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
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 Student
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 defend her PhD Thesis in 2021.
Sarah Barakat PhD Student
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 will defend her PhD Thesis in 2021.
Pegah Zahedimaram PhD Student
Pegah came to the lab from Iran. She is performing 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.
Melike works at ILKO Pharmaceuticals and is conducting her thesis work in the lab at the same time. 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 is mutating anti-MDM4 nanobodies developed in the lab with these techniques to develop them as cell permeable drugs. She uses the fluorescent two hybrid technique to assess the activity of these nanobodies.
Melike Berksoz PhD Student
Busra Simsek PhD Student
Busra also works at ILKO Pharmaceuticals and is concurrently conducting her PhD thesis 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.
Recent Lab Members
Hakan Taşkıran MSc 2018
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.
Liyne Noğay MSc 2019
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.
Sanem Sarıyar MSc 2019
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.
Past Lab Members
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
Diana Omarova '20
Minel Arinel '19 Duke University
Ezgi Sengun '18 Radboud University
Mehmet Oguz Gok '18 Baylor College of Medicine
Fulya Türker '17 Johns Hopkins University
Zeynep Ilgın Kolabaş '17 - Radboud Universtiy, The Netherlands
Eda Erata '16 - Duke University
Cansu Yıldırım '15 - EPFL, Lausanne
Liana Behmorias '15 - Brandeis University
Hazal Gizem Şentürk '15 - Duke University and Koc University
Nirva Mumcuyan '14 - Baylor College of Medicine
Vedat Burak Ozan '14
Yonca Betül Karadeniz '12
Saba Nur Basköylü '12 - Brown University
Can Altunbulaklı '11 - Swiss Allergy Institute
İrem Undeğer '11
Ceren Özek '10 - University of Pennsylvania
Didem Ağaç '10 - UT Southwestern
Duygu Deniz Baş '10 - EPFL, Lausanne
Kıvılcım Özturk '10
Begüm Irmak On '09 - Boğaziçi University
Duygu Saatçioğlu '09 - Uppsala University and UT Southwestern
Erkin Kuru '09 - Indiana University
Sine Yağanoğlu '08 - ETH, Zürich
Başak Burcu Çiçek '08 - Charite Universitat Medizin, Berlin
Emir Tınaztepe '08 - Boğaziçi University / NYU School of Medicine
Pınar Ayata '07 - Rockefeller University