Members

Team Leader

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.

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Lab Members

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.

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.

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.

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.

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.

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.

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I earned my B.Sc. degree from Abant İzzet Baysal University in Bolu and Jagiellonian University (Uniwersytet Jagielloński) in Kraków, Poland, majoring in Biology. Subsequently, I pursued my M. Sc. degree at Istanbul University, specializing in Genetics. For my master’s thesis, I delved into the realm of data science, immersing myself in topics such as machine learning applications, data structuring, dataset creation, pre-processing techniques, various training models, and algorithms.

Within the scope of my thesis, I endeavored to develop a multiple linear regression model aimed at computing the heteroplasmy ratio of muscular tissue in patients exhibiting clinical manifestations attributed to the m.3243A>G mutation, known to cause mitochondrial diseases. Concurrently with my academic pursuits, I was actively engaged in practical work encompassing various laboratory responsibilities at Istanbul Medical Faculty’s Molecular Genetics Laboratory, within the Department of Medical Genetics.

Presently, I am actively engaged in pursuing my Ph.D. in the Bioinformatics and Systems Biology program at Gebze Technical University. My research primarily revolves around the application of machine learning methodologies, with a particular emphasis on deep learning techniques.

I have graduated from Istanbul Bilgi University with a Bachelor of Science in Genetics and Bioengineering, did my internship in Kocaeli University’s Antibody Production Unit. I am currently working as a Research Asistant at Gebze Technical University and working on my Master’s Degree in the department of Bioinformatics and Systems Biology.

I graduated from the Electrical and Electronics Engineering department of Eskişehir Osmangazi University in 2015. After graduation, I worked in the automotive and finance sectors. Currently, I am working as an artificial intelligence engineer at Livewell, a subsidiary of Türkiye İş Bankası, focusing on wearable health technologies. I am involved in the development of software that detects diseases from signals using various software tools, primarily for heart diseases and ECG signals, through the processing, analysis, and application of machine learning methods to various biosignals. Additionally, I am a master’s student in the Bioinformatics and Systems Biology department at Gebze Technical University. I am working on a thesis that aims to explain the relationship between newly discovered cell death mechanisms and cancer.

I received my BSc degree in Biology from the Department of Biology at Kocaeli University. Currently, I am pursuing my MSc degree in Bioinformatics and Systems Biology Graduate Program in Bioengineering Department on Multi-Scale Mathematical Modelling of Tumor and its Microenvironment. My research specifically focuses on the implementation of genome-scale metabolic models into agent-based cellular systems in the context of cancer TME.

Mehmet İzmirli
MSc Student

I received my Bachelor’s degree from the department of Molecular Biology and Genetics at İnönü University in 2022. I completed internships at Baumeister Lab (January-April 2023), Albert-Ludwigs-Universität Freiburg; and MitoSTaRs Lab (June-September 2023), University of Helsinki. I am a Master’s student at Bioinformatics and Systems Biology Program, Gebze Technical University since September 2023.

I graduated from Trakya University with a bachelor’s degree in Genetics and Bioengineering. I did my internship in Ege University’s Bioinformatics and Molecular Genetics Laboratory on the Analysis of single-cell RNA Sequencing Data. Currently, I am doing master’s degree at Gebze Technical University in the department of Bioinformatics and Systems Biology.

I have completed my undergraduate studies in the Bioengineering Department at Yıldız Technical University. Currently, I am pursuing a Master’s degree in the Bioinformatics and Systems Biology Program. My research focuses on immunoinformatics and single-cell RNA-seq analysis.

Lab Alumni

2018

2019

2021

Tuğberk Talak
MSc Student

2024

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.