Principal Investigator
Batu graduated from Robert College, Istanbul in 1987, received a BA in Molecular Biology from Hamilton College, NY in 1991, a PhD in Biology from Brandeis University, MA in 1998. He was a post-doctoral fellow in Dr. Alfred Singer's laboratory at the Experimental Immunology Branch of the National Cancer Institute, National Institutes of Health from 1998 to 2004. He joined the faculty of Sabanci University in 2004 and since 2015 is a Professor of Molecular Biology, Genetics and Bioengineering. In 2020 he moved his lab to Bogazici University and serves as a Professor in the Molecular Biology and Genetics Department.
Post-Doctoral Fellows and Graduate Students
Busra Simsek PhD Student |
Busra is a PhD student in the lab. Her interests lie in identifying safe harbor sites, cis and trans elements in the genome of CHO cell lines that are used as factories to produce proteins in the industrial scale. She is targeting the genome of CHO cells with CRISPR/Cas9 to identify these elements and will develop novel biologicals using these modified transgenic cell lines. She is also involved in generating novel naive nanobody phage display libraries which she will use to screen for nanobodies that bind to either IL-1R or CD19.
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Ecem Ultanir MSc Student
Undergraduates
Undergraduate Students:,,,
Recent Lab Members
Sofia Piepoli PhD 2020
Holding a degree in general Biological sciences, Sofia obtained her Master's degree in Bioinformatics at the University of Bologna (Italy) in 2013. Then, enthusiastically she moved to Istanbul and she started her PhD in Sabanci University. The solid computational background gave her a good start for the study of protein structures through the analysis of molecular dynamic simulations. Her first main project has focused on the extraordinary complexity of TALE proteins. TALE transcription factors are of great interest for developing gene-editing technologies. She studied the specific interactions between the protein and the target DNA and she calculated the thermodynamic effect of mutations in different points of the protein. Her results will contribute to define accurate guidelines for the design of new TAL effectors.
Besides learning how to manipulate protein structures with computer tools, she wanted to get a structure on her own. So she started learning crystallography in E. Mancini's lab at the University of Sussex where she visits regularly. She solved the structure of the BTB domain of Patz1, a transcription factor largely important for the regulation of cancer related genes and for the known interaction with p53. She is also interested in other BTB domains that belong to different proteins of the same structural family (BTB-ZF) for characterization of in vitro and in vivo functional interactions. She received her PhD in 2020 and continues to work on the structure of Patz1 as a post-doctoral fellow. |
Melike Gezen PhD 2022
Melike came to Sabanci University with an MSc in Biology from Istanbul University. She works on the function of the Patz1 transcription factor. She has identified the target genes that Patz1 controls. She has analyzed the target genes in cells that have lost Patz-1 by targeting using CRISPR-Cas9. Melike will defended her PhD Thesis in 2022 and is now going to the US for a postdoc at the University of Pittsburg.
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Pegah Zahedimaram PhD 2022
Pegah came to the lab from Iran. She performed biochemistry experiments aiming to express and purify a protein called interleukin-1 receptor antagonist, which our bodies make as an anti-inflammatory cytokine to suppress IL-1 signaling. This molecule is marketed as Anakinra, a drug that works wonders in various inflammatory diseases. Pegah expresses this protein in E.coli in the periplasm of these bacteria and purifies the protein using affinity and size exclusion chromatography. As Anakinra is in several clinical trials against COVID-19, we hope to collaborate with drug companies Kocak Pharma and Turgut Ilaclari to produce this protein as a drug.
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Sarah Barakat PhD 2022
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Sarah came to the lab from Yemen. For her PhD thesis she makes nanbodies. Most recently she has screened a phage display library for nanobies that bind to the Patz1 transcription factor. She is performing biochemical experiments with these nanobodies to understand their affinity for Patz1 and also microscopic experiments to express the nanobodies in cells to visualize the binding in vivo. Sarah defended her PhD Thesis in 2022.
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Melike Berksoz PhD Student
Melike is conducting her thesis work in the lab and also with her advisor, Prof. Canan Atilgan at Sabanci University. Her interests are to perform molecular dynamics simulations to computationally model nanobody proteins and to predict surface modifications that can render these proteins cell permeable. She mutated anti-MDM4 nanobodies developed in the lab to develop them as cell permeable drugs. She is continuing her PhD work in the lab of Prof. Canan Atilgan at Sabanci University .
Hakan Taşkıran MSc 2018
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Hakan came to the lab from ODTU and spent two years to identify inhibitors of the p53 and MDM2 cancer proteins. He set up a fluorescent two hybrid screen to identify small molecules that bind to MDM2, releasing it from p53, activating p53 and causing apoptosis in cancer cells. The most famous example of this kind of small molecule is called Nutlin-3 because it was discovered in Nutley New Jersey. We call our inhibitors Istin's. Hakan is pursuing his PhD at the Max-Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany.
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Liyne Noğay MSc 2019
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Liyne came to the lab from ODTU and spent two years to identify the interactions between zinc finger BTB domain transcription factor BTB proteins. She set up a fluorescent two hybrid (F2H) assay to identify BTB domains that homodimerize and those that heterodimerize in baby hamster kidney cells. Liyne is pursuing her PhD at the Max-Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany.
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Sanem Sarıyar MSc 2019
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Sanem developed optimized nanobodies targeting the MDM4-p53 interaction. She expressed these nanobodies in E.coli and purified and tested their activity as potential anti-cancer drugs in vitro using affinity, size exclusion chromatography and surface plasmon resonance. She is continuing with her PhD in Sweden.
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Past Lab Members
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Sofia Piepoli, PhD. Didem Özkazanç Ünsal, PhD. Seden Bedir, MSc. Liyne Nogay, MSc. Freiburg, Germany. Sanem Sariyar, MSc. Hakan Taskiran, MSc. Freiburg, Germany. Ronay Çetin, MSc - Goethe University Frankfurt Sinem Usluer, MSc - Medical University of Graz Nazife Tolay, MSc - University of Würzburg Ece Canan Sayitoğlu, PhD - Stanford University, California Bahar Shamloo, PhD - Legacy Health Research Institute, Oregon Asma Al Murtadha, MSc - University of Edinburgh Ahsen Özcan, MSc- Max Planck Institute, Marburg Gülperi Yalçın, MSc - Korea University Emre Deniz, PhD- Assistant Professor, Acıbadem University Nazlı Keskin, PhD- Assistant Professor, Acıbadem University Emre Taskin (post-doc)- Assistant Professor, Karabuk University Ceren Tuncer (post-doc)- Duzen Laboratories Belkis Atasever - Assistant Professor, Üsküdar University Jitka Eryilmaz - ISKO Kenan Ates (post-doc)- Istanbul University DETAE Safak Isil Cevik, PhD - Beckton Dickenson Şeyda Temiz, MSc Tuğçe Altınuşak, MSc Izmir Biogenome Institute İzzet Akçay, MSc Manolya Un, MSc Sema Kurtuluş, MSc - University of Cincinnati İbrahim Aksoylar, MSc - University of Cincinnati Pınar Önal, MSc - Max Plank Institute Berlin Serkan Belkaya, MSc - UT Southwestern/Rockefeller U. Now Assistant Professor at Bilkent University!! Abdalsalam Kmail, MSc - Arab American University-Jenin Gamze Günal, MSc - Dresden University of Technology Meral İlçim Özlü, MSc - King's College London |
Undergraduates
Sabancı University graduates:
Diana Omarova SU'20 Minel Arinel SU'19 Duke University Ezgi Sengun SU'18 Radboud University Mehmet Oguz Gok SU'18 Baylor College of Medicine Fulya Türker SU'17 Johns Hopkins University Zeynep Ilgın Kolabaş SU'17 - Radboud Universtiy, The Netherlands Eda Erata SU'16 - Duke University Cansu Yıldırım SU'15 - EPFL, Lausanne Liana Behmorias SU'15 - Brandeis University Hazal Gizem Şentürk SU'15 - Duke University and Koc University Nirva Mumcuyan SU'14 - Baylor College of Medicine Vedat Burak Ozan SU'14 Yonca Betül Karadeniz SU'12 Saba Nur Basköylü SU'12 - Brown University Can Altunbulaklı SU'11 - Swiss Allergy Institute İrem Undeğer SU'11 Ceren Özek SU'10 - University of Pennsylvania Didem Ağaç SU'10 - UT Southwestern Duygu Deniz Baş SU'10 - EPFL, Lausanne Kıvılcım Özturk SU'10 Begüm Irmak On SU'09 - Boğaziçi University Duygu Saatçioğlu SU'09 - Uppsala University and UT Southwestern Erkin Kuru SU'09 - Indiana University Sine Yağanoğlu SU'08 - ETH, Zürich Başak Burcu Çiçek SU'08 - Charite Universitat Medizin, Berlin Emir Tınaztepe SU'08 - Boğaziçi University / NYU School of Medicine Pınar Ayata SU'07 - Rockefeller University |
Bogazici University graduates:
Mustafa Tuncay BU'22 Boston University |