Computational Systems Biology Group

Batuhan Çakır

Ph.D Student

Gebze Technical University
Department of Bioengineering
Computational Systems Biology Group
Gebze-Kocaeli
TURKEY
Mailto:	bcakir [at] gtu.edu.tr
Room:	Bioengineering Building, 205
Phone:	+90 262 605 32 55

Introduction

I completed my bachelor’s degree in Bioengineering at Yıldız Technical University. In my thesis, I prepared a literature review on effects of radiation on a human body. Later, I continued to study computationally and started my master’s degree in Bioinformatics and Systems Biology at Gebze Technical University. During my masters, I had an Erasmus internship at Wellcome Sanger Institute in Cellular Genetics Informatics to work on benchmarking of single-cell visualization tools. Currently I am working on single-cell analyses of differentiation and reprogramming processes of stem cells.

I am currently a MSc student in Bioinformatics and Systems Biology Program at Gebze Technical University, and a research assistant in Department of Bioengineering at Gebze Technical University.

MSc Thesis

The aim of my thesis project is the analysis of single-cell omics data to investigate and model the transformation of pluripotent stem cells into neurons, and is expected to generate new theories on the progress of these transformation processes. Single-cell data from iPSCs will be retrieved from the literature. Trajectory inference will be made using Monocle 3. The output from Monocle will provide the details of the transformation process including which transcriptional path the cells follow.

Publications

• Comparison of visualization tools for single-cell RNAseq data
  • by Batuhan Cakir, Martin Prete, Ni Huang, Stijn van Dongen, Pinar Pir, Vladimir Yu Kiselev
  • NAR Genomics and Bioinformatics, Volume 2, Issue 3, September 2020, https://doi.org/10.1093/nargab/lqaa052
• Nöronal hücre farklılaşma süreçlerinin tek hücre transkriptom analizi
  • by Batuhan Çakır, Pınar Pir
  • VI. Türk Tıp Dünyası Kurultayı, Istanbul / TURKEY (October 29-31, 2019) (poster presentation)
• Single-cell transcriptome analysis of neuronal cell differentiation processes
  • by Batuhan Çakır, Pınar Pir
  • The International Symposium on Health Informatics and Bioinformatics 2019, Izmir / TURKEY (October 17-18, 2019) (poster presentation)
• Benchmarking of interactive data visualization tools for single-cell RNAseq data
  • by Batuhan Çakır, Pınar Pir, Vladimir Yu Kiselev
  • GTÜ Lisansüstü Araştırmalar Sempozyumu 2019, Kocaeli / TURKEY (June 17-18, 2019) (poster presentation)

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Computational Systems Biology Group