NeTLAB

NeTLAB – Network Modeling Lab

We work on network modelling of human diseases at the top level, specifically in cancer. All the projects we contribute consist of steps starting at the data production, computational modeling and hypothesis generations, and finally experimental validation. We have experience both in structural bioinformatics and computational systems biology. These two different but complementing areas are combined and improved to address new questions in the systems biology area in our research group.

Obviously, biology is still moving toward generation of big data. No single data type is capable to fully represent the cellular activity. Beyond the list of molecules from each data type, there is a necessity to consider multiple data jointly and reconstruct the relations between these molecules which implies the necessity of personalized network-based approaches. We develop new integrative network modelling approaches to combine multiple high-throughput data with interactomes. Our current and planned research covers several branches of the systems biology of diseases. The main topics can be listed as follows:

  • revealing tumour specific structural networks by integrating alternative splicing events,
  • modelling temporal signalling networks in tumour tissues,
  • analysis of temporal ischemic effects at sample freezing stage in ovarian cancer,
  • integrating multi-omic data to reconstruct patient-specific cancer pathways.

Group Members

  • Nurcan Tuncbag, Principal Investigator, METU
  • Gungor Budak, PhD student at Computer Engineering, METU
  • Seyma Unsal Beyge, PhD Student at Medical Informatics, METU
  • Melike Caglayan, PhD Student at Medical Informatics, METU
  • Mecit Sari, PhD Student at Information Systems, METU
  • Rumeysa Fayetorbay, MSc student at Bioinformatics, METU
  • Tugba Kaya, MSc student at Bioinformatics Program
  • Cansu Demirel, MSc student at Bioinformatics, METU
  •  Gokce Senger, MSc Student at Bioinformatics, METU
  • Cansu Dincer, MSc student at Bioinformatics, METU

Projects 

  • 2017 Bilimsel Araştırma Projeleri (BAP) Desteği (Yürütücü)
  • 2015 Bilim Akademisi Genç Bilim İnsanları Ödül Programı (BAGEP) Ödülü
  • 2016 –2018 T.C. Kalkınma Bakanlığı, Altyapı Desteği; Kanser Sistem Biyolojisi Laboratuvarı (KanSiL) (Araştırmacı)  
  • 2014 – 2016 FP7 the Marie Curie Action and TÜBİTAK Co-funded Uluslararası Deneyimli Araştırmacı Dolaşımı Destek Programı (Yürütücü)

Publications

  • 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, Schöndorf 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, Gosline SJC, Kedaigle A, Soltis AR, Gitter A, Fraenkel E (2016). Network-based interpretation of diverse high-throughput datasets through the Omics Integrator software package, PLOS Comp Bio, 12(4):e1004879. doi: 10.1371/journal.pcbi.1004879. 
  • Keskin O, Tuncbag N, Gursoy A (2016). Predicting Protein-Protein Interactions from the Molecular to the Proteome Level. Chemical Reviews. 116(8):4884-909. doi: 10.1021/acs.chemrev.5b00683.
  • 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 (2016). The potential impact of recent developments in three-dimensional quantitative interaction proteomics on structural biology. Expert Rev Proteomics. 13(5):447-9. doi: 10.1080/14789450.2016. 
  • Budak G, Eren-Ozsoy O, Aydin-Son Y, Can T, Tuncbag N (2015). Reconstruction of temporal signaling networks in Salmonella-infected human cells, Frontiers in Microbiology, 6(730):1-14.
  • Ersahin T, Tuncbag N, Cetin-Atalay R (2015). The PI3K/AKT/mTOR interactive pathway, Molecular Biosystems, 11(7):1946-54.
  • Tuncbag N, Braunstein A, Pagnani A, Huang SSC, 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, pp. 1-13.
  • Tuncbag N, McCallum S, Huang SSC, Fraenkel E (2012). SteinerNet: A Web Server for Integrating “Omic” data to Discover Hidden Components of Response Pathways, Nucleic Acids Research (Web Server Issue), doi: 10.1093/nar/gks445.
  • Tuncbag N, Keskin O, Nussinov R, Gursoy A (2012). Fast and Accurate Modeling of Protein-Protein Interactions by Combining Template-Interface-Based Docking with Flexible Refinement, Proteins: Structure, Function and Bioinformatics, 80(4):1239-49.
  • Tuncbag N, Gursoy A, Nussinov R, Keskin O (2011). Predicting Protein-Protein Interactions on a Proteome Scale by Matching Evolutionary and Structural Similarities at Interfaces Using PRISM, Nature Protocols, 6(9):1341-54.
  • Tuncbag N, Gursoy A, Keskin O (2011). Prediction of protein-protein interactions: Unifying evolution and structure at protein interfaces, Physical Biology, 8(3):035006.
  • Tuncbag N, Keskin O, Gursoy A (2010). “HotPoint: Hot Spot Prediction Server for Protein Interfaces” Nucleic Acids Research, 38(Web Server issue):W402-6.
  • Tuncbag N, Salman FS, Keskin O, Gursoy A (2010). “Analysis and network representation of hot spots in protein interfaces using minimum cut trees” Proteins: Structure, Function and Bioinformatics, 78(10):2283-94.
  • Tuncbag N, Kar G, Gursoy A, Keskin O, Nussinov R (2009). “Towards inferring time-dimensionality in protein-protein interaction networks by intergrating structures: the p53 example” Molecular Biosystems, 5:1770-1778.
  • Tuncbag N, Gursoy A, Keskin O (2009). “Identification of computational hot spots in protein interfaces: Combining solvent accessibility and inter-residue potentials improves the accuracy” Bioinformatics, 25(12):1513-1520.
  • Tuncbag N, Kar G, Gursoy A, Keskin O, Nussinov R (2009). “A survey of available tools and web servers for analysis of protein–protein interactions and interfaces” Briefings in Bioinformatics, 10:217-232.
  • Guney E, Tuncbag N, Keskin O, Gursoy A. “HotSprint: database of computational hot spots in protein interfaces” Nucleic Acids Research, 36(Database Issue):D662-666, 2008.
  • Keskin O, Tuncbag N, Gursoy A (2008). “Characterization and Prediction of Protein Interfaces to Infer Protein-Protein Interaction Networks” Curr. Phar. Biotech., 9(2):67-76.
  • Tuncbag N, Guney E, Gursoy A, Keskin O, Nussinov R (2008). “Architectures and Functional Coverage of Protein-Protein Interfaces” Journal of Molecular Biology, 381:785-802.

External Collaborators

  • Ernest Fraenkel, PhD - MIT
  • Ozlem Keskin, PhD - Koc University
  • Attila Gursoy, PhD - Koc University
  • Betul Kacar, PhD - Harvard University
  • Ruth Nussinov, PhD, NIH
  • Rengul Cetin-Atalay, MD, PhD - METU
  • Yesim Aydin-Son, MD, PhD - METU
  • Tolga Can, PhD - METU
  • Nurhan Ozlu, PhD - Koc University

Links

http://mistral.ii.metu.edu.tr