Advisors
Now showing items 1-17 of 17
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BRCA:Cohort-vs-TCGA: a webtool for comprehensive exploration and comparison of mutational landscape of breast cancer cohorts with TCGA-BRCA
(Bilkent University, 2022-08)Comparisons of mutational landscapes between independent breast cancer (BRCA) cohorts in a comprehensive and statistical manner using online tools are likely to help advance our understanding of the diversity of somatic ... -
Co-expression pairs and modules (CoEX-PM): a shiny application and an example case study on chromogranins
(Bilkent University, 2018-09)Gene expression signatures have been proved to be effective biomarkers of tumorigenesis and metastasis especially when alternative methods are inconvenient or ineffective. Nevertheless, handling very large datasets obtained ... -
Development of a shiny application for comparative transcriptomics and differential gene expression analysis
(Bilkent University, 2022-09)RNA sequencing has proven to be an effective technique for divulging information about the transcriptome in molecular biology research. Compared to microarrays and early methods of cDNA sequencing, high-throughput RNA ... -
Development of a specialized zebrafish xenotransplantation database and establishment of ALU-based tumor DNA quantification method in zebrafish: focus on models of overexpression and microenvironment
(Bilkent University, 2020-09)Successful xenotransplantation of human cancer cells into zebrafish host marked a new era in cancer research enabling high throughput in vivo screens. Zebrafish xenotransplantation literature continues to rapidly accumulate, ... -
Development of novel tools for cancer diagnosis, prognosis and treatment using intra- or inter-species transcriptome metaanalysis
(Bilkent University, 2017-08)In the past decades, a considerable number of studies have performed meta-analysis on large data collections to prioritize sets of genes, pathways or types/categories of disease focusing on either differential expression, ... -
Effects of Cholinergic Receptor Nicotinic Alpha 5 (CHRNA5) RNAi on apoptosis, DNA damage response, drug sensitivity, and HSA-MIR-495-3P overexpression in breast cancer
(Bilkent University, 2018-12)Cholinergic Receptor Nicotinic Alpha 5 (CHRNA5) is associated with nicotine addiction and it has an important role in the prognosis of lung cancer. Despite its important cellular functions, its role in breast cancer remains ... -
Effects of depletion of CHRNA5 and/or TP53, and transient and stable overexpression of wildtype or mutant TP53 on expression of DLK1-MEG3 locus in MCF7 cells
(Bilkent University, 2022-09)The expression of CHRNA5 has a prominent role in lung cancer and nicotine addiction. Besides, depletion of CHRNA5 has been identified as being tumour suppressive in breast cancer. Moreover, CHRNA5 depletion causes increases ... -
Effects of miR-376 family miRNAs on CHRNA5 depleted MCF7 cell line model and co-culture competition studies
(Bilkent University, 2019-07)Cholinergic receptor nicotinic alpha 5 (CHRNA5) is a ligand-gated ion channel and one of the subunits of nicotinic acetylcholine receptors. Role of CHRNA5 in tumorigenesis has been initially shown in the lung tissue in ... -
Identification of modulatory functions of TP53, estrogen signaling, and 14q32.31 miRNA cluster on CHRNA5 knock-down expression profile and development of syneRgy APP
(Bilkent University, 2021-09)Cholinergic receptor subunit alpha 5 (CHRNA5) is a ligand-gated ion channel expressed in not only the nervous system but also other tissues. Differential expression and the polymorphisms of CHRNA5 have been associated with ... -
Identification of preclinical implications for novel indole-benzimidazoles and phenothiazines using in vitro cancer cell line and in vivo zebrafish models
(Bilkent University, 2020-09)Breast cancer (BC) and hepatocellular carcinoma (HCC) are two major health problems with significant mortality rates. Although drug therapies are available, therapeutic success remains limited. Because of low bioavailability, ... -
Investigation of novel RNAi and nanoparticle approaches for their anti-proliferative and drug-sensitizing effects in breast cancer
(Bilkent University, 2017-08)Drug resistivity remains a major challenge in treating different cancer types. Among several strategies adapted to increase drug sensitivity in breast cancer cells, in the present thesis I studied an RNAi molecule targeting ... -
Mineralocorticoid and glucocorticoid receptors as novel targets in breast and liver cancer therapies
(Bilkent University, 2020-12)Cell signaling is a complex phenomenon and is maintained through intertwined signal transmissions within and in-between the cells. Anti-cancer therapies are often challenged by this fact due to crosstalk-associated ... -
A shiny application for pancan survival analysis with paralog/miRNA pairs and in vitro validation of miRNA synergism in liver cancer
(Bilkent University, 2022-09)Emerging cancer survival tools can predict risk of disease and identify prognostic biomarkers. Multivariable Cox proportional hazards models with mRNA and microRNAs (miRNAs) expression can differentiate survival outcomes. ... -
Survival analysis and its applications in identifying genes, signatures, and pathways in human cancers
(Bilkent University, 2021-09)Cancer literature makes use of survival analyses focused on gene expression based on univariable or multivariable regression. However, there is still a need to understand whether a) incorporating exon or isoform information ... -
Tissue specific transcriptome of zebrafish in ache mutant embryos
(Bilkent University, 2019-06)Differential expression of specific genes in certain tissues provides information about tissue specificity which might define phenotypes of various tissues. It is possible to understand the tissue-specific effects of ... -
A web tool to explore, annotate and classify the Acıbadem Breast Cancer Cohort RNA-seq data with gene signatures and clinical/mutation data, according to molecular subtypes
(Bilkent University, 2022-06)Transcriptomics-based approaches have revealed the molecular heterogeneity and distinct gene expression patterns across breast cancer subtypes since the early 2000s. This led to the usage of molecular subtypes in clinics ... -
Zebrafish as an in vivo model of drug screens for liver cancer: the role of phenothiazines
(Bilkent University, 2021-08)Hepatocellular carcinoma (HCC) is one of the most dangerous cancer types and sorafenib (SFB) is a commonly used drug against HCC, being the only FDA-approved medication until 2018. However, its limited efficacy and severe ...
