Members

Team Leader

Pınar Pir
Team Leader

Twitter: @pnarpir

I have received my B.Sc, M.Sc and Ph.D degrees from Department of Chemical Engineering at Bogazici University, Istanbul. My PhD thesis research mainly involved integrative analysis of omics data (metabolomics and transcriptomics) from yeast growing in carbon or nitrogen limited chemostats, and it was partly a collaborative project with Prof. Stephen G Oliver.

I worked as a postdoctoral research associate in the UK between 2006-2015. I worked on yeast systems biology (Oliver Lab), metabolic modelling of biofuel production by microbes (Novacta Biosystems ) and kinetic modelling of signalling pathways in stem cells (Le Novere Lab).

As of November 2015, I am leading the Pirism Lab in CSB group at the Department of Bioengineering in Gebze Technical University, TURKEY.


Lab Members

Enes Ak
MSc Student

Email: eak2018@gtu.edu.tr
Linkedin: linkedin.com/in/enes-ak/

I graduated my bachelor’s degree in Molecular Biology and Genetics department of Yıldız Technical University in 2018. Then I started my Master’s degree in Bioinformatics and Systems Biology at Gebze Technical University. Now, I am working on the identification of TF-mediated dynamics of signaling pathways in stem cell reprogramming using transcriptomics data, reversibility of stem cell differentiation in TUBITAK ARDEB 1001 project.

Barış Altunkara
MSc Student

Email:

Gülben Avşar
PhD Candidate / Research Assistant

Email: g.avsar@gtu.edu.tr
Linkedin: linkedin.com/in/gülben-avşar/

I graduated from Department of Bioengineering with a BSc degree in Ege University and MSc degree in Marmara University. Now, I am in the Bioinformatics and Systems Biology PhD program in Gebze Technical University. Besides the epitranscriptomics, NGS data analysis and mathematical modeling of biological systems,  I currently focus more on machine learning applications in the field of bioinformatics.

Batuhan Çakır
PhD Student / Research Assistant

Email: bcakir@gtu.edu.tr
Twitter: @cakirb_
Github: github.com/cakirb
Linkedin: linkedin.com/in/batuhancakir/

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 finished my master’s degree in Bioinformatics and Systems Biology at Gebze Technical University. In my thesis, I worked on single-cell analyses of differentiation and reprogramming processes of stem cells. 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 studying on single-cell analyses and structural bioinformatics.

Emre Taylan Duman
PhD Candidate

Email: etduman2018@gtu.edu.tr
Twitter: @emretaylanduman
Github: github.com/emretaylanduman
Linkedin: linkedin.com/in/emre-taylan-duman/

I completed my BSc and MSc in Ege University Department of Bioengineering. My research area focused on patented bioreactor design, rapid prototyping and computational fluid dynamics (CFD) simulations. I made internship in Karunya University Bioinformatics department on genome scale metabolic network simulations and also structural bioiformatics for designing new polymers. Currently I’m a PhD student in GTU Systems Biology and Bioinformatics and a scholar in GTU Computer Science Department on Machine Learning and AI field. Currently I’m working on compression on omics data and applying deep learning applications into bioinformatics data.

Habib Burak Can Erdönmez
MSc Student

Email:

Hamza Umut Karakurt
PhD Student

Email: hkarakurt@gtu.edu.tr
Linkedin: linkedin.com/in/hamza-umut-karakurt/

I received my BSc degree from Biochemistry Department of Ege University. I received MSc degrees from Molecular Biology and Genetics program of Gebze Technical University and Bioinformatics and Systems Biology program of Gebze Technical University. I had internships in Babraham Institute, UK and Institut Curie, France. I am doing my PhD in Bioinformatics and Systems Biology in Bioengineering Department. I am interested in transcriptome data analyses, network modelling, genome-scale metabolic modelling and artifical intelligence applications in bioinformatics. I also have self-interest in cognitive and psychiatric bioinformatics.

Merve Keskin
MSc Student

Email:

Emel Kökrek
PhD Candidate

Email: ekokrek@gtu.edu.tr
Twitter: @ekokrek
Linkedin: linkedin.com/in/emel-kökrek/

I received my BSc degree from Chemical Engineering Department of Boğaziçi University and my MSc degree in Erasmus Mundus BioHealth Computing Master Program. At the moment, I am doing my PhD in Bioinformatics and Systems Biology PhD Program in Bioengineering Department. I am interested in unraveling the transcriptional regulatory mechanism through network analysis of protein complexes, and integration of genome accessibility and architecture data to the (qualitative and quantitative) complex prediction pipelines.

Merve Say
MSc Student

Email:

Gülçin Selçuk
MSc Student

Email:

Simge Şengül
MSc Student

Email: ssengul2018@gtu.edu.tr
Linkedin: linkedin.com/in/simge-sengul/

I achieved my bachelor’s degree from the Department of Molecular Biology and Genetics, Uskudar University in 2018. My undergraduate thesis was about sphingolipid metabolism and its effect on cancer progression. I have continued master’s degree program in Department of Molecular Biology and Genetics, Institute of Natural and Applied Sciences, Gebze Technical University, since 2018 fall. During my masters, I had an internship opportunity at Yesil Science Company which is working on artificial intelligence applications in health sciences. Currently, I am working on quantitative modeling of molecular and gene networks in stem cells.

Tuğberk Talak
MSc Student

Email:

Cemal Yıldız
PhD Student

Email: cyildiz@gtu.edu.tr
Twitter: @cemalyildizzz
Linkedin: linkedin.com/in/cemal-yıldız/

I graduated from Inonu University with a bachelor’s degree in Molecular Biology and Genetics. Currently, I am doing MSc in Bioinformatics and Systems Biology at Gebze Technical University. I am working on identification cell-cell communication driven by receptor-ligand interactions in cancer, especially non-small cell lung cancer.


Lab Alumni

2018

Furkan Kurtoğlu
MSc Student

2019

Canan Has
Postdoctoral Fellow

Şükrü Öztürk
PhD Candidate / Research Assistant

2020