Unveiling Hidden Connections in Omics Data via pyPARAGON: an Integrative Hybrid Approach for Disease Network Construction. Arici M.K., Tuncbag N. bioRxiv (Preprint) 2023, doi: 10.1101/2023.07.13.547583

Pan-cancer clinical impact of latent drivers from double mutations.Yavuz, B.R., Tsai, CJ., Nussinov, R. Tuncbag N. Commun Biol 6, 202 (2023). https://doi.org/10.1038/s42003-023-04519-5

Neurodevelopmental disorders and cancer networks share pathways; but differ in mechanisms, signaling strength, and outcome. Yavuz B.Y., Arici M.K., Demirel H.C., Tsai C.J., Jang H., Nussinov R., Tuncbag N. bioRxiv (Preprint), 2023, doi: 10.1101/2023.04.16.536718

Neurodevelopmental disorders, like cancer, are connected to impaired chromatin remodelers, PI3K/mTOR, and PAK1-regulated MAPK. Nussinov, R., Yavuz, B.R., Arici, M.K., Demirel H.C., Zhang M., Liu Y., Tsai C.J., Jang H. & Tuncbag N. Biophys Rev 15, 163–181 (2023). doi: 10.1007/s12551-023-01054-9

Functional stratification of cancer drugs through integrated network similarity. Unsal-Beyge S, Tuncbag N.NPJ Syst Biol Appl. 2022 Apr 19;8(1):11. doi: 10.1038/s41540-022-00219-8.PMID: 35440787 Free PMC article.

Performance Assessment of the Network Reconstruction Approaches on Various Interactomes. Arici MK, Tuncbag N.Front Mol Biosci. 2021 Oct 5;8:666705. doi: 10.3389/fmolb.2021.666705. eCollection 2021.PMID: 34676243

Structural analysis of mammalian protein phosphorylation at a proteome level. Kamacioglu A, Tuncbag N, Ozlu N.Structure. 2021 Nov 4;29(11):1219-1229.e3. doi: 10.1016/j.str.2021.06.008. Epub 2021 Jun 29.PMID: 34192515

3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients. Dincer C, Kaya T, Keskin O, Gursoy A, Tuncbag N.PLoS Comput Biol. 2019 Sep 17;15(9):e1006789. doi: 10.1371/journal.pcbi.1006789. eCollection 2019 Sep.PMID: 31527881

Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington’s disease. Paraskevopoulou F, Parvizi P, Senger G, Tuncbag N, Rosenmund C, Yildirim F.Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2020293118. doi: 10.1073/pnas.2020293118.PMID: 33952696

Functional Constraints on Replacing an Essential Gene with Its Ancient and Modern Homologs. Kacar B, Garmendia E, Tuncbag N, Andersson DI, Hughes D.mBio. 2017 Aug 29;8(4):e01276-17. doi: 10.1128/mBio.01276-17.PMID: 28851849

Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways. 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 BJ, 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.Cell Syst. 2017 Feb 22;4(2):157-170.e14. doi: 10.1016/j.cels.2016.12.011. Epub 2017 Jan 25.PMID: 28131822

• Comparative biological network analysis for differentially expressed proteins as a function of bacilysin biosynthesis in Bacillus subtilis.Kutnu M, İşlerel ET, Tunçbağ N, Özcengiz G.Integr Biol (Camb). 2022 Aug 3;14(5):99-110. doi: 10.1093/intbio/zyac010.PMID: 35901454
• Editorial overview: Artificial intelligence (AI) methodologies in structural biology.
  Cheng F, Tuncbag N.Curr Opin Struct Biol. 2022 Jun;74:102387. doi: 10.1016/j.sbi.2022.102387. Epub 2022 May 16.PMID: 35589509 Review.
• Context dependent isoform specific PI3K inhibition confers drug resistance in hepatocellular carcinoma cells.
  Narci K, Kahraman DC, Koyas A, Ersahin T, Tuncbag N, Atalay RC.BMC Cancer. 2022 Mar 24;22(1):320. doi: 10.1186/s12885-022-09357-y.PMID: 35331184
• Artificial intelligence based methods for hot spot prediction.Ovek D, Abali Z, Zeylan ME, Keskin O, Gursoy A, Tuncbag N.Curr Opin Struct Biol. 2022 Feb;72:209-218. doi: 10.1016/j.sbi.2021.11.003. Epub 2021 Dec 23.PMID: 34954608
• Ischemic Heart Disease Selectively Modifies the Right Atrial Appendage Transcriptome.
  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.Front Cardiovasc Med. 2021 Dec 2;8:728198. doi: 10.3389/fcvm.2021.728198. eCollection 2021.PMID: 34926599
• Epithelial Wnt secretion drives the progression of inflammation-induced colon carcinoma in murine model.
  Degirmenci B, Dincer C, Demirel HC, Berkova L, Moor AE, Kahraman A, Hausmann G, Aguet M, Tuncbag N, Valenta T, Basler K.iScience. 2021 Oct 28;24(12):103369. doi: 10.1016/j.isci.2021.103369. eCollection 2021 Dec 17.PMID: 34849464
• Computational approaches leveraging integrated connections of multi-omic data toward clinical applications.
  Demirel HC, Arici MK, Tuncbag N.Mol Omics. 2022 Jan 17;18(1):7-18. doi: 10.1039/d1mo00158b.PMID: 34734935
• Mechanism of activation and the rewired network: New drug design concepts.
  Nussinov R, Zhang M, Maloney R, Tsai CJ, Yavuz BR, Tuncbag N, Jang H.Med Res Rev. 2022 Mar;42(2):770-799. doi: 10.1002/med.21863. Epub 2021 Oct 25.PMID: 34693559
• Epitranscriptomics of Ischemic Heart Disease-The IHD-EPITRAN Study Design and Objectives. Sikorski V, Karjalainen P, Blokhina D, Oksaharju K, Khan J, Katayama 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.Int J Mol Sci. 2021 Jun 21;22(12):6630. doi: 10.3390/ijms22126630.PMID: 34205699
• Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics. Eren M, Tuncbag N, Jang H, Nussinov R, Gursoy A, Keskin O.J Phys Chem B. 2021 May 27;125(20):5210-5221. doi: 10.1021/acs.jpcb.1c00891. Epub 2021 May 12.PMID: 33978412
• Quantitative Proteomics Identifies Secreted Diagnostic Biomarkers as well as Tumor-Dependent Prognostic Targets for Clear Cell Renal Cell Carcinoma. Senturk A, Sahin AT, Armutlu A, Kiremit MC, Acar O, Erdem S, Bagbudar S, Esen T, Tuncbag N, Ozlu N.Mol Cancer Res. 2021 Aug;19(8):1322-1337. doi: 10.1158/1541-7786.MCR-21-0004. Epub 2021 May 11.PMID: 33975903
• A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules. Demirel HC, Dogan T, Tuncbag N.Curr Top Med Chem. 2018;18(8):700-713. doi: 10.2174/1568026618666180601080824.PMID: 29852872
• Systems-level Analysis Reveals Multiple Modulators of Epithelial-mesenchymal Transition and Identifies DNAJB4 and CD81 as Novel Metastasis Inducers in Breast Cancer. Uretmen Kagiali ZC, Sanal E, Karayel Ö, Polat AN, Saatci Ö, Ersan PG, Trappe K, Renard BY, Önder TT, Tuncbag N, Şahin Ö, Ozlu N.Mol Cell Proteomics. 2019 Sep;18(9):1756-1771. doi: 10.1074/mcp.RA119.001446. Epub 2019 Jun 20.PMID: 31221721
• Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis.Karayel Ö, Şanal E, Giese SH, Üretmen Kagıalı ZC, Polat AN, Hu CK, Renard BY, Tuncbag N, Özlü N.Sci Rep. 2018 Feb 2;8(1):2269. doi: 10.1038/s41598-018-20231-5.PMID: 29396449
• Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites. Atas H, Tuncbag N, Doğan T.Methods Mol Biol. 2018;1762:51-69. doi: 10.1007/978-1-4939-7756-7_4.PMID: 29594767
• Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information.Tuncbag N, Keskin O, Nussinov R, Gursoy A.Methods Mol Biol. 2017;1558:255-270. doi: 10.1007/978-1-4939-6783-4_12.PMID: 28150242