CV

Education

• University of Canterbury, Christchurch, New Zealand — PhD in Bioinformatics/Biotechnology Nov 2012 - Aug 2016
• METU, Ankara — MSc in Bioinformatics Sep 2009 - Aug 2012
• METU, Ankara — BS in Physics Sep 2001 - Aug 2005

Work experience

Department of Pathology, University of Oslo, Oslo, Norway — Researcher in Bioinformatics
Mar 2022 - Present

• Analysis of gut macrophages (and other immune cells, mucosal immunology) using bulk RNA sequencing, single-cell RNA sequencing, and spatial transcriptomics (specifically Visium platform) methods.
• Developing single-cell RNA sequencing workflows (cellsnake tool) and reproducible pipelines.
• Combining metagenomics, microbiome-related reads, and single-cell RNA sequencing and developing workflows for analysis.
• Developing ML models for spatial deconvolution analysis.
• Developing open-source software (to share in Bioconda and Docker).

Cancer Registry of Norway, Oslo, Norway — Senior Bioinformatics Scientist
Oct 2016 - Oct 2020, Research Advisor Oct 2020 - Sep 2022

• Analysis of serum RNA profiles using bulk RNA sequencing in the context of RNA biology, (My first paper on RNA profiling was among the most cited papers in the journal).
• Investigating prediagnostic serum samples for cancer footprints using bioinformatics and functional annotation.
• Prediction of early carcinogenesis using machine learning and survival models (including lung cancer and other cancer types).
• Developing bioinformatics pipelines using Snakemake (e.g. small RNA pipeline ), singularity, Python and R programming.
• Developing genome analysis pipelines for Variant calling in HPV genomes (e.g. TaME-seq workflow).
• Building ML models for microRNA prediction and developing a genome annotation tool (MirMachine).
• Prediction of RNA-RNA interactions (in the context of cancer biology).

University of Canterbury, Christchurch, New Zealand —PhD Scientist in Bioinformatics
Nov 2012 - Aug 2016

• Prokaryotic genome annotation for protein-coding genes and non-coding RNAs.
• DNA (Illumina, Pacbio, Nanopore) and RNA sequencing (Illumina).
• Benchmarking of RNA-RNA interaction algorithms using statistical models.
• Building parallel programming interfaces using Python programming.
• Modeling protein production in prokaryotes using regression models.
• Proposal of avoidance hypothesis which explains prokaryotic protein production. (My paper was on the cover of eLife web issue and I also got the best publication by a PhD student award).

Department of Chemistry, METU, Ankara, TR — Research Assistant in Computational Science
Aug 2006 - Oct 2012

• I finished my masters during this period and I was a computer scientist in the department of chemistry.
• I did take courses on biostatistics, molecular biology, and advanced computing.
• I combined my computer scientist background with my desire to be a scientist so I selected bioinformatics.