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).

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