Publications

  1. Demirel H.C., Arici K., Tuncbag N.* A Review on Computational Approaches Leveraging Integrated Connections of Multi-Omic Data toward Clinical Applications, Molecular Omics, under review.
  2. Unsal-Beyge S. and Tuncbag N.* Functional Stratification of Cancer Drugs through Integrated Network Similarity, under review.
  3. Paraskevopoulou F., Parvizi P., Senger G., Tuncbag N., Rosenmund C., Yildirim F. (2021) Impaired inhibitory GABAergic synaptic transmission and gene transcription studied in single neurons by Patch-seq in Huntington’s disease, PNAS, 118 (19): e2020293118; https://doi.org/10.1073/pnas.2020293118.
  4. Sikorski V., Karjalainen P., Blokhina D., Oksaharju K., Khan J., Katayma S., Rajala H., Suihko S., Tuohinen S., Teittinen K., Nummi A., Nykänen A., Eskin A., Stark C., Biancari F., Kiss J., Simpanen J., Ropponen J., Lemström K., Savinainen K., Lalowski M., Kaarne M., Jormalainen M., Elomaa O., Koivisto P., Raivio P., Bäckström P., Dahlbacka S., Syrjälä S., Vainikka T., Vähäsilta T., Tuncbag N., Karelson M., Mervaala E., Juvonen T., Laine M., Laurikka J., Vento A., Kankuri E. (2021) Epitranscriptomics of Ischemic Heart Disease—The IHD-EPITRAN Study Design and Objectives, International Journal of Molecular Sciences, 22, 6630. https://doi.org/10.3390/ijms22126630.
  5. Yavuz B.R., Tsai C.J., Nussinov R., Tuncbag N*. Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data Reveal their Clinical Impact, bioRxiv, https://doi.org/10.1101/2021.04.02.438239.
  6. Nussinov R., Zhang M., Maloney R., Tsai C.J., Yavuz B.R., Tuncbag N., Jang H. (2021) Targeting the mechanism of activation and the rewired network: New concepts in drug design, Medicinal Research Reviews, under review.
  7. Arici M.K., Tuncbag N.* A critical assessment of the performance of network reconstruction approaches based on interactome data sets, Frontiers in Molecular Biosciences, under review.
  8. Mulari S., Eskin A., Lampinen M., Nummi A., Nieminen T., Teittinen K., Ojala T., Kankainen M., Vento A., Laurikka J., Kupari M., Harjula A., Tuncbag N.*, Kankuri E.* Atrial Appendage Signature RNAs Associated with Ischemic Heart Disease Severity and Surgical Outcome, Frontiers in Cardiovasc. Med., under review.
  9. Senturk A., Sahin A., Armutlu A., Kiremit M., Acar O., Erdem S., Bagbudar S., Esen T., Tuncbag N., Ozlu N., Quantitative proteomics identifies secreted diagnostic biomarkers as well as tumor-dependent prognostic targets for clear cell Renal Cell Carcinoma, AACR Molecular Cancer Research, doi: 10.1158/1541-7786.MCR-21-0004.
  10. Kamacioglu A., Tuncbag N.*, Ozlu N.*, Structural Analysis of Mammalian Protein Phosphorylation at a Proteome Level, Structure, 29, 1–11; 10.1016/j.str.2021.06.008.
  11. Eren M., Tuncbag N., Jang H., Nussinov R., Gursoy A., Keskin O. (2021) Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics, Journal of Physical Chemistry, 125(20):5210-5221. doi: 10.1021/acs.jpcb.1c00891.
  12. Mohamed RI, Bargal SA, Mekawy AS, El-Shiekh I, Tuncbag N, Ahmed AS, Badr E, Elserafy M. (2021) The overexpression of DNA repair genes in invasive ductal and lobular breast carcinomas: Insights on individual variations and precision medicine. PLoS One. 16(3):e0247837. doi: 10.1371/journal.pone.0247837
  13. Dincer C, Kaya T, Keskin O, Gursoy A, Tuncbag N.* (2019) 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients. PLOS Computational Biology. 15(9):e1006789. doi: 10.1371/journal.pcbi.1006789.
  14. Uretmen Kagiali ZC, Sanal E, Karayel Ö, Polat AN, Saatci Ö, Ersan PG, TrappeK, Renard BY, Önder TT, Tuncbag N, Şahin Ö, Ozlu N. (2019) Systems-level analysis reveals multiple modulators of epithelial-mesenchymal transition and identifies DNAJB4 and CD81 as novel metastasis inducers in breast cancer. Mol Cell Proteomics. pii: mcp.RA119.001446. doi: 10.1074/mcp.RA119.001446.
  15. Demirel HC, Dogan T, Tuncbag N.* (2018) A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules. Curr Top Med Chem.;18(8):700-713. doi: 10.2174/1568026618666180601080824.
  16. Atas H, Tuncbag N, Doğan T. (2018) Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites. Methods Mol Biol.;1762:51-69. doi: 10.1007/978-1-4939-7756-7_4.
  17. Karayel O, Sanal E, Giese SH, Uretmen Kagıalı ZC, Polat AN, Hu CK, Renard BY, Tuncbag N, Ozlu N (2017) Comparative phosphoproteomic analysis reveals signaling networks that regulate cytokinesis, Scientific Reports 8(1):2269. doi: 10.1038/s41598-018-20231-5.
  18. 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.
  19. 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.
  20. 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. (book chapter).
  21. 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.
  22. 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.
  23. 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.Out of all 2016 articles, it was in the top 50 most downloaded.
  24. 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.
  25. Budak G, Eren-Ozsoy O, Aydin-Son Y, Can T, Tuncbag N*. Modeling and reconstruction of temporal signaling networks in Salmonella-infected human cells, Frontiers in Microbiology, 2015, 20(6):730.
  26. Ersahin T, Tuncbag N, Cetin-Atalay R. The PI3K/AKT/mTOR interactive pathway, Molecular Biosystems, 2015, 11(7):1946-54.
  27. Tuncbag N, Braunstein A, Pagnani A, Huang SSC, Chayes J, Borgs C, Zecchina R, Fraenkel E. Simultaneous reconstruction of multiple signaling pathways via the prize-collecting Steiner forest problem, Journal of Computational Biology, 2013, 20, pp. 1-13.
  28. Tuncbag N, McCallum S, Huang SSC, Fraenkel E. SteinerNet: A Web Server for Integrating “Omic” data to Discover Hidden Components of Response Pathways, Nucleic Acids Research (Web Server Issue), 2012, doi: 10.1093/nar/gks445.
  29. Tuncbag N, Keskin O, Nussinov R, Gursoy A. Fast and Accurate Modeling of Protein-Protein Interactions by Combining Template-Interface-Based Docking with Flexible Refinement, Proteins: Structure, Function and Bioinformatics, 2012, 80(4):1239-49.
  30. Tuncbag N, Gursoy A, Nussinov R, Keskin O. Predicting Protein-Protein Interactions on a Proteome Scale by Matching Evolutionary and Structural Similarities at Interfaces Using PRISM, Nature Protocols, 2011, 6(9):1341-54. Labelled “Highly cited paper” at Web of Science.
  31. Tuncbag N, Gursoy A, Keskin O. Prediction of protein-protein interactions: Unifying evolution and structure at protein interfaces, Physical Biology, 2011, 8(3):035006.
  32. Tuncbag N, Keskin O, Gursoy A. “HotPoint: Hot Spot Prediction Server for Protein Interfaces” Nucleic Acids Research, 2010, 38(Web Server issue):W402-6.
  33. Tuncbag N, Salman FS, Keskin O, Gursoy A. “Analysis and network representation of hot spots in protein interfaces using minimum cut trees” Proteins: Structure, Function and Bioinformatics, 2010, 78(10):2283-94.
  34. Tuncbag N, Kar G, Gursoy A, Keskin O, Nussinov R. “Towards inferring time-dimensionality in protein-protein interaction networks by intergrating structures: the p53 example” Molecular Biosystems, 2009, 5:1770-1778. Amongst the top ten accessed articles in June, July, August 2011 and in February 2012.
  35. Tuncbag N, Gursoy A, Keskin O. “Identification of computational hot spots in protein interfaces: Combining solvent accessibility and inter-residue potentials improves the accuracy” Bioinformatics, 2009, 25(12):1513-1520. “Fast Breaking Paper in Engineering” by Thomson Reuters and Science Watch in December 2010 in the field of Computer Science: Labelled “Highly cited paper” at Web of Science.
  36. Tuncbag N, Kar G, Gursoy A, Keskin O, Nussinov R. “A survey of available tools and web servers for analysis of protein–protein interactions and interfaces” Briefings in Bioinformatics, 2009, 10:217-232.
  37. 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.
  38. Keskin O, Tuncbag N, Gursoy A. “Characterization and Prediction of Protein Interfaces to Infer Protein-Protein Interaction Networks” Phar. Biotech., 9(2):67-76, 2008.
  39. Tuncbag N, Guney E, Gursoy A, Keskin O, Nussinov R. “Architectures and Functional Coverage of Protein-Protein Interfaces” Journal of Molecular Biology, 381:785-802, 2008.