Publications

Ivet Bahar, PhD

Mikulska-Ruminska K, Shrivastava I, Krieger J, Zhang S, Li H, Bayır H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. J Chem Inf Model. 2019 Feb 28; doi: 10.1021/acs.jcim.9b00006. PubMed PMID: 30762363.
Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux JP, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Di Pizio A, Niv MY, Nussinov R, Tsai CJ, Jang H, Padhorny D, Kozakov D, McLeish T. Allostery in Its Many Disguises: From Theory to Applications. Structure. 2019 Apr 2;27(4):566-578. doi: 10.1016/j.str.2019.01.003. PubMed PMID: 30744993.
Wang Y, Cobanoglu MC, Li J, Hidvegi T, Hale P, Ewing M, Chu AS, Gong Z, Muzumdar R, Pak SC, Silverman GA, Bahar I, Perlmutter DH. An analog of glibenclamide selectively enhances autophagic degradation of misfolded α1-antitrypsin Z. PLoS One. 2019;14(1):e0209748. doi: 10.1371/journal.pone.0209748. PubMed PMID: 30673724; PMCID: PMC6343872.
Lee JY, Krieger J, Herguedas B, García-Nafría J, Dutta A, Shaikh SA, Greger IH, Bahar I. Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain. Structure. 2019 Feb 5;27(2):241-252.e3. doi: 10.1016/j.str.2018.10.017. PubMed PMID: 30528594; PMCID: PMC6365164.
van Dijk L, Giladi M, Refaeli B, Hiller R, Cheng MH, Bahar I, Khananshvili D. Key residues controlling bidirectional ion movements in Na+/Ca2+ exchanger. Cell Calcium. 2018 Dec;7610-22. doi: 10.1016/j.ceca.2018.09.004. PubMed PMID: 30248574.
Ponzoni L, Zhang S, Cheng MH, Bahar I. Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization. Philos Trans R Soc Lond B Biol Sci. 2018 Jun 19;373(1749): doi: 10.1098/rstb.2017.0177. PubMed PMID: 29735731; PMCID: PMC5941172.
Ponzoni L, Bahar I. Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4164-4169. doi: 10.1073/pnas.1715896115. PubMed PMID: 29610305; PMCID: PMC5910821.
Mikulska-Ruminska K, Kulik AJ, Benadiba C, Bahar I, Dietler G, Nowak W. Author Correction: Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD. Sci Rep. 2018 Mar 6;8(1):4291. doi: 10.1038/s41598-018-21746-7. PubMed PMID: 29511214; PMCID: PMC5840351.
Lee JY, Feng Z, Xie XQ, Bahar I. Allosteric Modulation of Intact γ-Secretase Structural Dynamics. Biophys J. 2017 Dec 19;113(12):2634-2649. doi: 10.1016/j.bpj.2017.10.012. PubMed PMID: 29262358; PMCID: PMC5770568.
Liu B, Oltvai ZN, Bayır H, Silverman GA, Pak SC, Perlmutter DH, Bahar I. Quantitative assessment of cell fate decision between autophagy and apoptosis. Sci Rep. 2017 Dec 14;7(1):17605. doi: 10.1038/s41598-017-18001-w. PubMed PMID: 29242632; PMCID: PMC5730598.
Steinman J, Epperly M, Hou W, Willis J, Wang H, Fisher R, Liu B, Bahar I, McCaw T, Kagan V, Bayir H, Yu J, Wipf P, Li S, Huq MS, Greenberger JS. Improved Total-Body Irradiation Survival by Delivery of Two Radiation Mitigators that Target Distinct Cell Death Pathways. Radiat Res. 2018 Jan;189(1):68-83. doi: 10.1667/RR14787.1. PubMed PMID: 29140165; PMCID: PMC5808408.
Wenzel SE, Tyurina YY, Zhao J, St Croix CM, Dar HH, Mao G, Tyurin VA, Anthonymuthu TS, Kapralov AA, Amoscato AA, Mikulska-Ruminska K, Shrivastava IH, Kenny EM, Yang Q, Rosenbaum JC, Sparvero LJ, Emlet DR, Wen X, Minami Y, Qu F, Watkins SC, Holman TR, VanDemark AP, Kellum JA, Bahar I, Bayır H, Kagan VE. PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals. Cell. 2017 Oct 19;171(3):628-641.e26. doi: 10.1016/j.cell.2017.09.044. PubMed PMID: 29053969; PMCID: PMC5683852.
Tyurina YY, Shrivastava I, Tyurin VA, Mao G, Dar HH, Watkins S, Epperly M, Bahar I, Shvedova AA, Pitt B, Wenzel SE, Mallampalli RK, Sadovsky Y, Gabrilovich D, Greenberger JS, Bayır H, Kagan VE. "Only a Life Lived for Others Is Worth Living": Redox Signaling by Oxygenated Phospholipids in Cell Fate Decisions. Antioxid Redox Signal. 2018 Nov 1;29(13):1333-1358. doi: 10.1089/ars.2017.7124. PubMed PMID: 28835115; PMCID: PMC6157439.
Li H, Chang YY, Lee JY, Bahar I, Yang LW. DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Res. 2017 Jul 3;45(W1):W374-W380. doi: 10.1093/nar/gkx385. PubMed PMID: 28472330; PMCID: PMC5793847.
Sauerwald N, Zhang S, Kingsford C, Bahar I. Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic Acids Res. 2017 Apr 20;45(7):3663-3673. doi: 10.1093/nar/gkx172. PubMed PMID: 28334818; PMCID: PMC5397156.
Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y. Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis. EBioMedicine. 2017 Feb;1548-61. doi: 10.1016/j.ebiom.2016.12.014. PubMed PMID: 28040451; PMCID: PMC5233825.
Kagan VE, Mao G, Qu F, Angeli JP, Doll S, Croix CS, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayır H. Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nat Chem Biol. 2017 Jan;13(1):81-90. doi: 10.1038/nchembio.2238. PubMed PMID: 27842066; PMCID: PMC5506843.
Kurkcuoglu Z, Bahar I, Doruker P. ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution. J Chem Theory Comput. 2016 Sep 13;12(9):4549-62. doi: 10.1021/acs.jctc.6b00319. PubMed PMID: 27494296; PMCID: PMC5088496.
Liu B, Liu Q, Yang L, Palaniappan SK, Bahar I, Thiagarajan PS, Ding JL. Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways. Sci Signal. 2016 Jul 12;9(436):ra70. doi: 10.1126/scisignal.aac9340. PubMed PMID: 27405980; PMCID: PMC5087126.
Stern AM, Schurdak ME, Bahar I, Berg JM, Taylor DL. A Perspective on Implementing a Quantitative Systems Pharmacology Platform for Drug Discovery and the Advancement of Personalized Medicine. J Biomol Screen. 2016 Jul;21(6):521-34. doi: 10.1177/1087057116635818. PubMed PMID: 26962875; PMCID: PMC4917453.
Gur M, Zomot E, Cheng MH, Bahar I. Energy landscape of LeuT from molecular simulations. J Chem Phys. 2015 Dec 28;143(24):243134. doi: 10.1063/1.4936133. PubMed PMID: 26723619; PMCID: PMC4662675.
Li H, Chang YY, Yang LW, Bahar I. iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res. 2016 Jan 4;44(D1):D415-22. doi: 10.1093/nar/gkv1236. PubMed PMID: 26582920; PMCID: PMC4702874.
Hu D, Gur M, Zhou Z, Gamper A, Hung MC, Fujita N, Lan L, Bahar I, Wan Y. Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis. Nat Commun. 2015 Sep 30;68419. doi: 10.1038/ncomms9419. PubMed PMID: 26420673; PMCID: PMC4598737.
Bahar I, Cheng MH, Lee JY, Kaya C, Zhang S. Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions. Biophys J. 2015 Sep 15;109(6):1101-9. doi: 10.1016/j.bpj.2015.06.004. PubMed PMID: 26143655; PMCID: PMC4576147.
Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, Center for Causal Discovery team.. The center for causal discovery of biomedical knowledge from big data. J Am Med Inform Assoc. 2015 Nov;22(6):1132-6. doi: 10.1093/jamia/ocv059. PubMed PMID: 26138794; PMCID: PMC5009908.
Bakan A, Kapralov AA, Bayir H, Hu F, Kagan VE, Bahar I. Inhibition of Peroxidase Activity of Cytochrome c: De Novo Compound Discovery and Validation. Mol Pharmacol. 2015 Sep;88(3):421-7. doi: 10.1124/mol.115.097816. PubMed PMID: 26078313; PMCID: PMC4551054.
Mao W, Kaya C, Dutta A, Horovitz A, Bahar I. Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. Bioinformatics. 2015 Jun 15;31(12):1929-37. doi: 10.1093/bioinformatics/btv103. PubMed PMID: 25697822; PMCID: PMC4481699.
Eyal E, Lum G, Bahar I. The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics. 2015 May 1;31(9):1487-9. doi: 10.1093/bioinformatics/btu847. PubMed PMID: 25568280; PMCID: PMC4410662.

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