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Ivet Bahar - Publications

University of Pittsburgh, Pittsburgh, PA, United States 
General Biophysics, Bioinformatics Biology, Biostatistics Biology

229 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I. ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. Bioinformatics (Oxford, England). PMID 33822884 DOI: 10.1093/bioinformatics/btab187  1
2021 Porritt RA, Paschold L, Noval Rivas M, Cheng MH, Yonker LM, Chandnani H, Lopez M, Simnica D, Schultheiß C, Santiskulvong C, van Eyk J, McCormick JK, Fasano A, Bahar I, Binder M, et al. HLA class I-associated expansion of TRBV11-2 T cells in Multisystem Inflammatory Syndrome in Children. The Journal of Clinical Investigation. PMID 33705359 DOI: 10.1172/JCI146614  0.56
2021 Sorkina T, Cheng MH, Bagalkot TR, Wallace C, Watkins SC, Bahar I, Sorkin A. Direct coupling of oligomerization and oligomerization-driven endocytosis of the dopamine transporter to its conformational mechanics and activity. The Journal of Biological Chemistry. 100430. PMID 33610553 DOI: 10.1016/j.jbc.2021.100430  0.56
2021 Wang H, Pei F, Vanyukov MM, Bahar I, Wu W, Xing EP. Coupled mixed model for joint genetic analysis of complex disorders with two independently collected data sets. Bmc Bioinformatics. 22: 50. PMID 33546598 DOI: 10.1186/s12859-021-03959-2  0.68
2021 Sun WY, Tyurin VA, Mikulska-Ruminska K, Shrivastava IH, Anthonymuthu TS, Zhai YJ, Pan MH, Gong HB, Lu DH, Sun J, Duan WJ, Korolev S, Abramov AY, Angelova PR, Miller I, ... ... Bahar I, et al. Phospholipase iPLAβ averts ferroptosis by eliminating a redox lipid death signal. Nature Chemical Biology. PMID 33542532 DOI: 10.1038/s41589-020-00734-x  0.68
2021 Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. HiDeF: identifying persistent structures in multiscale 'omics data. Genome Biology. 22: 21. PMID 33413539 DOI: 10.1186/s13059-020-02228-4  0.8
2021 Dagvadorj J, Mikulska-Ruminska K, Tumurkhuu G, Ratsimandresy RA, Carriere J, Andres AM, Marek-Iannucci S, Song Y, Chen S, Lane M, Dorfleutner A, Gottlieb RA, Stehlik C, Cassel S, Sutterwala FS, ... Bahar I, et al. Recruitment of pro-IL-1α to mitochondrial cardiolipin, via shared LC3 binding domain, inhibits mitophagy and drives maximal NLRP3 activation. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33361152 DOI: 10.1073/pnas.2015632118  0.68
2020 Cheng MH, Porritt RA, Rivas MN, Krieger JM, Ozdemir AB, Garcia G, Arumugaswami V, Fries BC, Arditi M, Bahar I. A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry . Biorxiv : the Preprint Server For Biology. PMID 33269352 DOI: 10.1101/2020.11.24.395079  0.88
2020 Zhou Z, Huang F, Shrivastava I, Zhu R, Luo A, Hottiger M, Bahar I, Liu Z, Cristofanilli M, Wan Y. New insight into the significance of KLF4 PARylation in genome stability, carcinogenesis, and therapy. Embo Molecular Medicine. e12391. PMID 33231937 DOI: 10.15252/emmm.202012391  0.64
2020 Porritt RA, Paschold L, Rivas MN, Cheng MH, Yonker LM, Chandnani H, Lopez M, Simnica D, Schultheiß C, Santiskulvong C, Van Eyk J, Fasano A, Bahar I, Binder M, Arditi M. Identification of a unique TCR repertoire, consistent with a superantigen selection process in Children with Multi-system Inflammatory Syndrome. Biorxiv : the Preprint Server For Biology. PMID 33200133 DOI: 10.1101/2020.11.09.372169  0.56
2020 Anthonymuthu TS, Tyurina YY, Sun WY, Mikulska-Ruminska K, Shrivastava IH, Tyurin VA, Cinemre FB, Dar HH, VanDemark AP, Holman TR, Sadovsky Y, Stockwell BR, He RR, Bahar I, Bayır H, et al. Resolving the paradox of ferroptotic cell death: Ferrostatin-1 binds to 15LOX/PEBP1 complex, suppresses generation of peroxidized ETE-PE, and protects against ferroptosis. Redox Biology. 38: 101744. PMID 33126055 DOI: 10.1016/j.redox.2020.101744  0.68
2020 Arditi M, Bahar I. Multisystem Inflammatory Syndrome in Children in the United States. The New England Journal of Medicine. 383: 1794. PMID 33085853 DOI: 10.1056/NEJMc2026136#sa2  0.48
2020 Rivas MN, Porritt RA, Cheng MH, Bahar I, Arditi M. COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): a novel disease that mimics Toxic Shock Syndrome. The superantigen hypothesis. The Journal of Allergy and Clinical Immunology. PMID 33075409 DOI: 10.1016/j.jaci.2020.10.008  0.56
2020 Wingert B, Krieger J, Li H, Bahar I. Adaptability and specificity: how do proteins balance opposing needs to achieve function? Current Opinion in Structural Biology. 67: 25-32. PMID 33053463 DOI: 10.1016/  0.8
2020 Cheng MH, Zhang S, Porritt RA, Noval Rivas M, Paschold L, Willscher E, Binder M, Arditi M, Bahar I. Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Proceedings of the National Academy of Sciences of the United States of America. PMID 32989130 DOI: 10.1073/pnas.2010722117  0.8
2020 Song X, Zhou Z, Li H, Xue Y, Lu X, Bahar I, Kepp O, Hung MC, Kroemer G, Wan Y. Pharmacological suppression of B7-H4 glycosylation restores antitumor immunity in immune-cold breast cancers. Cancer Discovery. PMID 32938586 DOI: 10.1158/2159-8290.Cd-20-0402  0.8
2020 Zhang Y, Krieger J, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I. State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Progress in Biophysics and Molecular Biology. PMID 32866476 DOI: 10.1016/J.Pbiomolbio.2020.08.006  0.8
2020 Kaynak BT, Bahar I, Doruker P. Essential site scanning analysis: A new approach for detecting sites that modulate the dispersion of protein global motions. Computational and Structural Biotechnology Journal. 18: 1577-1586. PMID 32637054 DOI: 10.1016/J.Csbj.2020.06.020  1
2020 Clark LJ, Krieger J, White AD, Bondarenko V, Lei S, Fang F, Lee JY, Doruker P, Böttke T, Jean-Alphonse F, Tang P, Gardella TJ, Xiao K, Sutkeviciute I, Coin I, ... Bahar I, et al. Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation. Nature Chemical Biology. PMID 32632293 DOI: 10.1038/S41589-020-0567-0  1
2020 Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods. Current Opinion in Structural Biology. 64: 34-41. PMID 32622329 DOI: 10.1016/J.Sbi.2020.05.013  1
2020 Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. Decoding of persistent multiscale structures in complex biological networks. Biorxiv : the Preprint Server For Biology. PMID 32587977 DOI: 10.1101/2020.06.16.151555  0.8
2020 Zhao J, Dar HH, Deng Y, St Croix CM, Li Z, Minami Y, Shrivastava IH, Tyurina YY, Etling E, Rosenbaum JC, Nagasaki T, Trudeau JB, Watkins SC, Bahar I, Bayır H, et al. PEBP1 acts as a rheostat between prosurvival autophagy and ferroptotic death in asthmatic epithelial cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 32513718 DOI: 10.1073/Pnas.1921618117  0.64
2020 Cheng MH, Zhang S, Porritt RA, Arditi M, Bahar I. An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. Biorxiv : the Preprint Server For Biology. PMID 32511374 DOI: 10.1101/2020.05.21.109272  0.8
2020 Shi Q, Pei F, Silverman GA, Pak SC, Perlmutter DH, Liu B, Bahar I. Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis. International Journal of Molecular Sciences. 21. PMID 32325894 DOI: 10.3390/Ijms21082855  0.68
2020 Zhou Z, Zhou H, Ponzoni L, Luo A, Zhu R, He M, Huang Y, Guan KL, Bahar I, Liu Z, Wan Y. EIF3H orchestrates Hippo pathway-mediated oncogenesis via catalytic control of YAP stability. Cancer Research. PMID 32269044 DOI: 10.1158/0008-5472.Can-19-3718  0.64
2020 Ponzoni L, Nguyen NH, Bahar I, Brodsky JL. Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel. Plos Computational Biology. 16: e1007749. PMID 32251469 DOI: 10.1371/Journal.Pcbi.1007749  0.56
2020 Li H, Pei F, Taylor DL, Bahar I. QuartataWeb: integrated chemical-protein-pathway mapping for polypharmacology and chemogenomics. Bioinformatics (Oxford, England). PMID 32221612 DOI: 10.1093/Bioinformatics/Btaa210  0.8
2020 Thermozier S, Hou W, Zhang X, Shields D, Fisher R, Bayir H, Kagan V, Yu J, Liu B, Bahar I, Epperly MW, Wipf P, Wang H, Huq MS, Greenberger JS. Anti-Ferroptosis Drug Enhances Total-Body Irradiation Mitigation by Drugs that Block Apoptosis and Necroptosis. Radiation Research. PMID 32134361 DOI: 10.1667/Rr15486.1  0.68
2020 Li H, Doruker P, Hu G, Bahar I. Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding. Biophysical Journal. PMID 32130874 DOI: 10.1016/J.Bpj.2020.01.046  1
2020 Ponzoni L, Peñaherrera DA, Oltvai ZN, Bahar I. Rhapsody: Predicting the pathogenicity of human missense variants. Bioinformatics (Oxford, England). PMID 32101277 DOI: 10.1093/Bioinformatics/Btaa127  0.56
2020 Kapralov AA, Yang Q, Dar HH, Tyurina YY, Anthonymuthu TS, Kim R, St Croix CM, Mikulska-Ruminska K, Liu B, Shrivastava IH, Tyurin VA, Ting HC, Wu YL, Gao Y, Shurin GV, ... ... Bahar I, et al. Redox lipid reprogramming commands susceptibility of macrophages and microglia to ferroptotic death. Nature Chemical Biology. 16: 278-290. PMID 32080625 DOI: 10.1038/S41589-019-0462-8  0.68
2019 Zhang S, Chen F, Bahar I. Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation. Nucleic Acids Research. PMID 31828312 DOI: 10.1093/Nar/Gkz1102  0.8
2019 Belovich AN, Aguilar JI, Mabry SJ, Cheng MH, Zanella D, Hamilton PJ, Stanislowski DJ, Shekar A, Foster JD, Bahar I, Matthies HJG, Galli A. A network of phosphatidylinositol (4,5)-bisphosphate (PIP) binding sites on the dopamine transporter regulates amphetamine behavior in Drosophila Melanogaster. Molecular Psychiatry. PMID 31796894 DOI: 10.1038/S41380-019-0620-0  0.56
2019 Zhang Y, Doruker P, Kaynak B, Zhang S, Krieger J, Li H, Bahar I. Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior. Current Opinion in Structural Biology. 62: 14-21. PMID 31785465 DOI: 10.1016/J.Sbi.2019.11.002  1
2019 Chi JJ, Li H, Zhou Z, Izquierdo-Ferrer J, Xue Y, Wavelet CM, Schiltz GE, Zhang B, Cristofanilli M, Lu X, Bahar I, Wan Y. A novel strategy to block mitotic progression for targeted therapy. Ebiomedicine. PMID 31669221 DOI: 10.1016/J.Ebiom.2019.10.013  0.8
2019 Lee JY, Krieger JM, Li H, Bahar I. Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations. Protein Science : a Publication of the Protein Society. PMID 31576621 DOI: 10.1002/Pro.3732  0.88
2019 Kim Y, Jun I, Shin DH, Yoon JG, Piao H, Jung J, Park HW, Cheng MH, Bahar I, Whitcomb DC, Lee MG. Regulation of CFTR Bicarbonate Channel Activity by WNK1: Implications for Pancreatitis and CFTR-related disorders. Cellular and Molecular Gastroenterology and Hepatology. PMID 31561038 DOI: 10.1016/J.Jcmgh.2019.09.003  0.56
2019 Thermozier S, Zhang X, Hou W, Fisher R, Epperly MW, Liu B, Bahar I, Wang H, Greenberger JS. Radioresistance of Serpinb3a-/- Mice and Derived Hematopoietic and Marrow Stromal Cell Lines. Radiation Research. PMID 31295086 DOI: 10.1667/Rr15379.1  0.68
2019 Cheng MH, Bahar I. Monoamine transporters: structure, intrinsic dynamics and allosteric regulation. Nature Structural & Molecular Biology. 26: 545-556. PMID 31270469 DOI: 10.1038/S41594-019-0253-7  0.56
2019 Cheng MH, Ponzoni L, Sorkina T, Lee JY, Zhang S, Sorkin A, Bahar I. Trimerization of dopamine transporter triggered by AIM-100 binding: Molecular mechanism and effect of mutations. Neuropharmacology. 107676. PMID 31228486 DOI: 10.1016/J.Neuropharm.2019.107676  0.8
2019 Taylor DL, Gough A, Schurdak ME, Vernetti L, Chennubhotla CS, Lefever D, Pei F, Faeder JR, Lezon TR, Stern AM, Bahar I. Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology. Handbook of Experimental Pharmacology. PMID 31201557 DOI: 10.1007/164_2019_239  0.76
2019 Zhou Z, Feng Z, Hu D, Yang P, Gur M, Bahar I, Cristofanilli M, Gradishar WJ, Xie XQ, Wan Y. A novel small-molecule antagonizes PRMT5-mediated KLF4 methylation for targeted therapy. Ebiomedicine. PMID 31101597 DOI: 10.1016/J.Ebiom.2019.05.011  0.84
2019 Zhang S, Li H, Krieger JM, Bahar I. Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity. Molecular Biology and Evolution. PMID 31028708 DOI: 10.1093/Molbev/Msz102  0.88
2019 Pei F, Li H, Liu B, Bahar I. Quantitative Systems Pharmacological Analysis of Drugs of Abuse Reveals the Pleiotropy of Their Targets and the Effector Role of mTORC1. Frontiers in Pharmacology. 10: 191. PMID 30906261 DOI: 10.3389/Fphar.2019.00191  0.8
2019 Mikulska-Ruminska K, Shrivastava IH, Krieger J, Zhang S, Li H, Bayir H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. Characterization of differential dynamics, specificity, and allostery of lipoxygenase family members. Journal of Chemical Information and Modeling. PMID 30762363 DOI: 10.1021/Acs.Jcim.9B00006  0.8
2019 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, et al. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). PMID 30744993 DOI: 10.1016/J.Str.2019.01.003  0.36
2019 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. 14: e0209748. PMID 30673724 DOI: 10.1371/Journal.Pone.0209748  0.6
2018 Wang KZQ, Steer E, Otero PA, Bateman NW, Cheng MH, Scott AL, Wu C, Bahar I, Shih YT, Hsueh YP, Chu CT. PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons. Eneuro. 5. PMID 30783609 DOI: 10.1523/ENEURO.0466-18.2018  0.88
2018 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 (London, England : 1993). PMID 30528594 DOI: 10.1016/J.Str.2018.10.017  0.96
2018 Anthonymuthu TS, Kenny EM, Shrivastava IH, Tyurina YY, Hier ZE, Ting HC, Dar H, Tyurin VA, Nesterova A, Amoscato AA, Mikulska-Ruminska K, Rosenbaum JC, Mao G, Jinming Z, Conrad M, ... ... Bahar I, et al. Empowerment of 15-lipoxygenase catalytic competence in selective oxidation of membrane ETE-PE to ferroptotic death signals, HpETE-PE. Journal of the American Chemical Society. PMID 30525572 DOI: 10.1021/Jacs.8B09913  0.68
2018 van Dijk L, Giladi M, Refaeli B, Hiller R, Cheng MH, Bahar I, Khananshvili D. Key residues controlling bidirectional ion movements in Na/Ca exchanger. Cell Calcium. 76: 10-22. PMID 30248574 DOI: 10.1016/J.Ceca.2018.09.004  0.56
2018 Dar HH, Tyurina YY, Mikulska-Ruminska K, Shrivastava I, Ting HC, Tyurin VA, Krieger J, St Croix CM, Watkins S, Bayir E, Mao G, Ambruster C, Kapralov A, Wang H, Parsek MH, ... ... Bahar I, et al. Pseudomonas aeruginosa utilizes host polyunsaturated phosphatidylethanolamines to trigger theft-ferroptosis in bronchial epithelium. The Journal of Clinical Investigation. PMID 30198910 DOI: 10.1172/Jci99490  0.8
2018 Ponzoni L, Zhang S, Cheng MH, Bahar I. Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 373. PMID 29735731 DOI: 10.1098/Rstb.2017.0177  0.8
2018 Ponzoni L, Bahar I. Structural dynamics is a determinant of the functional significance of missense variants. Proceedings of the National Academy of Sciences of the United States of America. 115: 4164-4169. PMID 29610305 DOI: 10.1073/Pnas.1715896115  0.56
2018 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. Scientific Reports. 8: 4291. PMID 29511214 DOI: 10.1038/S41598-018-21746-7  0.68
2018 Krieger J, Lee JY, Greger IH, Bahar I. Activation and Desensitization of Ionotropic Glutamate Receptors by Selectively Triggering Pre-existing Motions. Neuroscience Letters. PMID 29481851 DOI: 10.1016/J.Neulet.2018.02.050  0.8
2017 Lee JY, Feng Z, Xie XQ, Bahar I. Allosteric Modulation of Intact γ-Secretase Structural Dynamics. Biophysical Journal. 113: 2634-2649. PMID 29262358 DOI: 10.1016/J.Bpj.2017.10.012  0.68
2017 Pei F, Li H, Henderson MJ, Titus SA, Jadhav A, Simeonov A, Cobanoglu MC, Mousavi SH, Shun T, McDermott L, Iyer P, Fioravanti M, Carlisle D, Friedlander RM, Bahar I, et al. Connecting Neuronal Cell Protective Pathways and Drug Combinations in a Huntington's Disease Model through the Application of Quantitative Systems Pharmacology. Scientific Reports. 7: 17803. PMID 29259176 DOI: 10.1038/S41598-017-17378-Y  0.8
2017 Liu B, Oltvai ZN, Bayır H, Silverman GA, Pak SC, Perlmutter DH, Bahar I. Quantitative assessment of cell fate decision between autophagy and apoptosis. Scientific Reports. 7: 17605. PMID 29242632 DOI: 10.1038/S41598-017-18001-W  0.68
2017 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, et al. Improved Total-Body Irradiation Survival by Delivery of Two Radiation Mitigators that Target Distinct Cell Death Pathways. Radiation Research. PMID 29140165 DOI: 10.1667/Rr14787.1  0.68
2017 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, ... ... Bahar I, et al. PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals. Cell. 171: 628-641.e26. PMID 29053969 DOI: 10.1016/J.Cell.2017.09.044  0.68
2017 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, et al. "Only a life lived for others is worth living:" Redox Signaling by Oxygenated Phospholipids in Cell Fate Decisions. Antioxidants & Redox Signaling. PMID 28835115 DOI: 10.1089/ars.2017.7124  0.68
2017 Mikulska-Ruminska K, Kulik AJ, Benadiba C, Bahar I, Dietler G, Nowak W. Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD. Scientific Reports. 7: 8852. PMID 28821864 DOI: 10.1038/S41598-017-09482-W  0.68
2017 Ma S, Cheng MH, Guthrie DA, Newman AH, Bahar I, Sorkin A. Targeting of dopamine transporter to filopodia requires an outward-facing conformation of the transporter. Scientific Reports. 7: 5399. PMID 28710426 DOI: 10.1038/S41598-017-05637-X  0.56
2017 Li H, Sharma N, General IJ, Schreiber G, Bahar I. Dynamic Modulation of Binding Affinity as a Mechanism for Regulating Interferon Signaling. Journal of Molecular Biology. PMID 28648616 DOI: 10.1016/J.Jmb.2017.06.011  0.8
2017 Cheng MH, Garcia-Olivares J, Wasserman S, DiPietro J, Bahar I. Allosteric Modulation of Human Dopamine Transporter Activity under Conditions Promoting its Dimerization. The Journal of Biological Chemistry. PMID 28584050 DOI: 10.1074/Jbc.M116.763565  0.56
2017 Cheng MH, Torres-Salazar D, Gonzalez-Suarez AD, Amara SG, Bahar I. Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters. Elife. 6. PMID 28569666 DOI: 10.7554/Elife.25850  0.56
2017 Li H, Chang YY, Lee JY, Bahar I, Yang LW. DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Research. PMID 28472330 DOI: 10.1093/Nar/Gkx385  0.88
2017 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 Research. PMID 28334818 DOI: 10.1093/Nar/Gkx172  0.8
2017 Gur M, Cheng MH, Zomot E, Bahar I. Effect of Dimerization on the Dynamics of Neurotransmitter: Sodium Symporters. The Journal of Physical Chemistry. B. PMID 28118712 DOI: 10.1021/Acs.Jpcb.6B09876  0.84
2016 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. PMID 28040451 DOI: 10.1016/J.Ebiom.2016.12.014  0.64
2016 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, ... ... Bahar I, et al. Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nature Chemical Biology. PMID 27842066 DOI: 10.1038/Nchembio.2238  0.68
2016 Kurkcuoglu Z, Bahar I, Doruker P. ClustENM: ENM-based sampling of essential conformational space at full atomic resolution. Journal of Chemical Theory and Computation. PMID 27494296 DOI: 10.1021/Acs.Jctc.6B00319  1
2016 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. Science Signaling. 9: ra70. PMID 27405980 DOI: 10.1126/Scisignal.Aac9340  0.68
2016 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. Journal of Biomolecular Screening. PMID 26962875 DOI: 10.1177/1087057116635818  1
2015 Gur M, Zomot E, Cheng MH, Bahar I. Energy landscape of LeuT from molecular simulations. The Journal of Chemical Physics. 143: 243134. PMID 26723619 DOI: 10.1063/1.4936133  1
2015 Jun I, Cheng MH, Sim E, Jung J, Suh BL, Kim Y, Son H, Park K, Kim CH, Yoon JH, Whitcomb DC, Bahar I, Lee MG. Pore dilation increases the bicarbonate permeability of CFTR, ANO1, and glycine receptor anion channels. The Journal of Physiology. PMID 26663196 DOI: 10.1113/Jp271311  1
2015 Li H, Chang YY, Yang LW, Bahar I. iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Research. PMID 26582920 DOI: 10.1093/Nar/Gkv1236  1
2015 Cheng MH, Bahar I. Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter. Structure (London, England : 1993). 23: 2171-81. PMID 26481814 DOI: 10.1016/J.Str.2015.09.001  1
2015 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. Nature Communications. 6: 8419. PMID 26420673 DOI: 10.1038/Ncomms9419  1
2015 Keskin O, Dyson HJ, Bahar I. Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions. Biophysical Journal. 109: E01-2. PMID 26377787 DOI: 10.1016/J.Bpj.2015.08.005  1
2015 Dutta A, Krieger J, Lee JY, Garcia-Nafria J, Greger IH, Bahar I. Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences. Structure (London, England : 1993). 23: 1692-704. PMID 26256538 DOI: 10.1016/J.Str.2015.07.002  1
2015 Krieger J, Bahar I, Greger IH. Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains. Biophysical Journal. 109: 1136-48. PMID 26255587 DOI: 10.1016/J.Bpj.2015.06.061  1
2015 Bahar I, Cheng MH, Lee JY, Kaya C, Zhang S. Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions. Biophysical Journal. PMID 26143655 DOI: 10.1016/J.Bpj.2015.06.004  1
2015 Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R. The Center for causal discovery of biomedical knowledge from Big Data. Journal of the American Medical Informatics Association : Jamia. PMID 26138794 DOI: 10.1093/Jamia/Ocv059  1
2015 Cheng MH, Block E, Hu F, Cobanoglu MC, Sorkin A, Bahar I. Insights into the Modulation of Dopamine Transporter Function by Amphetamine, Orphenadrine, and Cocaine Binding. Frontiers in Neurology. 6: 134. PMID 26106364 DOI: 10.3389/Fneur.2015.00134  1
2015 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. Molecular Pharmacology. 88: 421-7. PMID 26078313 DOI: 10.1124/Mol.115.097816  1
2015 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 (Oxford, England). 31: 1929-37. PMID 25697822 DOI: 10.1093/Bioinformatics/Btv103  1
2015 Eyal E, Lum G, Bahar I. The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics (Oxford, England). 31: 1487-9. PMID 25568280 DOI: 10.1093/Bioinformatics/Btu847  0.56
2015 Zomot E, Gur M, Bahar I. Microseconds simulations reveal a new sodium-binding site and the mechanism of sodium-coupled substrate uptake by LeuT. The Journal of Biological Chemistry. 290: 544-55. PMID 25381247 DOI: 10.1074/Jbc.M114.617555  1
2015 Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I. BalestraWeb: efficient online evaluation of drug-target interactions. Bioinformatics (Oxford, England). 31: 131-3. PMID 25192741 DOI: 10.1093/Bioinformatics/Btu599  1
2014 Cheng MH, Bahar I. Complete mapping of substrate translocation highlights the role of LeuT N-terminal segment in regulating transport cycle. Plos Computational Biology. 10: e1003879. PMID 25299050 DOI: 10.1371/Journal.Pcbi.1003879  0.56
2014 Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar I. Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies. Scientific Reports. 4: 6245. PMID 25175563 DOI: 10.1038/Srep06245  1
2014 LaRusch J, Jung J, General IJ, Lewis MD, Park HW, Brand RE, Gelrud A, Anderson MA, Banks PA, Conwell D, Lawrence C, Romagnuolo J, Baillie J, Alkaade S, Cote G, ... ... Bahar I, et al. Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis. Plos Genetics. 10: e1004376. PMID 25033378 DOI: 10.1371/Journal.Pgen.1004376  1
2014 Korotchenko VN, Saydmohammed M, Vollmer LL, Bakan A, Sheetz K, Debiec KT, Greene KA, Agliori CS, Bahar I, Day BW, Vogt A, Tsang M. In vivo structure-activity relationship studies support allosteric targeting of a dual specificity phosphatase. Chembiochem : a European Journal of Chemical Biology. 15: 1436-45. PMID 24909879 DOI: 10.1002/Cbic.201402000  1
2014 Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I. Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinformatics (Oxford, England). 30: 2681-3. PMID 24849577 DOI: 10.1093/Bioinformatics/Btu336  1
2014 O'Reilly LP, Long OS, Cobanoglu MC, Benson JA, Luke CJ, Miedel MT, Hale P, Perlmutter DH, Bahar I, Silverman GA, Pak SC. A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of α1-antitrypsin deficiency. Human Molecular Genetics. 23: 5123-32. PMID 24838285 DOI: 10.1093/Hmg/Ddu236  0.4
2014 General IJ, Liu Y, Blackburn ME, Mao W, Gierasch LM, Bahar I. ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones. Plos Computational Biology. 10: e1003624. PMID 24831085 DOI: 10.1371/Journal.Pcbi.1003624  1
2014 Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B. Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. Plos Computational Biology. 10: e1003521. PMID 24699246 DOI: 10.1371/Journal.Pcbi.1003521  1
2014 Jiang J, Bakan A, Kapralov AA, Silva KI, Huang Z, Amoscato AA, Peterson J, Garapati VK, Saxena S, Bayir H, Atkinson J, Bahar I, Kagan VE. Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids. Free Radical Biology & Medicine. 71: 221-30. PMID 24631490 DOI: 10.1016/J.Freeradbiomed.2014.02.029  1
2014 Lui VW, Peyser ND, Ng PK, Hritz J, Zeng Y, Lu Y, Li H, Wang L, Gilbert BR, General IJ, Bahar I, Ju Z, Wang Z, Pendleton KP, Xiao X, et al. Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer. Proceedings of the National Academy of Sciences of the United States of America. 111: 1114-9. PMID 24395800 DOI: 10.1073/Pnas.1319551111  1
2013 Cobanoglu MC, Liu C, Hu F, Oltvai ZN, Bahar I. Predicting drug-target interactions using probabilistic matrix factorization. Journal of Chemical Information and Modeling. 53: 3399-409. PMID 24289468 DOI: 10.1021/Ci400219Z  0.48
2013 Gur M, Madura JD, Bahar I. Global transitions of proteins explored by a multiscale hybrid methodology: application to adenylate kinase. Biophysical Journal. 105: 1643-52. PMID 24094405 DOI: 10.1016/J.Bpj.2013.07.058  1
2013 Gur M, Zomot E, Bahar I. Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions. The Journal of Chemical Physics. 139: 121912. PMID 24089724 DOI: 10.1063/1.4816375  1
2013 Chu CT, Ji J, Dagda RK, Jiang JF, Tyurina YY, Kapralov AA, Tyurin VA, Yanamala N, Shrivastava IH, Mohammadyani D, Qiang Wang KZ, Zhu J, Klein-Seetharaman J, Balasubramanian K, Amoscato AA, ... ... Bahar I, et al. Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells. Nature Cell Biology. 15: 1197-205. PMID 24036476 DOI: 10.1038/Ncb2837  1
2013 Cheng MH, Bahar I. Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT. Biophysical Journal. 105: 630-9. PMID 23931311 DOI: 10.1016/J.Bpj.2013.06.032  0.56
2013 Zomot E, Bahar I. Intracellular gating in an inward-facing state of aspartate transporter Glt(Ph) is regulated by the movements of the helical hairpin HP2. The Journal of Biological Chemistry. 288: 8231-7. PMID 23386619 DOI: 10.1074/Jbc.M112.438432  0.56
2012 Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL. FlexE: Using elastic network models to compare models of protein structure. Journal of Chemical Theory and Computation. 8: 3985-3991. PMID 25530735 DOI: 10.1021/Ct300148F  1
2012 Kurkcuoglu Z, Bakan A, Kocaman D, Bahar I, Doruker P. Coupling between catalytic loop motions and enzyme global dynamics. Plos Computational Biology. 8: e1002705. PMID 23028297 DOI: 10.1371/Journal.Pcbi.1002705  1
2012 Bhatt D, Bahar I. An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates. The Journal of Chemical Physics. 137: 104101. PMID 22979844 DOI: 10.1063/1.4748278  1
2012 Isin B, Tirupula KC, Oltvai ZN, Klein-Seetharaman J, Bahar I. Identification of motions in membrane proteins by elastic network models and their experimental validation. Methods in Molecular Biology (Clifton, N.J.). 914: 285-317. PMID 22976035 DOI: 10.1007/978-1-62703-023-6_17  0.68
2012 Dutta A, Shrivastava IH, Sukumaran M, Greger IH, Bahar I. Comparative dynamics of NMDA- and AMPA-glutamate receptor N-terminal domains. Structure (London, England : 1993). 20: 1838-49. PMID 22959625 DOI: 10.1016/J.Str.2012.08.012  0.96
2012 Zomot E, Bahar I. A conformational switch in a partially unwound helix selectively determines the pathway for substrate release from the carnitine/γ-butyrobetaine antiporter CaiT. The Journal of Biological Chemistry. 287: 31823-32. PMID 22843728 DOI: 10.1074/Jbc.M112.397364  0.56
2012 Bakan A, Nevins N, Lakdawala AS, Bahar I. Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules. Journal of Chemical Theory and Computation. 8: 2435-2447. PMID 22798729 DOI: 10.1016/J.Bpj.2012.11.3081  1
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071  1
2012 Lezon TR, Bahar I. Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter GltPh. Biophysical Journal. 102: 1331-40. PMID 22455916 DOI: 10.1016/J.Bpj.2012.02.028  0.76
2012 Liu Y, Bahar I. Sequence evolution correlates with structural dynamics. Molecular Biology and Evolution. 29: 2253-63. PMID 22427707 DOI: 10.1093/Molbev/Mss097  0.76
2012 Liu L, Byeon IJL, Bahar I, Gronenborn AM. Domain swapping proceeds via complete unfolding: A 19F- and 1H-NMR study of the cyanovirin-N protein Journal of the American Chemical Society. 134: 4229-4235. PMID 22296296 DOI: 10.1021/Ja210118W  1
2012 Liu L, Gronenborn AM, Bahar I. Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion Proteins: Structure, Function and Bioinformatics. 80: 616-625. PMID 22105881 DOI: 10.1002/Prot.23225  1
2011 Eyal E, Dutta A, Bahar I. Cooperative dynamics of proteins unraveled by network models. Wiley Interdisciplinary Reviews. Computational Molecular Science. 1: 426-439. PMID 32148561 DOI: 10.1002/Wcms.44  0.96
2011 Jiang J, Shrivastava IH, Watts SD, Bahar I, Amara SG. Large collective motions regulate the functional properties of glutamate transporter trimers. Proceedings of the National Academy of Sciences of the United States of America. 108: 15141-6. PMID 21876140 DOI: 10.1073/Pnas.1112216108  1
2011 Meireles L, Gur M, Bakan A, Bahar I. Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Protein Science : a Publication of the Protein Society. 20: 1645-58. PMID 21826755 DOI: 10.1002/Pro.711  1
2011 Morel PA, Srinivas M, Turner MS, Fuschiotti P, Munshi R, Bahar I, Feili-Hariri M, Ahrens ET. Gene expression analysis of dendritic cells that prevent diabetes in NOD mice: analysis of chemokines and costimulatory molecules. Journal of Leukocyte Biology. 90: 539-50. PMID 21628331 DOI: 10.1189/Jlb.0311126  1
2011 Zomot E, Bahar I. Protonation of glutamate 208 induces the release of agmatine in an outward-facing conformation of an arginine/agmatine antiporter. The Journal of Biological Chemistry. 286: 19693-701. PMID 21487006 DOI: 10.1074/Jbc.M110.202085  0.56
2011 Bakan A, Meireles LM, Bahar I. ProDy: protein dynamics inferred from theory and experiments. Bioinformatics (Oxford, England). 27: 1575-7. PMID 21471012 DOI: 10.1093/Bioinformatics/Btr168  1
2011 Mustata G, Li M, Zevola N, Bakan A, Zhang L, Epperly M, Greenberger JS, Yu J, Bahar I. Development of small-molecule PUMA inhibitors for mitigating radiation-induced cell death. Current Topics in Medicinal Chemistry. 11: 281-90. PMID 21320058 DOI: 10.2174/156802611794072641  1
2011 Sukumaran M, Rossmann M, Shrivastava I, Dutta A, Bahar I, Greger IH. Dynamics and allosteric potential of the AMPA receptor N-terminal domain. The Embo Journal. 30: 972-82. PMID 21317871 DOI: 10.1038/Emboj.2011.17  0.96
2011 DeChancie J, Shrivastava IH, Bahar I. The mechanism of substrate release by the aspartate transporter GltPh: insights from simulations. Molecular Biosystems. 7: 832-42. PMID 21161089 DOI: 10.1039/C0Mb00175A  0.64
2011 Bakan A, Bahar I. Computational generation inhibitor-bound conformers of p38 MAP kinase and comparison with experiments. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 181-92. PMID 21121046  1
2011 Zomot E, Bakan A, Shrivastava IH, De Chancie J, Lezon TR, Bahar I. Sodium-coupled secondary transporters: Insights from structure-based computations Molecular Machines. 199-230. DOI: 10.1142/9789814343466_0011  1
2010 Liu Y, Gierasch LM, Bahar I. Role of Hsp70 ATPase domain intrinsic dynamics and sequence evolution in enabling its functional interactions with NEFs. Plos Computational Biology. 6. PMID 20862304 DOI: 10.1371/Journal.Pcbi.1000931  1
2010 Dutta A, Bahar I. Metal-binding sites are designed to achieve optimal mechanical and signaling properties. Structure (London, England : 1993). 18: 1140-8. PMID 20826340 DOI: 10.1016/J.Str.2010.06.013  0.96
2010 Lezon TR, Bahar I. Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology. Plos Computational Biology. 6: e1000816. PMID 20585542 DOI: 10.1371/Journal.Pcbi.1000816  0.76
2010 Zomot E, Bahar I. The sodium/galactose symporter crystal structure is a dynamic, not so occluded state. Molecular Biosystems. 6: 1040-6. PMID 20358053 DOI: 10.1039/B927492H  0.56
2010 Bahar I, Lezon TR, Yang LW, Eyal E. Global dynamics of proteins: bridging between structure and function. Annual Review of Biophysics. 39: 23-42. PMID 20192781 DOI: 10.1146/Annurev.Biophys.093008.131258  1
2010 Liu Y, Bahar I. Toward understanding allosteric signaling mechanisms in the ATPase domain of molecular chaperones. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 269-80. PMID 19908379 DOI: 10.1142/9789814295291_0029  0.76
2010 Bahar I, Lezon TR, Bakan A, Shrivastava IH. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chemical Reviews. 110: 1463-97. PMID 19785456 DOI: 10.1021/Cr900095E  1
2009 Lezon TR, Sali A, Bahar I. Global motions of the nuclear pore complex: insights from elastic network models. Plos Computational Biology. 5: e1000496. PMID 19730674 DOI: 10.1371/Journal.Pcbi.1000496  0.76
2009 Bakan A, Bahar I. The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proceedings of the National Academy of Sciences of the United States of America. 106: 14349-54. PMID 19706521 DOI: 10.1073/Pnas.0904214106  1
2009 Liu L, Koharudin LMI, Gronenborn AM, Bahar I. A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations Proteins: Structure, Function and Bioinformatics. 77: 927-939. PMID 19688820 DOI: 10.1002/Prot.22518  1
2009 Molina G, Vogt A, Bakan A, Dai W, Queiroz de Oliveira P, Znosko W, Smithgall TE, Bahar I, Lazo JS, Day BW, Tsang M. Zebrafish chemical screening reveals an inhibitor of Dusp6 that expands cardiac cell lineages. Nature Chemical Biology. 5: 680-7. PMID 19578332 DOI: 10.1038/Nchembio.190  1
2009 Yang Z, Bahar I, Widom M. Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity. Biophysical Journal. 96: 4438-48. PMID 19486668 DOI: 10.1016/J.Bpj.2009.03.016  1
2009 Yang Z, Májek P, Bahar I. Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL. Plos Computational Biology. 5: e1000360. PMID 19381265 DOI: 10.1371/Journal.Pcbi.1000360  0.64
2009 Mustata G, Follis AV, Hammoudeh DI, Metallo SJ, Wang H, Prochownik EV, Lazo JS, Bahar I. Discovery of novel Myc-Max heterodimer disruptors with a three-dimensional pharmacophore model. Journal of Medicinal Chemistry. 52: 1247-50. PMID 19215087 DOI: 10.1021/Jm801278G  1
2009 Gu Y, Shrivastava IH, Amara SG, Bahar I. Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter. Proceedings of the National Academy of Sciences of the United States of America. 106: 2589-94. PMID 19202063 DOI: 10.1073/Pnas.0812299106  1
2009 Yang LW, Eyal E, Bahar I, Kitao A. Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Bioinformatics (Oxford, England). 25: 606-14. PMID 19147661 DOI: 10.1093/Bioinformatics/Btp023  1
2008 Bakan A, Lazo JS, Wipf P, Brummond KM, Bahar I. Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening. Current Medicinal Chemistry. 15: 2536-44. PMID 18855677 DOI: 10.2174/092986708785909003  1
2008 Shrivastava IH, Jiang J, Amara SG, Bahar I. Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter. The Journal of Biological Chemistry. 283: 28680-90. PMID 18678877 DOI: 10.1074/Jbc.M800889200  1
2008 Engen JR, Wales TE, Hochrein JM, Meyn MA, Banu Ozkan S, Bahar I, Smithgall TE. Structure and dynamic regulation of Src-family kinases. Cellular and Molecular Life Sciences : Cmls. 65: 3058-73. PMID 18563293 DOI: 10.1007/S00018-008-8122-2  1
2008 Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. Computational insights on the competing effects of nitric oxide in regulating apoptosis. Plos One. 3: e2249. PMID 18509469 DOI: 10.1371/Journal.Pone.0002249  1
2008 Isin B, Schulten K, Tajkhorshid E, Bahar I. Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes. Biophysical Journal. 95: 789-803. PMID 18390613 DOI: 10.1529/Biophysj.107.120691  0.68
2008 Liu Y, Eyal E, Bahar I. Analysis of correlated mutations in HIV-1 protease using spectral clustering. Bioinformatics (Oxford, England). 24: 1243-50. PMID 18375964 DOI: 10.1093/Bioinformatics/Btn110  0.76
2008 Chennubhotla C, Yang Z, Bahar I. Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL. Molecular Biosystems. 4: 287-92. PMID 18354781 DOI: 10.1039/B717819K  0.76
2008 Eyal E, Bahar I. Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models. Biophysical Journal. 94: 3424-35. PMID 18223005 DOI: 10.1529/Biophysj.107.120733  0.56
2007 Bahar I, Chennubhotla C, Tobi D. Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Current Opinion in Structural Biology. 17: 633-40. PMID 18024008 DOI: 10.1016/J.Sbi.2007.09.011  0.76
2007 Chennubhotla C, Bahar I. Signal propagation in proteins and relation to equilibrium fluctuations. Plos Computational Biology. 3: 1716-26. PMID 17892319 DOI: 10.1371/Journal.Pcbi.0030172  0.76
2007 Chennubhotla C, Bahar I. Markov methods for hierarchical coarse-graining of large protein dynamics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 765-76. PMID 17691893 DOI: 10.1089/Cmb.2007.R015  0.76
2007 Eyal E, Chennubhotla C, Yang LW, Bahar I. Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Bioinformatics (Oxford, England). 23: i175-84. PMID 17646294 DOI: 10.1093/bioinformatics/btm186  1
2007 Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I. Insights into Equilibrium Dynamics of Proteins from Comparison of NMR and X-Ray Data with Computational Predictions Structure. 15: 741-749. PMID 17562320 DOI: 10.1016/J.Str.2007.04.014  1
2007 Lazo JS, Skoko JJ, Werner S, Mitasev B, Bakan A, Koizumi F, Yellow-Duke A, Bahar I, Brummond KM. Structurally unique inhibitors of human mitogen-activated protein kinase phosphatase-1 identified in a pyrrole carboxamide library. The Journal of Pharmacology and Experimental Therapeutics. 322: 940-7. PMID 17538006 DOI: 10.1124/Jpet.107.122242  1
2007 Vries JK, Liu X, Bahar I. The relationship between n-gram patterns and protein secondary structure. Proteins. 68: 830-8. PMID 17523186 DOI: 10.1002/Prot.21480  0.8
2007 Eyal E, Pietrokovski S, Bahar I. Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices. Bioinformatics (Oxford, England). 23: 1837-9. PMID 17496318 DOI: 10.1093/Bioinformatics/Btm256  0.56
2007 Iyer AK, Tran KT, Borysenko CW, Cascio M, Camacho CJ, Blair HC, Bahar I, Wells A. Tenascin cytotactin epidermal growth factor-like repeat binds epidermal growth factor receptor with low affinity. Journal of Cellular Physiology. 211: 748-58. PMID 17311283 DOI: 10.1002/Jcp.20986  1
2006 Farkas IJ, Wu C, Chennubhotla C, Bahar I, Oltvai ZN. Topological basis of signal integration in the transcriptional-regulatory network of the yeast, Saccharomyces cerevisiae. Bmc Bioinformatics. 7: 478. PMID 17069658 DOI: 10.1186/1471-2105-7-478  0.76
2006 Isin B, Rader AJ, Dhiman HK, Klein-Seetharaman J, Bahar I. Predisposition of the dark state of rhodopsin to functional changes in structure. Proteins. 65: 970-83. PMID 17009319 DOI: 10.1002/Prot.21158  1
2006 Eyal E, Yang LW, Bahar I. Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics (Oxford, England). 22: 2619-27. PMID 16928735 DOI: 10.1093/Bioinformatics/Btl448  1
2006 Yang LW, Rader AJ, Liu X, Jursa CJ, Chen SC, Karimi HA, Bahar I. oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Research. 34: W24-31. PMID 16845002 DOI: 10.1093/Nar/Gkl084  1
2006 Chennubhotla C, Bahar I. Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Molecular Systems Biology. 2: 36. PMID 16820777 DOI: 10.1038/Msb4100075  0.76
2006 Shrivastava IH, Bahar I. Common mechanism of pore opening shared by five different potassium channels. Biophysical Journal. 90: 3929-40. PMID 16533848 DOI: 10.1529/Biophysj.105.080093  0.64
2006 Munshi R, Coalson RD, Ermentrout GB, Madura JD, Meirovitch H, Stiles JR, Bahar I. An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research. Biotechnology Progress. 22: 179-85. PMID 16454509 DOI: 10.1021/Bp0501773  1
2006 Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout GB, Bahar I. Bistability in apoptosis: roles of bax, bcl-2, and mitochondrial permeability transition pores. Biophysical Journal. 90: 1546-59. PMID 16339882 DOI: 10.1529/Biophysj.105.068122  1
2005 Berberich JA, Yang LW, Bahar I, Russell AJ. A stable three enzyme creatinine biosensor. 2. Analysis of the impact of silver ions on creatine amidinohydrolase. Acta Biomaterialia. 1: 183-91. PMID 16701795 DOI: 10.1016/J.Actbio.2004.11.007  1
2005 Berberich JA, Yang LW, Madura J, Bahar I, Russell AJ. A stable three-enzyme creatinine biosensor. 1. Impact of structure, function and environment on PEGylated and immobilized sarcosine oxidase. Acta Biomaterialia. 1: 173-81. PMID 16701794 DOI: 10.1016/J.Actbio.2004.11.006  1
2005 Chennubhotla C, Rader AJ, Yang LW, Bahar I. Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies. Physical Biology. 2: S173-80. PMID 16280623 DOI: 10.1088/1478-3975/2/4/S12  1
2005 Bahar I, Rader AJ. Coarse-grained normal mode analysis in structural biology. Current Opinion in Structural Biology. 15: 586-92. PMID 16143512 DOI: 10.1016/J.Sbi.2005.08.007  1
2005 Yang LW, Bahar I. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure (London, England : 1993). 13: 893-904. PMID 15939021 DOI: 10.1016/J.Str.2005.03.015  1
2005 Yang LW, Liu X, Jursa CJ, Holliman M, Rader AJ, Karimi HA, Bahar I. iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics (Oxford, England). 21: 2978-87. PMID 15860562 DOI: 10.1093/Bioinformatics/Bti469  1
2005 Rader AJ, Vlad DH, Bahar I. Maturation dynamics of bacteriophage HK97 capsid. Structure (London, England : 1993). 13: 413-21. PMID 15766543 DOI: 10.1016/J.Str.2004.12.015  1
2005 Ramaswamy A, Bahar I, Ioshikhes I. Structural dynamics of nucleosome core particle: comparison with nucleosomes containing histone variants. Proteins. 58: 683-96. PMID 15624215 DOI: 10.1002/Prot.20357  1
2004 Vries JK, Munshi R, Tobi D, Klein-Seetharaman J, Benos PV, Bahar I. A sequence alignment-independent method for protein classification. Applied Bioinformatics. 3: 137-48. PMID 15693739 DOI: 10.2165/00822942-200403020-00008  1
2004 Vodovotz Y, Kim PK, Bagci EZ, Ermentrout GB, Chow CC, Bahar I, Billiar TR. Inflammatory modulation of hepatocyte apoptosis by nitric oxide: in vivo, in vitro, and in silico studies. Current Molecular Medicine. 4: 753-62. PMID 15579022 DOI: 10.2174/1566524043359944  1
2004 Sluis-Cremer N, Temiz NA, Bahar I. Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding. Current Hiv Research. 2: 323-32. PMID 15544453 DOI: 10.2174/1570162043351093  1
2004 Seki M, Masutani C, Yang LW, Schuffert A, Iwai S, Bahar I, Wood RD. High-efficiency bypass of DNA damage by human DNA polymerase Q. The Embo Journal. 23: 4484-94. PMID 15496986 DOI: 10.1038/Sj.Emboj.7600424  0.88
2004 Wang Y, Rader AJ, Bahar I, Jernigan RL. Global ribosome motions revealed with elastic network model. Journal of Structural Biology. 147: 302-14. PMID 15450299 DOI: 10.1016/J.Jsb.2004.01.005  1
2004 Temiz NA, Meirovitch E, Bahar I. Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data. Proteins. 57: 468-80. PMID 15382240 DOI: 10.1002/Prot.20226  1
2004 Chen SC, Bahar I. Mining frequent patterns in protein structures: a study of protease families. Bioinformatics (Oxford, England). 20: i77-85. PMID 15262784 DOI: 10.1093/bioinformatics/bth912  0.92
2004 Brisson M, Nguyen T, Vogt A, Yalowich J, Giorgianni A, Tobi D, Bahar I, Stephenson CR, Wipf P, Lazo JS. Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase. Molecular Pharmacology. 66: 824-33. PMID 15231869 DOI: 10.1124/Mol.104.001784  1
2004 Rader AJ, Anderson G, Isin B, Khorana HG, Bahar I, Klein-Seetharaman J. Identification of core amino acids stabilizing rhodopsin. Proceedings of the National Academy of Sciences of the United States of America. 101: 7246-51. PMID 15123809 DOI: 10.1073/Pnas.0401429101  1
2004 Liu X, Karimi HA, Yang LW, Bahar I. Protein functional motion query and visualization Proceedings - International Computer Software and Applications Conference. 2: 86-89. DOI: 10.1109/CMPSAC.2004.1342683  1
2004 Rader AJ, Bahar I. Folding core predictions from network models of proteins Polymer. 45: 659-668. DOI: 10.1016/J.Polymer.2003.10.080  1
2003 Bagci Z, Kloczkowski A, Jernigan RL, Bahar I. The origin and extent of coarse-grained regularities in protein internal packing. Proteins. 53: 56-67. PMID 12945049 DOI: 10.1002/Prot.10435  1
2003 Ozkan SB, Dill KA, Bahar I. Computing the transition state populations in simple protein models. Biopolymers. 68: 35-46. PMID 12579578 DOI: 10.1002/Bip.10280  1
2002 Temiz NA, Bahar I. Inhibitor binding alters the directions of domain motions in HIV-1 reverse transcriptase. Proteins. 49: 61-70. PMID 12211016 DOI: 10.1002/Prot.10183  1
2002 Ozkan SB, Dill KA, Bahar I. Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Protein Science : a Publication of the Protein Society. 11: 1958-70. PMID 12142450 DOI: 10.1110/Ps.0207102  1
2002 Keskin O, Durell SR, Bahar I, Jernigan RL, Covell DG. Relating molecular flexibility to function: a case study of tubulin. Biophysical Journal. 83: 663-80. PMID 12124255 DOI: 10.1016/S0006-3495(02)75199-0  1
2002 Doruker P, Jernigan RL, Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. Journal of Computational Chemistry. 23: 119-27. PMID 11913377 DOI: 10.1002/Jcc.1160  1
2002 Isin B, Doruker P, Bahar I. Functional motions of influenza virus hemagglutinin: a structure-based analytical approach. Biophysical Journal. 82: 569-81. PMID 11806902 DOI: 10.1016/S0006-3495(02)75422-2  1
2002 Keskin O, Bahar I, Flatow D, Covell DG, Jernigan RL. Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry. 41: 491-501. PMID 11781087 DOI: 10.1021/Bi011393X  0.48
2001 Ozkan SB, Bahar I, Dill KA. Transition states and the meaning of Phi-values in protein folding kinetics. Nature Structural Biology. 8: 765-9. PMID 11524678 DOI: 10.1038/Nsb0901-765  1
2001 Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophysical Journal. 80: 505-15. PMID 11159421 DOI: 10.1016/S0006-3495(01)76033-X  1
2000 Keskin O, Jernigan RL, Bahar I. Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophysical Journal. 78: 2093-106. PMID 10733987 DOI: 10.1016/S0006-3495(00)76756-7  0.68
1999 Bahar I, Jernigan RL. Cooperative fluctuations and subunit communication in tryptophan synthase. Biochemistry. 38: 3478-90. PMID 10090734 DOI: 10.1021/Bi982697V  0.52
1999 Keskin O, Bahar I. Packing of sidechains in low-resolution models for proteins. Folding & Design. 3: 469-79. PMID 9889162 DOI: 10.1016/S1359-0278(98)00064-9  0.4
1999 Bahar I, Erman B, Jernigan RL, Atilgan AR, Covell DG. Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. Journal of Molecular Biology. 285: 1023-37. PMID 9887265 DOI: 10.1006/Jmbi.1998.2371  0.56
1999 Keskin O, Bahar I, Badretdinov AY, Ptitsyn OB, Jernigan RL. Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Science : a Publication of the Protein Society. 7: 2578-86. PMID 9865952 DOI: 10.1002/Pro.5560071211  0.56
1999 Sen TZ, Bahar I, Erman B, Lauprêtre F, Monnerie L. Local dynamics of cis-1,4-polybutadiene and cis-1,4-polyisoprene. A comparative study based on cooperative kinematics theory and NMR experiments Macromolecules. 32: 3017-3024. DOI: 10.1021/Ma9811167  1
1999 Jernigan RL, Demirel MC, Bahar I. Relating Structure to Function Through the Dominant Slow Modes of Motion of DNA Topoisomerase II International Journal of Quantum Chemistry. 75: 301-312. DOI: 10.1002/(Sici)1097-461X(1999)75:3<301::Aid-Qua19>3.0.Co;2-0  1
1998 Demirel MC, Atilgan AR, Jernigan RL, Erman B, Bahar I. Identification of kinetically hot residues in proteins. Protein Science : a Publication of the Protein Society. 7: 2522-32. PMID 9865946 DOI: 10.1002/Pro.5560071205  1
1998 Lustig B, Bahar I, Jernigan RL. RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access. Nucleic Acids Research. 26: 5212-7. PMID 9801321 DOI: 10.1093/Nar/26.22.5212  1
1998 Bahar I, Jernigan RL. Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms. Journal of Molecular Biology. 281: 871-84. PMID 9719641 DOI: 10.1006/Jmbi.1998.1978  0.52
1998 Bahar I, Kaplan M, Jernigan RL. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins. 29: 292-308. PMID 9365985 DOI: 10.1002/(Sici)1097-0134(199711)29:3<292::Aid-Prot4>3.0.Co;2-D  0.36
1998 Bahar I, Atilgan AR, Demirel MC, Erman B. Vibrational dynamics of folded proteins: Significance of slow and fast motions in relation to function and stability Physical Review Letters. 80: 2733-2736. DOI: 10.1103/Physrevlett.80.2733  1
1997 Bahar I, Erman B, Haliloglu T, Jernigan RL. Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations. Biochemistry. 36: 13512-23. PMID 9354619 DOI: 10.1021/Bi971611F  0.52
1997 Bahar I, Atilgan AR, Jernigan RL, Erman B. Understanding the recognition of protein structural classes by amino acid composition. Proteins. 29: 172-85. PMID 9329082 DOI: 10.1002/(Sici)1097-0134(199710)29:2<172::Aid-Prot5>3.0.Co;2-F  0.56
1997 Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding & Design. 2: 173-81. PMID 9218955 DOI: 10.1016/S1359-0278(97)00024-2  0.44
1997 Doruker P, Bahar I. Role of water on unfolding kinetics of helical peptides studied by molecular dynamics simulations. Biophysical Journal. 72: 2445-56. PMID 9168021 DOI: 10.1016/S0006-3495(97)78889-1  0.4
1997 Bahar I, Jernigan RL. Coordination geometry of nonbonded residues in globular proteins. Folding & Design. 1: 357-70. PMID 9080182 DOI: 10.1016/S1359-0278(96)00051-X  0.52
1997 Bahar I, Jernigan RL. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. Journal of Molecular Biology. 266: 195-214. PMID 9054980 DOI: 10.1006/Jmbi.1996.0758  0.44
1997 Baysal C, Erman B, Bahar I, Lauprêtre F, Monnerie L. Local dynamics of bulk polybutadienes of various microstructures: Comparison of theory with NMR measurements Macromolecules. 30: 2058-2066. DOI: 10.1021/Ma9604707  1
1996 Jernigan RL, Bahar I. Structure-derived potentials and protein simulations. Current Opinion in Structural Biology. 6: 195-209. PMID 8728652 DOI: 10.1016/S0959-440X(96)80075-3  0.52
1995 Besbes S, Bokobza L, Monnerie L, Bahar I, Erman B. Molecular orientation in deformed bimodal networks. 2. Fourier transform infrared measurements on poly(dimethylsiloxane) networks and comparison with theory Macromolecules. 28: 231-235. DOI: 10.5072/Zenodo.20262  1
1994 Bahar I, Jernigan RL. Cooperative structural transitions induced by non-homogeneous intramolecular interactions in compact globular proteins. Biophysical Journal. 66: 467-81. PMID 8161700 DOI: 10.1016/S0006-3495(94)80798-2  0.64
1994 Bahar I, Jernigan RL. Stabilization of intermediate density states in globular proteins by homogeneous intramolecular attractive interactions. Biophysical Journal. 66: 454-66. PMID 8161699 DOI: 10.1016/S0006-3495(94)80797-0  0.52
1993 Bokobza L, Besbes S, Monnerie L, Bahar I, Erman B. Segmental orientation in model networks of poly(dimethylsiloxane): Fourier transform infrared dichroism measurements and theoretical interpretation Polymeric Materials Science and Engineering, Proceedings of the Acs Division of Polymeric Materials Science and Engineering. 68: 272. DOI: 10.1021/Ma00033A018  1
1993 Besbes S, Bokobza L, Monnerie L, Bahar I, Erman B. An infra-red dichroism investigation of segmental orientation in dry and swollen poly(dimethylsiloxane) networks Polymer. 34: 1179-1182. DOI: 10.1016/0032-3861(93)90769-7  1
1993 Erman B, Bahar I, Besbes S, Bokobza L, Monnerie L. Interpretation of segmental orientation in deformed networks in terms of constrained junction model of rubber elasticity Polymer. 34: 1858-1864. DOI: 10.1016/0032-3861(93)90427-C  1
1992 Akcasu AZ, Erman B, Bahar I. Nonlinear kinetics of spinodal decomposition, and dissolution of inhomogeneities formed by spinodal decomposition in polymer blends Makromolekulare Chemie. Macromolecular Symposia. 62: 43-60. DOI: 10.1002/Masy.19920620107  0.32
1990 Bahar I, Erman B, Monnerie L. Effect of surrounding medium on intramolecular conformational changes in probe molecules Macromolecules. 23: 3805-3811. DOI: 10.1021/Ma00218A015  1
1990 Bahar I, Erman B, Monnerie L. Local orientational motions in flexible polymeric chains Macromolecules. 23: 1174-1180. DOI: 10.1021/Ma00206A041  1
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