Nurcan Tuncbag, PhD

Associate Professor at
METU Informatics Institute


To reach out the web page of my new research lab please refer to mistral.ii.metu.edu.tr

Office address:
Middle East Technical University
Informatics Institute B-204
Cankaya/Ankara

E-mail: ntuncbag[at]metu[dot]edu[dot]tr

Research Interests

Systems biology of human glioblastoma
  • Combination of proteome, interactome and transcriptional data to infer sub-components of signaling and regulatory networks.
  • Revealing how the networks of interactions among proteins and genome are altered in cells during disease.
  • Simultenous re-construction of multiple pathways via prize-collecting Steiner forest.
Structural analysis and characterization of protein interactions using computational methods.
  • Construction of the non-redundant dataset of protein interfaces
  • Architectures and functional coverage of protein interfaces
  • Prediction of hot spots in protein interfaces
  • Prediction of protein-protein interactions using structural matching and flexible refinement
  • Incorporation of time dimensionality into protein interaction networks
  • Binding site cooperativity in multi-partner proteins

Publications

  • Kacar B, Garmendia E, Tuncbag N, Andersson DI, Hughes D. (2017) Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs, mBio, doi: 10.1128/mBio.01276-17.

  • Tuncbag N, Keskin O, Nussinov R, Gursoy A (2017) Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information, Methods in Molecular Biology, 1558:255-270.

  • Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter-Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis B, Scharf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S (2017) Genome-scale networks link neurodegenerative disease genes to alpha-synuclein through specific molecular pathways, Cell Systems, doi:10.1016/j.cels.2016.12.011.

  • Tuncbag N, Milani P, Pokorny JL, Johnson H, Sio TT, Dalin S, Iyekegbe DO, White F, Sarkaria JN, Fraenkel E (2016) Network Modeling Identifies Patient-specific Pathways in Glioblastoma, Scientific Reports, 6:28668. doi: 10.1038/srep28668.

  • Tuncbag N, Gursoy A, Keskin O, Nussinov R. The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology. Expert Rev Proteomics. 2016 May;13(5):447-9. doi: 10.1080/14789450.2016.

  • Tuncbag N, Gosline SJC, Kedaigle A, Soltis AR, Gitter A, Fraenkel E. Network-based interpretation of diverse high-throughput datasets through the Omics Integrator software package, PLOS Comp Bio, 2016, 12(4):e1004879. doi: 10.1371/journal.pcbi.1004879.

  • Keskin O, Tuncbag N, Gursoy A. Predicting Protein-Protein Interactions from the Molecular to the Proteome Level. Chemical Reviews. 2016 Apr 27;116(8):4884-909. doi: 10.1021/acs.chemrev.5b00683.

  • Ersahin T, Tuncbag N, Cetin-Atalay R, (2015) PI3K/AKT/mTOR Interactive Pathway, Molecular Biosystems, 2015, 11(7):1946-54

  • Budak G, Eren-Ozsoy O, Aydin-Son Y, Can T, Tuncbag N (2015) Modeling and reconstruction of temporal signaling networks in Salmonella-infected human cells, 2015, 20(6):730

  • Tuncbag N, Braunstein A, Pagnani A, Huang SS, Chayes J, Borgs C, Zecchina R, Fraenkel E (2013) Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem, Journal of Computational Biology, 20(2):124-36

  • Tuncbag N, McCallum S, Huang SS, Fraenkel E (2012) SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways, Nucleic Acids Research, 40(Web Server issue):W505-9.

  • N.Tuncbag, O.Keskin, R.Nussinov, A.Gursoy, Fast and Accurate Modeling of Protein-Protein Interactions by Combining Template-Interface-Based Docking with Flexible Refinement, Proteins:Structure, Function and Bioinformatics, 2012, pubmed

  • N.Tuncbag, A.Gursoy, R.Nussinov, O.Keskin, Predicting Protein-Protein Interactions on a Proteome Scale by Matching Evolutionary and Structural Similarities at Interfaces Using PRISM, Nature Protocols, 2011, pubmed.
    Featured Protocol

  • N.Tuncbag, A.Gursoy, O.Keskin, Prediction of protein-protein interactions: Unifying evolution and structure at protein interfaces, Physical Biology, 2011, pubmed.

  • N.Tuncbag, O.Keskin, A.Gursoy, HotPoint:Hot spot prediction server for protein interfaces, Nucleic Acids Research, 2010, 38(Web Server issue):W402-6 pubmed.

  • N.Tuncbag, S.Salman, O.Keskin, A.Gursoy, Analysis and Network Representation of Hot Spots in Protein Interfaces Using Minimum Cut Trees, Proteins:Structure, Function & Bioinformatics, 2010, 78(10):2283-94. pubmed.

  • N. Tuncbag, G. Kar, A. Gursoy, O. Keskin, R. Nussinov, Towards inferring time dimensionality in protein-protein interaction networks by integrating structures: the p53 example, Molecular Biosystems, 2009, 5(12):1770-8. pubmed
    Amongst the top ten accessed articles in June and in July

  • N. Tuncbag, A. Gursoy, O. Keskin, Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy, Bioinformatics, 2009, 25(12):1513-20. pubmed
    "Fast Breaking Paper in Engineering" by Thomson Reuters and Science Watch in December 2010 in the field of Computer Science

  • N. Tuncbag, G. Kar, O. Keskin, A. Gursoy, R. Nussinov, A survey of available tools and web servers for analysis of protein - protein interactions and interfaces, Briefings in Bioinformatics, 2009, 10(3):217-32. pubmed

  • N. Tuncbag, E. Guney, R. Nussinov , A. Gursoy, O. Keskin. Architectures and Functional Coverage of Protein-Protein Interfaces, Journal of Molecular Biology Vol.:381, Issue:3, Pages:785-802, Sep, 2008. pubmed

  • O. Keskin, N. Tuncbag, A. Gursoy, Characterization and Prediction of Protein Interfaces to Infer Protein-Protein Interaction Networks, Curr Pharmacet Biotech, Vol.:9, Issue:2, Pages:67-76, Apr, 2008. pubmed

  • E. Guney, N. Tuncbag, O. Keskin, A. Gursoy. HotSprint: database of computational hot spots in protein interfaces. Nucleic Acids Res. 2008 Jan;36(Database issue):D662-6. pubmed

Softwares, Webservers and Databases

  • Omics Integrator - Network-Based Interpretation of Diverse High-Throughput Datasets
  • SteinerNet - integrating "omic" data to discover hidden components of response pathways
  • PRISM Server - a method to predict protein-protein interactions and structural modeling of protein complexes
  • HotPoint server - an efficient method for calculation of computational hot spots in protein interfaces
  • PRINT Database - a database of protein-protein interfaces available in PDB