Mehmet Burak Taşkaya
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Curriculum vitae

Mehmet Burak Taşkaya · PhD Candidate in Molecular Biology and Genetics · Bilkent University, Ankara

contact@mehmetburaktaskaya.com · mehmetburaktaskaya.com/cv/

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Education

  1. PhD, Molecular Biology and Genetics

    Bilkent University, Ankara

    – present

    Advisor: Asst. Prof. Onur Çizmecioğlu. Full scholarship. Qualifying examination passed (written and oral).

  2. B.Sc., Molecular Biology and Genetics

    Acıbadem University

    –

    Full scholarship. Graduation project, supervised by Assoc. Prof. Erkan Mozioğlu: Decoding Sequence Patterns and Conserved Motifs in Housekeeping Gene Upstream Regions: Unveiling Deeper Implications in Escherichia coli.

Research experience

  1. PhD candidate

    Department of Molecular Biology and Genetics, Bilkent University

    – present

    Functional analysis of two genes associated with pediatric kidney developmental disorders, in kidney epithelial cell lines.

  2. Project intern

    Mayack Lab, Sabancı University

    –

    RNA expression dynamics and post-transcriptional regulation in honey bees. Assisted with experimental design.

    Supervisor: Asst. Prof. Christopher Mayack.

  3. Student intern

    Acıbadem University

    –

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

    Methods: DNA and RNA isolation, cDNA library preparation, and RT-PCR.

    Supervisor: Prof. Uğur Sezerman.

  4. Undergraduate student researcher

    Acıbadem University

    –

    Bacteriophage culture, bacterial quorum sensing, and biofilm formation in the wet lab. Compared protein expression across strains after plasmid transformation; the work also covered viral transcription factors. Included a summer internship, Jun 2022 – Jul 2022.

    Methods: DNA isolation, plasmid purification, SDS-PAGE, agarose gel electrophoresis, and PCR.

    Supervisor: Assoc. Prof. Erkan Mozioğlu.

  5. Student intern

    Acıbadem University

    –

    Improved and evaluated protein and amino-acid databases in R and Python; produced a stability predictor algorithm to compare protein-stability datasets.

    Supervisor: Prof. Emel Timuçin.

  6. Student intern

    Life Sciences and Biotechnology Institute, Bezmialem Vakıf University

    –

    Studied and presented an in-silico student project on antibiotic-resistance protein mechanisms in multidrug-resistant tuberculosis (MDR-TB).

    Methods: Introduction to molecular docking and visualization (AutoDock Tools, Easy Dock Vina, Discovery Studio, and PyMOL).

    Supervisor: Prof. Mohammad Asif Khan.

Teaching and mentoring

  1. Teaching assistant, MBG 338 Microbiology Laboratory

    Bilkent University

    Spring 2025, Spring 2026

    About 50–60 students per term.

  2. Supervising interns at the bench

    Bilkent University

    –present

Honors and scholarships

Skills

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)
  • IBM SPSS Statistics

Programming

  • Python
  • R/Bioconductor
  • SQL

Professional development

Languages

Extracurricular activities