CV

Education

• PhD in Entomology, Louisiana State University (LSU), 2026 (expected)
• MSc in Molecular Biology, Genetics and Bioengineering, Sabanci University, 2022
• BSc in Genetics and Bionengineering, Istanbul Bilgi University University, 2020

Work experience

• PhD Researcher with Drs. Qian Sun and Kate Ihle, LSU Agricultural Center and USDA Honey Bee Breeding, Genetics, and Physiology Lab, 2022-Present
  • Currently working on creating bulk RNA-seq data analysis pipelines and writing a research proposal that builds on my MSc research
• MSc Researcher with Drs. Christopher Mayack and Stuart Lucas, Sabanci University, 2020-2022
  • The Genetic Underpinnings of Varroa Mite and Disease Resistance in Honey Bees
    • Performed screening tests for common bacterial and fungal honey bee pathogens using PCR and qPCR
    • Built three RNA-seq workflows to identify differentially expressed genes
    • Developed Python scripts to extract RNA-seq reads aligned to genomes of viruses that infect honey bees
    • Performed network-based and functional enrichment analyses to identify hub genes and mechanisms
  • The Genetic Underpinnings of Varroa Mite and Disease Resistance in Honey Bees
    • Systematically mined PubMed, Gene Expression Omnibus (GEO), Sequence Read Archive (SRA) and European Nucleotide Archive (ENA) databases for eligible raw RNA-seq datasets
    • Preprocessed datasets, reduced study-specific batch effect and variation, and identified differentially expressed genes
    • Performed network-based and functional enrichment analyses to identify a common response against pesticides
• Undergraduate Researcher with Dr. Yuk Yin Ng, Istanbul Bilgi University, 2019-2020
  • Evaluation of Differentially Expressed Genes Associated with Breast Cancer Subtypes
    • Identified differentially expressed genes and enriched gene sets in breast cancer subtype-representative cell lines
    • Validated the expression of three differentially expressed genes and two markers involved in epithelial-to￾mesenchymal transition using qPCR in three subtype-representative breast cancer cell lines
• Bioinformatics Intern with Dr. Ali Osmay Gure, Bilkent University, Summer 2019
  • Investigated subtype switch in breast tumors due to chemotherapy treatment and metastasis
  • Studied the relationship between chemosensitivity and metabolite profiles in breast cancer
  • Identified differentially abundant metabolites in breast cancer subtype-representative cell lines
• Undergraduate Researcher with Dr. Yuk Yin Ng, Istanbul Bilgi University, 2018-2019
  • Optimized a PCR protocol to amplify the gene SERPINE1 from patient samples
• Molecular Biology Intern with Dr. N. C. Tolga Emre, Bogazici University, Summer 2018
  • Routine work with mammalian cell culture, PCR, qPCR, and western blotting

Skills

• Computational skills
  • RNA-seq data analysis (quality control, preprocessing, exploratory data analysis, batch effect correction, differential gene expression analysis, functional enrichment analysis)
  • Construction and analysis of gene co-expression and protein-protein interaction networks using Cytoscape
  • Data manipulation and visualization with R and Python
  • Working with Slurm-based HPC clusters
  • Statistical analysis of data with R
  • Machine learning with Python
  • Version control with Git
• Laboratory skills
  • RNA and DNA isolation and quantitation (spectrophotometer, fluorescence-based assays)
  • RNA quality control (gel electrophoresis, Agilent 2100 Bioanalyzer)
  • PCR and qPCR (RT-qPCR)
  • Gel electrophoresis
  • Molecular cloning
  • Cell culture (mammalian, insect, bacterial)
• Field skills
  • Basic beekeeping

Publications

Plasticity as an Underlying Mechanism of Tumor Heterogeneity in Breast Cancer

Akbar, M. W., Isbilen, M., Kuckkaraduman, B., Canli, S. D., Dedeoglu, E., Azizolli, S., Cela, I., Akcay, A. G., Hakanoglu, H., & Gure, A. O. (2020). "Plasticity as an Underlying Mechanism of Tumor Heterogeneity in Breast Cancer." BioRxiv.

Teaching

BIO 303: Genetics

MATH 306: Statistical Modeling

Service and leadership

• Vice President, Istanbul Bilgi University Genetics & Bioengineering Student Club - BILGEN, 2018-2020
  • Organized BILGEN’s 3. National Genetics and Bioengineering Congress
  • Designed booklets, poster, and related posts for social media using Adobe Photoshop
  • Helped first and second year department students in securing internships and maximizing learning experience