Principal Investigators
Attila Gürsoy
Research Area
For more information see Dr. Gursoy’s home page.
Özlem Keskin
Research
For more information see Dr. Keskin’s homepage.
PhD Students
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Jackson WeakoPhD Candidate in Computational Science and Engineering
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Meryem ErenPhD Student in Molecular Biology and Genetics
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Erxiati PaerhatiPhD Student in Computational Science
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Melisa Ece ZeylanPhD Student in Computational Science and Engineering
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Fatma CankaraPhD Student in Computational Science and Engineering
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Esra BaşaranPhD Student in Computational Science and Engineering

Jackson Weako
Research
Short Bio
Ph.D. Candidate Koç University-
M.Sc. Kadir Has University-Computational Biology and Bioinformatics
B.Sc. Cuttington University-Chemistry
For more information see Jackson’s homepage
Meryem Eren
Research
Short Bio
Erxiati Paerhati
Research
Investigation of the association between type2 diabetes and human gut microbiota
Short Bio
Ph.D. Student Koç University-Computational Science and Engineering
B.Sc. Hacettepe University-Biology

Melisa Ece Zeylan
Research Area
Short Bio

Fatma Cankara
Research
Short Bio

Esra Başaran
Research
Short Bio
MSc Students
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Damla ÖvekMSc Candidate in Computational Science and Engineering
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Kayra KösoğluMSc Student in Molecular Biology and Genetics
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Zeynep AbalıMSc Student in Data Science
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Sukejna ValjevacMSc Student in Computer Science and Engineering
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Simge ŞenyüzMSc Student in Computational Science
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Yunus Emre KöroğluMSc Student in Data Science
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Emre KüçükMSc Student in Data Science
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Ece TezsezenM.Sc. Student in Molecular Biology and Genetics
Damla Övek
Research
Short Bio
M.Sc. Candidate Koç University-Computational Science & Engineering
B.Sc. Koç University-Molecular Biology & Genetics
B.Sc. Koç University-Computer Engineering (Double Major)
Kayra Kösoğlu
Research
Short Bio
M.Sc. Student Koç University-Molecular Biology and Genetics
B.Sc. Istanbul Bilgi University-Genetics and Bio-engineering
Zeynep Abalı
Sukejna Valjevac
Research
Short Bio
M.Sc. Student Koç University-Computer Science & Engineering
B.Sc. Boğaziçi University-Molecular Biology &Genetics
Simge Şenyüz
Short Bio
M.Sc. Candidate Koç University-Computational Science and Engineering
B.Sc. Boğaziçi University-Chemistry
Research Area
Structural and System Biology
Yunus Emre Köroğlu
Short Bio
M.Sc. Student Koç University-Data Science
B.Sc. Boğaziçi University-Chemistry (Double Major)
B.Sc. Boğaziçi University-Molecular Biology and Genetics
Emre Küçük
Short Bio
M.Sc. Student Koç University-Data Science
B.Sc. Istanbul Technical University-Mathematical Engineering

Ece Tezsezen
Research Area
Short Bio
M.Sc. Student Koç University-Molecular Biology and Genetics
B.Sc. Yeditepe University-Genetic and Bioengineering
Undergrad Students
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Can Berk AlakırUndergrad DM Student in Chemical and Biological Engineering & Computer Engineering
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Alihan HatunoğluUndergrad Student in Chemical and Biological Engineering
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Yiğit Can AteşUndergrad Student in Molecular Biology and Genetics
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Zeynep AydınUndergrad Student in Industrial Engineering
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Ece SağıroğluUndergrad Student in Molecular Biology and Genetics
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Burcu ÖzerUndergrad DM Student in Chemical and Biological Engineering & Computer Engineering
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Demet TümkayaUndergrad DM Student in Chemical and Biological Engineering & Computer Engineering
Can Berk Alakır
Research
Short Bio

Alihan Hatunoğlu
Short Bio

Yiğit Can Ateş
Short Bio

Zeynep Aydın
Short Bio

Ece Sağıroğlu
Short Bio

Burcu Özer
Research
Assessment of PRISM Software by using Apoptosis Pathway
Short Bio
B.Sc. Koç University – Chemical-Biological Engineering & Computer Engineering

Demet Tümkaya
Research
Assessment of PRISM Software by using Apoptosis Pathway
Short Bio
B.Sc. Koç University – Chemical-Biological Engineering & Computer Engineering
Alumni
Recent
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Ayşe Derya CavgaPhD in Chemical and Biological Engineering
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Ali Tuğrul BalcıMSc in Computer Science and Engineering
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Ayşe Seda YazgılıMSc in Molecular Biology and Genetics
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Emine Sıla ÖzdemirPhD candidate in Chemical and Biological Engineering
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Serena MuratcıoğluPhD in Chemical and Biological Engineering
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Efe ElbeyliMSc in Biomedical Science and Engineering
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Bilgesu ErdoğanMSc in Biomedical Science and Engineering
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Asma HakouzMSc in Computer Science and Engineering
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Meltem Eda ÖmürMSc in Molecular Biology and Genetics
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Farideh HalakouPhD candidate in Computer Science and Engineering
Ayşe Derya Cavga
Research
Prostate cancer affects 1 in 7 men. A long non-coding RNA acts as an enhancer and influences transcription of the Kallikrein gene family involved in prostate cancer. My main project aims to identify the protein partners of this lncRNA and structurally model the complex they form.
Side Projects:
- Structural analysis of the oligomerization & interactions of the steroid hormone glucocorticoid receptor
- RNA-Sequencing Analysis of Cryptochrome mutation in a p53 knockout background
Short Bio
M.Sc. Bilkent University-Molecular Biology and Genetics
Ph.D. Koç University-Chemical and Biological Engineering
Ali Tuğrul Balcı
Research
Since proteins are pivotal for the most of the crucial activities that are happening in organisms and the proteins, most of the time, do not act alone, studying protein-protein interactions is very important. Predicting which proteins can interact with each other is a very valuable skill on which I am working by using both statistical and deterministic algorithms.
Short Bio
M.Sc. Koç University-Computer Science and Engineering
Ayşe Seda Yazgılı
Research
Ras protein is shown to interact with the proteins involved in crucial pathways such as MAPK and PI3K. Our group recently showed that specific mutations on Ras protein interfere with the p-ERK level within the cell. Using molecular dynamics simulation methods and computational analysis, we aim to have a deeper understanding how these mutations affects the interaction .Therefore, I am simulating the interactions of KRAS protein and Ras-Binding-Domain (RBD) of c-Raf protein.
Short Bio
M.Sc. Koç University-Molecular Biology and Genetics
B.Sc. İstanbul Technical University-Molecular Biology and Genetics
For more information see Ayşe Seda’s homepage
Emine Sıla Özdemir
Research
IQGAP2 is a scaffold protein which plays central roles in cell-cell adhesion, polarity and cell motility. Rho GTPases Cdc42 and Rac1, in their GTP-bound active forms, interact with all three human IQGAP isoforms. IQGAP-Cdc42 interaction promotes metastasis by enhancing actin polymerization. However, despite their high degree of sequence identity, Cdc42 and Ra1 intrections with IQGAP show differences. We aim to reveal the interaction mechanisms of these proteins.
Publications
Unraveling the molecular mechanism of interactions of the Rho GTPases Cdc42 and Rac1 with the scaffolding protein IQGAP2. Ozdemir ES, Jang H, Gursoy A, Keskin O, Li Z, Sacks DB, Nussinov R (2018) . The Journal of Biological Chemistry. doi:10.1074/jbc.RA117.001596
Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations. Ozgur B*, Ozdemir ES*, Gursoy A, Keskin O (2017) Journal of Physical Chemistry B 121 (15):3686-3700.doi:10.1021/
Red emitting, cucurbituril-capped, pH-responsive conjugated oligomer-based nanoparticles for drug delivery and cellular imaging. Pennakalathil J, Jahja E, Ozdemir ES, Konu O, Tuncel D (2014) Biomacromolecules 15 (9):3366-3374. doi:10.1021/bm500839j
Short Bio
M.Sc. Bilkent University-Molecular Biology and Genetics
Ph.D. Koç University-Chemical and Biological Engineering
For more information see Sıla’s homepage
Serena Muratcıoğlu
Research
Ras proteins recruit and activate effectors, including Raf, that transmit receptor-initiated signals and regulates gene expression. Ras is believed to function as a monomer; however, since Raf dimerizes, it was suspected that Ras may also dimerize. Here we show that GTP-bound K-Ras4B forms stable homodimers using two interfaces. We aim to confirm RAS dimerization in vivo and understand the effect of
Short Bio
Ph.D. Koç University-Chemical and Biological Engineering
B.Sc. Istanbul Technical University-Chemistry and Molecular Biology & Genetics
Efe Elbeyli
Research
Capri is community wide experiment to test protein-protein docking methods in blind predictions based on three-dimensional structures. Targets are selected from experimentally known but unpublished complex structures. Predictors can use any of the information in literature about the components for prediction.
Short Bio
M.Sc. Koç University-Biomedical Science and Engineering
Bilgesu Erdoğan
Research
Diseases are commonly the result of dysregulated complex interactions involving large sets of genes and proteins as products of these genes, and their cooperation with other cellular components. Interpreting protein-protein interactions at both network and molecular interaction levels with mutation knowledge requires a comprehensive research process that is fed from different sources. In this project, we developed a web-based tool, Gene2Phen, by integrating large-scale protein-protein interaction network, 3D protein structure information and interface mutation knowledge to aid researchers in exploring and comparing the molecular mechanism of different phenotypes. Gene2Phen works as an automatized pipeline tool to build, visualize and compare phenotype specific subnetworks, to examine protein- protein interactions associated with their structure and mutation data. Gene2Phen web tool prioritizes the human protein-protein network based on seed genes specific to a phenotype. From the prioritized-PPI
network, users can generate a phenotype specific subnetwork. The phenotype-specific subnetworks can be visualized and compared interactively. Genome annotations and topological properties of each protein are shown in this interactive network representation. A unique feature of Gene2Phen is its ability to display 3D structural models of protein-protein interactions and their predicted protein-protein interfaces. Users can see the list of mutations which are mapped on predicted protein-protein interfaces. This allows users to study mutations altering protein-protein interfaces and their role in the phenotype-specific subnetworks. Gene2Phen, by automating the integration of protein-protein networks, protein structure, and disease – related mutations at large scale, will not only boost the productivity and efficiency, but it may be the leveraging step to the novel solutions/studies.
Short Bio
M.Sc. Koç University-Biomedical Science and Engineering
B.Sc. Bilkent University-Computer Engineering
Asma Hakouz
Research
Short Bio
M.Sc. Koç University – Computer Science and Engineering
B.Sc. The University of Jordan – Electrical Engineering
For more information see Asma’s homepage
Meltem Eda Ömür
Research
Classification of structures of protein-protein interactions may provide valuable insights for modeling and abstracting design principles. We aim to cluster protein-protein interactions by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites and expand previously created interface datasets. The novelty in this work is in generating structurally non-redundant protein-protein interfaces which are sensitive to small perturbations in protein binding sites that have a significant impact in template-based docking.
Short Bio
M.Sc. Koç University-Molecular Biology and Genetics
B.Sc. Üsküdar University-Computer Engineering (Double Major)
B.Sc. Üsküdar University-Molecular Biology and Genetics
Farideh Halakou
Research
The common practice in structural PPI networks is to consider just one specific conformation for each protein. Yet it is not a comprehensive representation as it neglects the conformational changes of proteins which may lead to different protein interactions, functions, and downstream signaling. We propose a new representation for structural PPI networks which inspects the different conformations of proteins.
Publications
Enriching Traditional Protein-protein Interaction Networks with Alternative Conformations of Proteins. Halakou F, Kilic ES, Cukuroglu E, Keskin O, Gursoy A. Sci Rep. 2017 Aug 3;7(1):7180.
Topological, functional, and structural analyses of protein-protein interaction networks of breast cancer lung and brain metastases, Halakou F, Gursoy A., Kilic E. S. and Keskin O. 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Manchester, 2017, pp. 1-7.
doi: 10.1109/CIBCB.2017.8058539
Short Bio
M.Sc. Kerman Graduate University of Technology-Information Technology Engineering
For more information see Farideh’s homepage
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