Mehmet Burak Taşkaya
Türkçe

Research

For my PhD at Bilkent University, I study two genes linked to pediatric kidney developmental disorders. In kidney epithelial cell lines, I test how their disease-associated variants affect cell function.

Research statement

The question

Genetic studies can link a gene to a disease, but they do not show what a disease-associated variant changes in the cell, or whether it changes anything at all. Experiments in cells can test that directly. In my PhD, I run such experiments for two genes associated with pediatric kidney developmental disorders. For each gene, I ask what it contributes to kidney epithelial cells, and what its disease-associated variants change in those cells.

What I bring

I work at the bench and with data. At the bench, my methods include cloning and site-directed mutagenesis, colony screening with Sanger verification, mammalian cell culture, transfection, RNA isolation, and Western blotting. On the computational side of my PhD, I analyze RNA-seq data with Salmon and DESeq2 and run KEGG pathway enrichment with clusterProfiler in R/Bioconductor. I also analyze metabolomics data in MetaboAnalystR and integrate results across omics layers in R and Python.

My training before the PhD covered both sides. As a project intern in Asst. Prof. Christopher Mayack's lab at Sabancı University, I worked on RNA expression dynamics and post-transcriptional regulation in honey bees and assisted with experimental design. At Acıbadem University, I analyzed SARS-CoV-2 variants in saliva samples and did microbiome analysis. In the wet lab, I cultured bacteriophages and worked on quorum sensing and biofilm formation. In R and Python, I improved and evaluated protein and amino-acid databases and produced a protein-stability predictor. A student internship at Bezmialem Vakıf University introduced me to molecular docking.

At Bilkent, I was a teaching assistant for MBG 338 Microbiology Laboratory in Spring 2025 and Spring 2026. I also supervise interns at the bench.

Where I'm heading

The work I want to keep doing runs from variant to function: building cell models of disease-associated variants, and analyzing omics data such as RNA-seq and metabolomics. I am most interested in questions that the cell models and the omics data can answer together, with the bench work and the analysis both my own.

Current project

  1. Disease-associated variants in kidney epithelial cells

    PhD thesis project · Bilkent University

    – present

    A functional analysis of two genes associated with pediatric kidney developmental disorders.

    My role:
    PhD candidate; this is my thesis project.
    Outcome and status:
    PhD thesis; in progress.
    Lab and supervisor:
    Asst. Prof. Onur Çizmecioğlu, Department of Molecular Biology and Genetics, Bilkent University

Earlier research

  1. Conserved motifs upstream of E. coli housekeeping genes

    B.Sc. graduation project

    Python code that compares the upstream regions of six housekeeping genes across 300 bacterial sequences, then applies the same analysis to 49 upstream sequences from E. coli K-12 MG1655. It analyzes nucleotide composition and frequent subsequences, and searches for ribosome-binding-site (Shine–Dalgarno) motifs.

    My role:
    I wrote the analysis code in Python for my B.Sc. graduation project.
    Methods:
    Python; comparison of upstream sequences; nucleotide composition; conserved-motif search.
    Outcome and status:
    Graduation project and Python analysis code; completed.
    Lab and supervisor:
    Assoc. Prof. Erkan Mozioğlu, Acıbadem University

  2. RNA expression and regulation in honey bees

    Project internship · Sabancı University

    –

    A project internship on RNA expression dynamics and post-transcriptional regulation in honey bees.

    My role:
    Project intern; I assisted with experimental design.
    Outcome and status:
    Completed.
    Lab and supervisor:
    Asst. Prof. Christopher Mayack, Mayack Lab, Sabancı University

  3. SARS-CoV-2 variants and microbiome analysis

    Student internship · Acıbadem University

    –

    Analysis of SARS-CoV-2 variants in saliva samples, and microbiome analysis of stool samples.

    My role:
    Student intern (wet lab and analysis)
    Methods:
    DNA and RNA isolation, cDNA library preparation, and RT-PCR.
    Outcome and status:
    Completed.
    Lab and supervisor:
    Prof. Uğur Sezerman, Acıbadem University

  4. Bacteriophages, quorum sensing, and biofilm formation

    Undergraduate research · Acıbadem University

    –

    Wet-lab research on bacteriophage culture, bacterial quorum sensing, and biofilm formation. The work also covered viral transcription factors, and I compared protein expression across strains after plasmid transformation.

    My role:
    Undergraduate student researcher (wet lab), including a summer internship, Jun 2022 – Jul 2022
    Methods:
    DNA isolation, plasmid purification, SDS-PAGE, agarose gel electrophoresis, and PCR.
    Outcome and status:
    Completed.
    Lab and supervisor:
    Assoc. Prof. Erkan Mozioğlu, Acıbadem University

  5. Protein-stability prediction

    Student internship · Acıbadem University

    –

    I improved and evaluated protein and amino-acid databases in R and Python, and produced a stability predictor algorithm to compare protein-stability datasets.

    My role:
    Student intern (computational)
    Methods:
    R, Python, and protein-stability prediction (machine-learning approach).
    Outcome and status:
    A protein-stability predictor algorithm; completed.
    Lab and supervisor:
    Prof. Emel Timuçin, Acıbadem University

  6. Antibiotic-resistance proteins in multidrug-resistant tuberculosis

    Student internship · Bezmialem Vakıf University

    –

    An in-silico student project on antibiotic-resistance protein mechanisms in multidrug-resistant tuberculosis (MDR-TB), which I presented. It introduced me to molecular docking and visualization tools.

    My role:
    Student intern; I worked on the student project and presented it.
    Methods:
    Introduction to molecular docking and visualization (AutoDock Tools, Easy Dock Vina, Discovery Studio, and PyMOL).
    Outcome and status:
    A student project and its presentation; completed.
    Lab and supervisor:
    Prof. Mohammad Asif Khan, Life Sciences and Biotechnology Institute, Bezmialem Vakıf University

Methods

Wet lab

  • Cloning and site-directed mutagenesis
  • Plasmid transformation
  • Plasmid purification
  • Colony screening with Sanger verification
  • Mammalian cell culture (HEK293, kidney epithelial cell lines)
  • Transfection
  • DNA isolation
  • RNA isolation
  • cDNA library preparation
  • PCR
  • RT-PCR
  • Agarose gel electrophoresis
  • Protein extraction and BCA quantification
  • SDS-PAGE
  • Western blotting
  • Bacteriophage culture
  • Quorum-sensing and biofilm-formation studies

Computational

  • RNA-seq (Salmon, DESeq2)
  • Pathway enrichment (clusterProfiler, KEGG)
  • Metabolomics (MetaboAnalystR)
  • Cross-omics integration
  • Protein-stability prediction
  • Introduction to molecular docking (AutoDock Tools, PyMOL)

Programming

  • Python
  • R/Bioconductor

Full CV