Pınar Pir, Group Leader
Assistant Professor
| Gebze Technical University |
Detailed CV |
|
| Department of Bioengineering | ||
| Computational Systems Biology Group | ||
| Gebze-Kocaeli | ||
| TURKEY | ||
| Mail: | pinarpir [at] gtu.edu.tr | |
| Room: | Bioengineering Building, 145 | |
| Phone: | +90 262 605 33 23 | |
 |
||
Introduction
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.
Research Areas
Research in Pirism Lab is mostly based on use of NGS data in systems modelling. We are particularly interested in analysis and modelling of dynamic processes such as stem cell differentiation and tumour growth. We use single cell NGS data to be able to represent the heterogeneity in the cell populations accurately in our models, which involves use of machine learning methods as well as rigorous statistical analysis of the data. We aim to extend our models to 3-dimensions to accurately describe the cells in the context of their extracellular environment, which in turn regulates the intracellular dynamics via signalling pathways. Better understanding the dynamics of cellular processes and interactions may lead to discovery of targets to regulate these processes by human intervention.
Research Projects
- TÜBİTAK ARDEB 1001 - 120S987 - PI - Reconstruction of 3D mathematical models of tumors and their microenvironments - Budget is under approval process as of December 2020
- TÜSEB 2019-TA-01 - 3936 - PI - Identification of rare cell types in tumour samples and investigation of their prognostic potential - 15/05/2020 - 15/05/2022
- TÜBİTAK ARDEB 1001 - 116S388 - PI - Mathematical Modelling and Improvement of Reprogramming and Differentiation Processes Induced Pluripotent Stem Cells - 01/05/2017 - 01/05/2020
- TÜBİTAK ARDEB 1003 - 216S489 - Researcher - Creation of dormancy models of non-small cell lung carcinoma and investigation of its etiopathogenesis using omics methods - 15/12/2017-15/12/2020 - Consortium lead by Prof. Devrim Gözüaçık
- TÜBİTAK BİDEB 2232 - 116C062 - PI - New generation biofuel production via modelling of metabolic pathways and carbon assimilation in Eubacterium limosum strains - 01/05/2016 - 01/05/2018
Teaching
- Biostatistics
- Programming in Python
- Systems Biology of Stem Cells and Cell Fate
- Advanced Modelling in Systems Biology
Selected Publications
For a full list of publications, see my Google Scholar page.
-
Integration of transcriptomic profile of SARS-CoV-2 infected normal human bronchial epithelial cells
with metabolic and protein-protein interaction networks
- Turkish Journal of Biology, 44, (2020), 168-177