Bio-Engineering

Research Interests

Fabrication of lab-on-a-chip, microfluidics, tissue engineering, vascularization, 3D in vitro controlled microenvironment, biomaterials, adhesion, invasion and extravasation in breast cancer, hepatocellular carcinoma, senescence, cancer biology, imaging techiques & analysis, confocal microscopy, lithography, electron beam lithography

Associated Faculty

Gizem BATI AYAZ, Ph.D
Associated Faculty
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  • Work Experience
  • Ph.D., Graduate Program in Bioengineering
    (GPA: 3.43/4.00), Izmir Institute of Technology, Izmir, Turkey, February 2015 – January 2021
    Dissertation Title: “Engineering target tissue in lab-on-a-chip devices for predicting homing choices of metastatic cancer”
  • M.Sc., Graduate Program in Biotechnology
    (GPA: 3.19/4.00), Izmir Institute of Technology, Izmir, Turkey, December 2014
    Thesis Title: “Invadopodia Formation on Nanometer Scale Protein Patterns’’
  • B.Sc., Department of Biology, Biology Majored in Molecular Biology and Genetics in Faculty of Science
    (GPA 3.03/4.00), Ege University, Izmir, Turkey, September 2012
  • Pedagogical Formation
    (GPA 2.73/4.00), Faculty of Education, Ege University, Izmir, Turkey, June 2012
  • Bachelor Erasmus Programme Exchange Student
    (GPA 4.00/4.00) , Department of Molecular Biology and Genetics, Sofia University St. Kliment Ohridski, Sofia, Bulgaria, September 2010-February 2011
  • Assistant Professor, September  2015 - January 2018
    Istanbul Aydin University (IAU), Engineering Faculty, Food Engineering Dept. 
  • Research Assistant, December 2006 – January 2015
    Istanbul Technical University, Food Engineering Department
  • Visiting Scholar, October2011 – August 2012
    Michigan State University Dept. of Food Science & Human Nutrition
  • Project Specialist, May 2008
    GESPRO Consultancy
  • Summer Practice, August 2005 – September  2005
    Technologie-Transfer-Zentrum Bremerhaven - GERMANY
  • Summer Practice, May 2004 – June 2004
    UNO Unmaş Packaged Br
  • Work Experience
  • Izmir Biomedicine and Genome Center (March 2021-March 2023)
    Postdoc Researcher, in the project titled “Role of Factors Secreted by Stellate Cells in Formation of c-Met Mediated Hybrid EMT Phenotype” granted by The Scientific and Technological Research Council of Turkey (TUBITAK-BIDEB-2218, 118C473)
  • Izmir Institute of Technology (July 2012-August 2012)
    Internship, studied in vitro interactions of comb-type PEG polymer with cancer cells Supervisor: Prof. Volga Bulmus, Chemical Engineering Department, Izmir Institute of Technology, Turkey
  • Hacettepe University Faculty of Medicine (June 2011-July 2011)
    Internship, studied the diagnosis of phenylketonuria by using PCR/RFLP techniques Supervisor: Assoc. Prof. Didem Dayangac Erden, Medical Biology Department, Hacettepe University Faculty of Medicine, Ankara
  • Ege University Faculty of Medicine, Department of Pathology (September 2009)
    Internship, worked at Immnunohistochemistry Laboratory
  • Research Experience
  • Principle researcher in the project titled “Role of Factors Secreted by Stellate Cells in Formation of c-Met Mediated Hybrid EMT Phenotype” granted by The Scientific and Technological Research Council of Turkey (TUBITAK-BIDEB-2218, 118C473), (March 2021-March 2023).
  • Graduate Researcher in the project titled “A New lab-on-a-chip Device in Early Diagnosis of Metastasis” granted by The Scientific and Technological Research Council of Turkey (TUBITAK-1003, 115E057), (2016-2019).
  • Graduate Researcher in the project titled “Lab-on-a-chip for tissue engineering” 2017IYTE95 Scientific Research Project granted by İYTE. (2018).
  • Graduate Researcher in the project titled “Lab on a chip that identifies consecutive intravasation and extravasation of breast cancer cells” in 2014IYTE33 Scientific Research Project granted by IYTE. (2015).
  • Graduate Researcher in the project titled “Drug Delivery via Targeted Microbubbles as Ultrasound Contrast Agent and Their Use in Cancer Treatment via Controlled Local Drug Release”, granted by The Scientific and Technological Research Council of Turkey TUBITAK-1003 Primary Subjects R&D Funding Program, 213M668, (2015-2016).
  • Graduate Researcher in the project titled “Invadopodia Formation on Nanometer Scale Protein Patterns” granted by The Scientific and Technological Research Council of Turkey (COST Bioinspired Nanotechnologies – TUBITAK-1001, 111T547), (April 2013-September 2014).
  • Grants
  • BIDEB (TUBITAK Directorate of Science Fellowships and Grant Programmes)-2218, (March 2021- March 2023)
  • BIDEB (TUBITAK Directorate of Science Fellowships and Grant Programmes)-2211C, (December 2019- December 2020)
  • 100/2000 YOK Scholarship in the field of “Tissue Engineering and Biomaterials” (March 2017- December 2020)
  • TUBITAK Funded Research Project (A New lab-on-a-chip Device in Early Diagnosis of Metastasis) Scholarship (April 2016-April 2019)
  • EACR Meeting Bursary, Amsterdam, 2018
  • TUBITAK Funded Research Project (Drug Delivery via Targeted Microbubbles as Ultrasound Contrast Agent and Their Use in Cancer Treatment via Controlled Local Drug Release) Scholarship (April2015- April 2016)
  • TUBITAK Funded Research Project (Invadopodia Formation on Nanometer Scale Protein Patterns) Schoolarship (September 2013- September 2014)
  • Erasmus-LLP (Lifelong Learning Programme) (September 2010- February 2011)
  • Prime Minister’s Schoolarship, Turkey (September 2008- June 2012)

Publications

Peer-reviewed Journal Articles
  1. Gulsun Bagci, Dehan Comez, Hande Topel, Ezgi Bagirsakci, Yeliz Yilmaz, Aysim Gunes, Gizem Bati-Ayaz, Gulhas Solmaz, Devrim Pesen-Okvur, Nese Atabey. c-Met Activation Promotes Liver- Specific Extravasation of Hepatocellular Carcinoma Cells
    (Manuscript in preperation).
  2. Bati-Ayaz, G., M., Pesen-Okvur, D., & Yalcin-Ozuysal, O. Engineering vascularized target tissues in lab-on-a-chip devices for predicting organ-specific metastasis. (Manuscript in preperation).
  3. Elvan Dogan, Asli Kisim, Gizem Bati-Ayaz, Gregory J. Kubicek, Devrim Pesen-Okvur, Amir K. Miri (2021). Cancer Stem Cells in Tumor Modeling: Challenges and Future Directions. Advanced Nanobiomed Research.
  4.  Firatligil-Yildirir, B., Bati-Ayaz, G., Tahmaz, I., Bilgen, M., Pesen-Okvur, D., & Yalcin- Ozuysal, O. (2021). On‐chip determination of tissue‐specific metastatic potential of breast cancer cells. Biotechnology and Bioengineering. (Equal contribution authorship).
  5. Onal, S., Turker-Burhan, M., Bati-Ayaz, G., Yanik, H., & Pesen-Okvur, D. (2021). Breast Cancer Cells and Macrophages in a Paracrine-Juxtacrine Loop. Biomaterials.
  6. G. Bati-Ayaz, Ali Can, D. Pesen-Okvur. Cellular distribution of invadopodia is regulated by nanometer scale surface protein patterns. European Journal of Cell Biology, Volume 96, Issue 7, October 2017, Pages 673-684.
  7. G. Bati, D. Pesen-Okvur. Invadopodia: Proteolytic feeet of cancer cells. Turk J Biol (2014) 38.
Conference Proceedings
  1.  Gizem Bati-Ayaz, Muge Bilgen, Ismail Tahmaz, Devrim Pesen Okvur, “Optimization of lab-on-a-chip device and method for quantification of extravasation” , EACR (European Association of Cancer Research), Amsterdam, Holland, 30 June-3 July 2018.
  2.  Atabey H Topel, Y Yilmaz, A Gunes, E Bagirsakci, BA Gizem, D Comez, G Bagci, E Kahraman, D Pesen Okvur, “Predicting homing ability of hepatocellular carcinoma cells by using a lab-on-a-chip system” European Association of Cancer Research), Amsterdam, Holland, 30 June-3 July 2018.
  3. B Firatligil, G Bati-Ayaz, D Pesen-Okvur, O Yalcin-Ozuysal, “Tissue specific extravasation and invasion of MDA-MB-231 cells in a lab-on-a-chip system” Amsterdam, Holland, 30 June-3 July 2018.
  4.  S Onal, M Turker, G Bati Ayaz, D Pesen Okvur, “Breast cancer cells and macrophages in a paracrine-juxtacrine loop” Amsterdam, Holland, 30 June-3 July 2018.
  5.  Gizem Bati-Ayaz, Muge Bilgen, Ismail Tahmaz, Devrim Pesen Okvur, “Development of Blood Vessel Mimicking 3D Lab-on-a-chip Device” 19th National Biotechnology Congress with International Attendance, Eskişehir, Turkey 1-3 December 2017.
  6.  G. Bati and D. Pesen Okvur, Invadopodia formation on nanometer scale protein patterns, American Society for Cell Biology Annual Meeting, New Orleans, LA, USA. 2013 (Poster).
  7. Gizem Bati, Devrim Pesen Okvur, “Invadopodia Formation on Nanometer Scale Protein Patterns” XIII. National Medical Biology and Genetics, Pine Bay Hotel, Kusadası-Aydın (27-30 October 2013).
  8. Gizem Bati, Devrim Pesen Okvur, “Invadopodia Formation on Nanometer Scale Protein Patterns” XXV. International Congress of Biochemistry, Kaya Otel and Convention Center, Izmir, Turkey (3-6 September 2013).
PRESENTATIONS
  1. Gizem Bati-Ayaz, Muge Bilgen, Ismail Tahmaz, Devrim Pesen Okvur, “Optimization of lab-on-a-chip device and method for quantification of extravasation” , EACR (European Association of Cancer Research), Amsterdam, Holland, 30 June-3 July 2018 (Poster)
  2. N Atabey H Topel, Y Yilmaz, A Gunes, E Bagirsakci, BA Gizem, D Comez, G Bagci, E Kahraman, D Pesen Okvur, “Predicting homing ability of hepatocellular carcinoma cells by using a lab-on-a-chip system” European Association of Cancer Research), Amsterdam, Holland, 30 June-3 July 2018 (Poster).
  3. B Firatligil, G Bati-Ayaz, D Pesen-Okvur, O Yalcin-Ozuysal, “Tissue specific extravasation and invasion of MDA-MB-231 cells in a lab-on-a-chip system” Amsterdam, Holland, 30 June-3 July 2018 (Poster).
  4.  S Onal, M Turker, G Bati Ayaz, D Pesen Okvur, “Breast cancer cells and macrophages in a paracrine-juxtacrine loop” Amsterdam, Holland, 30 June-3 July 2018 (Poster).
  5. Gizem Bati-Ayaz, Muge Bilgen, Ismail Tahmaz, Devrim Pesen Okvur, “Development of Blood Vessel Mimicking 3D Lab-on-a-chip Device” 19th National Biotechnology Congress with International Attendance, Eskişehir, Turkey 1-3 December 2017 (Poster).
  6. G. Bati and D. Pesen Okvur, Invadopodia formation on nanometer scale protein patterns, American Society for Cell Biology Annual Meeting, New Orleans, LA, USA. 2013 (Poster).
  7. Gizem Bati, Devrim Pesen Okvur, “Invadopodia Formation on Nanometer Scale Protein Patterns” XIII. National Medical Biology and Genetics, Pine Bay Hotel, Kusadası-Aydın (27-30 October 2013) (Poster).
  8. Gizem Bati, Devrim Pesen Okvur, “Invadopodia Formation on Nanometer Scale Protein Patterns” XXV. International Congress of Biochemistry, Kaya Otel and Convention Center, Izmir, Turkey (3-6 September 2013) (Poster).

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