RESEARCH ASSISTANT PINAR KOCABAŞ    
Name : PINAR
Surname : KOCABAŞ
E-Mail : pkocabas@ankara.edu.tr
Phone Number : 2033526
Title : RESEARCH ASSISTANT
Unit : FACULTY OF ENGINEERING
Department : Chemical Engineering Department
Personal Information

High School (1998): Izmir Bornova Anatolian High School

BSc (2002) : in Chemical Engineering, Middle East Technical University, Ankara

MSc (2004) : in Chemical Engineering, Middle East Technical University, Ankara

Master Thesis Title: Aromatic Amino Acid Synthesis Performance of Bacillus acidocaldarius

Supervised by Prof. Dr. Pınar ÇALIK, METU Chemical Engineering Department

PhD (27.2.2017) : in Chemical Engineering, Ankara University, Ankara

Supervised by Prof. Dr. H. Tunçer ÖZDAMAR, Ankara University Chemical Engineering Department


Professional Experience

2003-2004: Research Assistant in Chemical Engineering Department, Middle East Technical University, Ankara

2004-2005: Research Assistant in UC Davis Chemical Engineering and Materials Science Department 

2006-2010:  PhD scholarship by The Scientific and Technological Research Council of Turkey (TÜBİTAK: BİDEB -2211)

2010-Present: Research Assistant in Chemical Engineering Department, Ankara University, Ankara

 Publications

6. Kocabaş, P., Çalik, G., Çalik, P., Özdamar, T.H. 2017. Analyses of extracellular protein production in Bacillus subtilis- II: Responses of reaction network to oxygen transfer at transcriptional level. Biochemical Engineering Journal. Accepted in 11 July 2017.

5. Kocabaş, P., Çalik, P., Çalik, G., Özdamar, T.H. 2017. Analyses of extracellular protein production in Bacillus subtilis- I: Genome-scale metabolic model reconstruction based on updated gene-enzyme-reaction data. Biochemical Engineering Journal. Accepted in 11 July 2017.

4. Çalık, G., Kocabaş, P., Afşar, H., Çalık, P., Özdamar, T.H. 2016. Parametric continuous feed stream design to fine-tune fed-batch bioreactor performance:  Recombinant human growth hormone production in Bacillus subtilisJournal of Chemical Technology & Biotechnology. Accepted.

3. Özdamar, T.H., Şentürk, B.,Yilmaz, Ö.D., Kocabaş, P., Çalik, G., Çalik, P. 2010. Bioreaction network flux analysis for human protein producing Bacillus subtilis based on genome-scale model. Chemical Engineering Science 65, 574–580.

2. Kocabaş, P., Çalik, P. , Çalik, G., Özdamar, T.H. 2009. Microarray studies in Bacillus subtilis. Biotechnology Journal 4, 1012–1027. 

1. Kocabaş, P., Çalık, P., Özdamar, T.H. 2006. Fermentation characteristics of l-tryptophan production by thermoacidophilic Bacillus acidocaldarius in a defined medium. Enzyme & Microbial Technology 39, 1077–1088.

 International symposiums 

a)      Oral presentations

1) Kocabaş, P., Çalık, G., Özdamar, T.H. (2012). Metabolic Flux Analysis by Transcriptome-Data Supported Genome-Scale Model for Human Protein Producing Bacillus subtilis. 9th European Symposium on Biochemical Engineering Science (ESBES-9), İstanbul, Turkey. (Presented by: Pınar Kocabaş)

2) T.H. Özdamar, B. Şentürk, Ö.D. Yılmaz, P. Kocabaş, G. Çalık. Bioreaction network flux analysis for human protein producing Bacillus subtilis based on genome-scale model. 20th International Symposium on Chemical Reaction Engineering (ISCRE 20), Kyoto, 2008, Japan.                                    

b) Poster presentations

3) Özdamar, T.H., Kocabaş, P., Yılmaz, Ö.D. and Çalık, G. (2012). Flux analysis by microarray supported genome-scale model for human protein producing Bacillus subtilis. 22nd International Symposium on Chemical Reaction Engineering (ISCRE 22), Maastricht, Netherlands. (Presented by: Pınar Kocabaş)

4)  Kocabaş, P., Çalık, P., Çalık, G. and Özdamar, T.H. (2014). Assessment of genome-scale and biochemical reaction based network models for protein production in Bacillus subtilis10th European Symposium on Biochemical Engineering Sciences and 6th International Forum on Industrial Bioprocesses (ESBES-IFIBIOP 2014)-Lille-France. (Presented by: Pınar Kocabaş)

National symposiums: oral presentations

5) Kocabaş, P., Çalık, G., Özdamar, T.H. (2012). Protein Üretiminde B.subtilis Hücreiçi Tepkimelerinin Reaksiyon Mühendisliği Prensipleriyle Analizi. 10. Ulusal Kimya Mühendisliği Kongresi (UKMK-10), İstanbul. (Presented by: Pınar Kocabaş)

6) Kocabaş, P., Çalık, P., Çalık, G. and Özdamar, T.H. (2014). Terapatik Protein rhGH Üretiminde Oksijen Aktarımının Reaksiyon Hızlarına Etkisi. 11. Ulusal Kimya Mühendisliği Kongresi (UKMK-11), Eskişehir. (Presented by: Pınar Kocabaş)

7) Kocabaş, P., Çalık, P., Çalık, G., Özdamar, T.H. (2016). Oksijen aktarımının terapötik protein üretiminde hücreiçi tepkime hızlarına etkisinin reaksiyon mühendisliği prensipleriyle analizi. 12. Ulusal Kimya Mühendisliği Kongresi (UKMK-12), İzmir. (Presented by: Pınar Kocabaş)

Courses attended

Microalgae Process Design Course, 8-15 July 2016, The Graduate School VLAG, WAGENINGEN, The Netherlands.

 Research areas         

Biochemical engineering

Production of recombinant molecules and industrial enzymes

Genome scale reconstruction and analysis of intracellular reaction systems

Microarray analysis

Thermophiles, 

Systems biology, Metabolic engineering

Computational, theoretical biology, having basic knowledge for C programming 

Further Interests

Green and clean chemistry, energy, biotechnology

Metabolic control analysis

Bioprocess control, Control theory

Modelling, MATLAB, nature

Teaching assistantship experience:

Recitations and Laboratories: Computer Programming, Physical chemistry, Numerical Methods, Chemical Engineering Laboratory I-III 

Courses:  Mass and Energy Balances, Fluid Dynamics, Thermodynamics, Chemical Reaction Engineering, Chemical Engineering Mathematics, Process Design I-II, Process Control