| Name | Degree | Year | Thesis Title |
| Cem Kuscu | MS | 2004 | Effects of Rapamycin on the early development of zebrafish (Danio rerio) |
| Koray Dogan Kaya | MS | 2005 | Evaluation of miRNA sequence composition and expression |
| Ertugrul Dalkic | MS | 2006 | In vivo and in vitro analyses of mRNA expression of Robo2 in zebrafish in the context of PI3K/AKT/TOR pathway |
| Rumeysa Biyik | MS | 2009 | Nicotine-modulated gene expression profiles in MCF7 breast cancer cell line and involvement of estrogen in CHRNA5 expression |
| Onur Kaya | MS | 2009 | Investigation of the effects of nicotine on the expression profile of SW620 colon adenocarcinoma cells using a functional genomics approach |
| Muammer Ucal | MS | 2010 | Investigation of the effects of nicotine and levamisole on SW620 colon adenocarcinoma cells using a customized R routine for automated microarray analysis |
| Ahmet Rasit Ozturk | MS | 2010 | Investigation of the effects of MAS5, RMA and GCRMA preprocessing methods on an affymetrix zebrafish genechip dataset using statistical and network parameters |
| Ceren Sucularli | PhD | 2011 | Zebrafish as a model for analysis of signaling pathways involved in cell growth and proliferation and development |
| Gizem Olmezer | MS | 2011 | Smoking and nicotine alter UGT1A expression |
| Koray Dogan Kaya | PhD | 2011 | Development of a WEB application/ database for the integrative analysis of microRNA expression patterns |
| Azer Aylin Acikgoz | MS | 2013 | Analysis of CHRNA5 expression in breast cancer cell lines in response to serum starvation and estrogen treatment |
| Sila Ozdemir | MS | 2014 | qPCR validation of diagnostic importance and regulation by estrogen of Chrna5 isoform expression in breast cancer |
| Bircan Coban | MSc | 2016 | Regulation of mineralocorticoid receptor and its downstream targets by estrogen and aldosterone in breast cancer |
| Ermira Jahja | PhD | 2017 | Investigation of novel RNAi and nanoparticle approaches for their anti-proliferative and drug-sensitizing effects in breast cancer |
| Basak Ozgursoy | MSc | 2017 | hsa-miR-497 as a modulator of the expression in the presence or absence of CHRNA5 in breast cancer |
| Huma Shehwana | PhD | 2017 | Development of novel tools for cancer diagnosis, prognosis and treatment using intra- or inter-species transcriptome meta-analysis |
| Damla Gunes | MSc | 2018 | Mineralocorticoid and Glucocorticoid receptors as novel targets in liver and breast cancers |
| Tugberk Kaya | MSc | 2018 | Co-expression pairs and modules (CoEX-PM): a shiny application and an example case study on chromogranins |
| Sahika Cingir-Koker | PhD | 2018 | 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 |
| Rafed Said Tiryaki | MSc | 2019 | Effects of miR-376 family miRNAs on CHRNA5 depleted MCF7 cell line model and co-culture competition studies |
| Fatma Betul Dincaslan | MSc | 2019 | Tissue specific transcriptome of zebrafish in ache mutant embryos |
| Seniye Targen | PhD | 2020 | 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 |
| Murat Yaman | PhD | 2020 | Identification of preclinical implications for novel indole-benzimidazoles and phenothiazines using in vitro cancer cell line and in vivo zebrafish models |
| Ayse Gokce Keskus | PhD | 2021 | Identification of modulatory functions of TP53, estrogen signaling, and 14q32 |
| Busra Korkmaz | MSc | 2021 | Zebrafish as an in vivo model of drug screens for liver cancer: the role of phenothiazines |
| Ayse Ozhan | PhD | 2021 | Survival analysis and its applications in identifying genes, signatures, and pathways in human cancers |
| Burcin Irem Arici | MSc | 2022 | 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 |
| Kubra Calisir | MSc | 2022 | 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 |
| Farid Ahadli | MSc | 2022 | BRCA:Cohort-vs-TCGA: a webtool for comprehensive exploration and comparison of mutational landscape of breast cancer cohorts with TCGA-BRCA |
| Melike Tombaz | MSc | 2022 | A shiny application for pancan survival analysis with paralog/miRNA pairs and in vitro validation of miRNA synergism in liver cancer |
| Ronaldo Leka | MSc | 2022 | Development of a shiny application for comparative transcriptomics and differential gene expression analysis |
| Ruya Tombuloglu | MSc | 2023 | Zebrafish glioma xenograft models: in vivo investigation of injection methods and development of a streamlit application |
| Gunes Tok | MSc | 2024 | Drug repurposing and investigation of novel combinations for glioblastoma therapeutics using in vitro and zebrafish in vivo models |
| Selvin Yildiz | MSc | 2024 | Diet-induced changes in mouse cells in vitro and in vivo zebrafish models of angiogenesis |
| Siber Gunes Celik (Kilinc) | MSc | 2024 | Sox2 in focus: Association of SOX2 copy number variation with TP53 mutation in TCGA PanCancer cohorts and codon optimized design for de novo SOX2 synthesis using novel shiny application |
| Abdul Moiz Aftab | MSc | 2024 | TP53 META, A webtool to visualize effects of TP53 modulators and mutations on expression profiles with a focus on breast cancer |
| Merve Vural-Ozdeniz | PhD | 2024 | CAP-RNAseq: An online platform for RNA-seq data clustering, annotation and prioritization based on gene essentiality and congruence between mRNA and protein levels |
| Mert Demirdizen | MSc | 2024 | Development of a multi-species scRNA-seq atlas of metabolic dysfunction-associated steatotic liver disease (MAFLD) |