed in the skin and signals through the melanocortin 1 receptor to switch pigment production of hair-follicle melanocytes from black to yellow. Ubiquitous over-expression of agouti protein in mice carrying the spontaneous dominant mutations A[superscript y] and A[superscript vy] causes a pleiotropic syn...
Article
Full-text available
Intraflagellar transport (IFT) proteins are essential for cilia assembly and have recently been associated with a number of developmental processes, such as left-right axis specification and limb and neural tube patterning. Genetic studies indicate that IFT proteins are required for Sonic hedgehog (Shh) signaling downstream of the Smoothened and Pa...
Article
Full-text available
Intraflagellar transport (IFT) proteins are essential for cilia assembly and have recently been associated with a number of developmental processes, such as left–right axis specification and limb and neural tube patterning. Genetic studies indicate that IFT proteins are required for Sonic hedgehog (Shh) signaling downstream of the Smoothened and Pa...
Article
Full-text available
We report a prenatally diagnosed balanced de novo translocation t(6;7)(p25;q31). Physical examination of the baby born at term revealed only a posterior cleft palate. Laboratory examinations and radiologic investigations were found normal. Two years follow-up of the patient showed her mental and motor development was appropriate with her age. Our r...
Article
Full-text available
Twenty-nail dystrophy (TND) is an autosomal dominantly inherited idiopathic nail dystrophy characterized by excessive longitudinal striations and numerous superficial pits on nails with a typical 'sand papered' rough appearance. It is evident at birth and progresses slowly. It can also be associated with various diseases including lichen planus, al...

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