Publications
List of publications that acknowledged the NIGMS MMBioS award P41GM103712.
Google Scholar Publication List
2021 2020 2019 2018 2017 2016 2015 2014 2013
2021
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Sutkeviciuta I, Lee JY, White AD, Maria CS, Peña KA, Savransky S, Doruker P, Li H, Lei S, Kaynak B, Tu C, Clark LJ, Sanker S, Gardella TJ, Chang W, Bahar I* and Vilardaga JP*. (2021) Precise druggability of the PTH type 1 receptor. Nature Chem Biol. [Online ahead of print]. TRD1
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Kaynak BT, Zhang S, Bahar I, Doruker P (2021) ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution. Bioinformatics. TRD1
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Mikulska-Ruminska K, Anthonymuthu TS, Levkina A, Shrivastava IH, Kapralov AA, Bayir H, Kagan VE, Bahar I. (2021) NO● Represses the Oxygenation of Arachidonoyl PE by 15LOX/PEBP1: Mechanism and Role in Ferroptosis. Int J Mol Sci. 22(10): 5253. TRD1
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Aggarwal J, Cheng MH, Salvino JM, Bahar I, Mortensen OV. (2021) Functional Characterization of the Dopaminergic Psychostimulant Sydnocarb as an Allosteric Modulator of the Human Dopamine Transporter. Biomedicines, 9(6), 634; https://doi.org/10.3390/biomedicines9060634. TRD1
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Aguilar JI, Cheng MH, Font J, Schwartz AC, Ledwitch K, Duran A, Mabry SJ, Belovich AN, Zhu Y, Carter AM, Shi L, Kurian MA, Fenollar-Ferrer C, Meiler J, Ryan RM, Mchaourab HS, Bahar I, Matthies HJG, Galli A. (2021) Psychomotor impairments and therapeutic implications revealed by a mutation associated with infantile Parkinsonism-Dystonia. ELife, 10, e68039 TRD1
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Chen F, Shi Q, Pei F, Vogt A, Porritt RA, Garcia Jr G, Gomez A, Cheng MH, Schurdak M, Liu B, Chan S, Arumugaswami V, Stern AM, Taylor DL, Arditi M, Bahar I. (2021) A systems-level study reveals host-targeted repurposable drugs against SARS-CoV-2 infection. Molecular Systems Biology, 17:e10239. TRD1
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Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I. (2021) ProDy 2.0: Increased Scale and Scope after 10 Years of Protein Dynamics Modelling with Python. Bioinformatics [Online ahead of print]. TRD1
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Pei F, Shi Q, Zhang H, Bahar I (2021) Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. J Chem Inf Model. TRD1
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Sorkina T, Cheng MH, Bagalkot TR, Wallace C, Watkins SC, Bahar I, Sorkin A. (2021) Direct coupling of oligomerization and oligomerization-driven endocytosis of the dopamine transporter to its conformational mechanics and activity. J Biol Chem. Feb 18:100430. TRD1 DBP3
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Zhou B, Yu H, Zeng X, Yang X, Zhang J, Xu M. (2021) One-Shot Learning With Attention-Guided Segmentation in Cryo-Electron Tomography. Front Mol Biosci. 7:613347. TRD4
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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, Beharier O, Mao GW, Dar HH, Kapralov AA, Amoscato AA, Hastings TG, Greenamyre TJ, Chu CT, Sadovsky Y, Bahar I, Bayır H, Tyurina YY, He RR, Kagan VE. (2021) Phospholipase iPLA2β averts ferroptosis by eliminating a redox lipid death signal. Nat Chem Biol. 2021 Feb 4. TRD1 CSP
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Li J, Shen R, Reddy B, Perozo E, Roux B. (2021) Mechanism of C-type inactivation in the hERG potassium channel. Sci Adv. 7(5):eabd6203. CSP
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Cheng MH, Krieger JM, Kaynak B, Arditi M, Bahar I. (2021) Impact of South African 501.V2 Variant on SARS-CoV-2 Spike Infectivity and Neutralization: A Structure-based Computational Assessment. BioRxiv [Online ahead of print] . TRD1
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Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T (2021) HiDeF: Identifying Persistent Structures in Multiscale ‘Omics Data. Genome Biol. 22: 21. TRD1
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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, Crother TR, Arditi M (2021) Recruitment of pro-IL-1a to Mitochondrial Cardiolipin, via Shared LC3 Binding Domain, Inhibits Mitophagy and Drives Maximal NLRP3 Activation. Proc Natl Acad Sci USA 118 (1) e2015632118. TRD1
2020
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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. (2020) Identification of a unique TCR repertoire, consistent with a superantigen selection process in Children with Multi-system Inflammatory Syndrome. bioRxiv 2020.11.09.372169. TRD1 CSP
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Zhou Z, Huang F, Shrivastava IH, Zhu R, Luo A, Hottiger M, Bahar I, Liu Z, Cristofanilli M, Wan Y (2020) New Insight into the Significance of KLF4 PARylation in Genome Stability, Carcinogenesis, and Therapy. EMBO Molecular Medicine, e12391. [Online ahead of print].TRD1
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Wingert B, Krieger JM, Li H, Bahar I (2020) Adaptability and Specificity: How Do Proteins Balance Opposing Needs to Achieve Function? Curr Opin Struct Biol 67:25-32. TRD1
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Li R, Yu L, Zhou B, Zeng X, Wang Z, Yang X, Zhang J, Gao X, Jiang R, Xu M. (2020) Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms. PLoS Comput Biol 16(11):e1008227. TRD4
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Rivas MN, Porritt RA, Cheng MH, Bahar I, Arditi M. (2020) COVID-19 Associated Multisystem Inflammatory Syndrome in Children (MIS-C): A Novel Disease that Mimics Toxic Shock Syndrome. The Superantigen Hypothesis. J Allergy Clin Immunol. S0091-6749: 31414-7. TRD1
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Anthonymuthu TS, Tyurina YY, Sun WY, Mikulska-Ruminska K, Shrivastava IH, Tyurin VA, Cinemre FB, Dar HH, VanDemark AP, Holman TR, Sadovsky YS, Stockwell BR, He RR, Bahar I, Bayir H, Kagan VE. (2020) 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 Biol. 38: 101744. TRD1
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Srivastava A, Malik L, Sarkar H, Zakeri M, Almodaresi F, Soneson C, Love MI, Kingsford C, Patro R. (2020) Alignment and mapping methodology influence transcript abundance estimation. Genome Biol 21(1):239. TRD1
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Song X, Zhou Z, Li H, Xue Y, Lu X, Bahar I, Kepp O, Hung MC, Kroemer G, and WanY (2020) Pharmacological suppression of B7-H4 glycosylation restores antitumor immunity in immune-cold breast cancers. Cancer Discovery 10(12):1872-1893.
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Zhang Y, Krieger JM, Mikulska-Ruminska K, Kaynak B, Sorzano COS, Carazo JM, Xing J, Bahar I (2020) State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps. Prog Biophys Mol Biol S0079-6107(20)30082-1.
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Yang Y, Ma Y, Zhang J, Gao X, Xu M. (2020) AttPNet: Attention-Based Deep Neural Network for 3D Point Set Analysis. Sensors (Basel) 20(19):5455. TRD4
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Cheng MH, Zhang S, Porritt RA, Noval Rivas M, Paschold L, Willscher E, Binder M, Arditi M, Bahar I. (2020) Superantigenic character of an insert unique to SARS-CoV-2 spike supported by skewed TCR repertoire in patients with hyperinflammation. Proc Natl Acad Sci USA 117(41):25254-25262. TRD1 CSP
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Shin DH, Kim M, Kim Y, Jun I, Jung J, Nam JH, Cheng MH, Lee MG. (2020) Bicarbonate permeation through anion channels: its role in health and disease. Pflugers Arch. 472(8):1003-1018. TRD1
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Zheng Y, Wang H, Zhang Y, Gao X, Xing EP, Xu M. (2020) Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species. PLoS Comput Biol 16(11):e1008297. TRD4 CSP
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Krieger JM, Doruker P, Scott AL, Perahia D, Bahar I. (2020) Towards Gaining Sight of Multiscale Events: Utilizing Network Models and Normal Modes in Hybrid Methods. Curr Opin Struct Biol [in press]. TRD1
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Zhang Y, Doruker P, Kaynak B, Zhang S, Krieger J, Li H, and Bahar I. (2020) Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior. Curr Opin Struct Biol. 62:14-21. PMID: 31785465 TRD1
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Ordyan M, Bartol T, Kennedy M, Rangamani P, Sejnowski T. (2020) Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator. PLoS Comput Biol 17;16(7):e1008015. TRD2 DBP2
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Li F, Shrivastava IH, Hanlon P, Dagda RK, Gasanoff ES. (2020) Molecular Mechanism by which Cobra Venom Cardiotoxins Interact with the Outer Mitochondrial Membrane. Toxins Jun 27; 12(7):42
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Liu S, Ban X, Zeng X, Zhao F, Gao Y, Wu W, Zhang H, Chen F, Hall T, Gao X, Xu M. (2020) A unified framework for packing deformable and non-deformable subcellular structures in crowded cryo-electron tomogram simulation. BMC Bioinformatics 21(1):399. TRD4
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Goncalves J, Bartol TM, Camus C, Levet F, Menegolla AP, Sejnowski TJ, Sibarita JB, Vivaudou M, Choquet D, Hosy E. (2020) Nanoscale Co-organization and Co-activation of AMPAR, NMDAR and mGluR at Excitatory Synapses. Proc Natl Acad Sci USA, Jun 23; . TRD2
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Zhang F, Meier-Schellersheim M. (2020) SBML Level 3 Package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 2. J. Integr. Bioinform., p. [in press], 2020. TRD3
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Clark LJ, Krieger JM, 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*, Jean-Pierre Vilardaga*. (2020) Allosteric Interactions in the Parathyroid Hormone GPCR–arrestin Complex Formation. Nat Chem Biol [in press]. TRD1
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Yao L, Wells M, Wu X, Xu Y, Zhang L, Xiong W. (2020) Membrane cholesterol dependence of cannabinoid modulation of glycine receptor. FASEB J 34(8):10920-10930 CSP
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Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. (2020) SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol 16(8):e9110 TRD3
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Ambler R, Edmunds GL, Toti G, Morgan DL, Wülfing C. (2020) PD-1 Suppresses the Maintenance of Cell Couples Between Cytotoxic T cells and Tumor Target Cells within the Tumor. Science Signaling, 2020. [in press]. https://doi.org/10.1101/443788. TRD4
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Zhang F, Smith LP, Blinov ML, Faeder J, Hlavacek WS, Juan Tapia J, Keating SM, Rodriguez N, Dräger A, Harris LA, Finney A, Hu B, Hucka M, Meier-Schellersheim M. (2020) Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. J Integr Bioinform. 17(2-3):20200015. TRD3 CSP
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Li H, Pei F, Taylor DL, Bahar I. (2020) QuartataWeb: Integrated Chemical-Protein-Pathway Mapping for Polypharmacology and Chemogenomics. Bioinformatics 36(12):3935-3937. TRD1
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Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. (2020) Decoding of persistent multiscale structures in complex biological networks. BioRxiv 2020.06.16.151555 TRD1 CSP
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Wang F, An G, Becker A, Cockrell C, Collier N, Craig M, Davis CL, Faeder JR, Ford Versypt AN, Gianlupi JF, Glazier JA, Heiland R, Hillen T, Islam MA, Jenner A, Liu B, Morel PA, Narayanan A, Ozik J, Rangamani P, Shoemaker JE, Smith AM, Macklin P. (2020) Rapid Community-driven Development of a SARS-CoV-2 Tissue Simulator. BioRxiv, p. 2020.04.02.019075, May 2020. TRD3
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Shi Q, Pei F, Silverman GA, Pak SC, Perlmutter DH, Liu B, Bahar I. (2020) Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis. Int J Mol Sci. 2020 Apr 19; 21(8):2855. doi: 10.3390/ijms21082855. PMID: 32325894 TRD1
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Cheng MH, Zhang S, Porritt RA, Arditi M, Bahar I. (2020) An insertion unique to SARS-CoV-2 exhibits superantigenic character strengthened by recent mutations. BioRxiv 2020.05.21.109272. TRD1 CSP
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Zeng X, Xu M. (2020) Gum-Net: Unsupervised Geometric Matching for Fast and Accurate 3D Subtomogram Image Alignment and Averaging. IEEE Conference on Computer Vision and Pattern Recognition. CVPR 2020, (conference paper) TRD4
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Ponzoni, L, Nguyen NH, Bahar I, Brodsky JL. (2020) Complementary Computational and Experimental Evaluation of Missense Variants in the ROMK Potassium Channel. PLoS Comput Biol. 2020 Apr 6; 16(4):e1007749. doi:10.1371/journal.pcbi.1007749 (2020). PMID: 32251469 PMCID: PMC7162551 TRD1
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Li H, Doruker P, Hu G, Bahar I. (2020) Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding. Biophysical Journal 2020 Apr 7; 118(7):1782-1794. doi:https://doi.org/10.1016/j.bpj.2020.01.046. PMID: 32130874 PMCID: 7136436 TRD1
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Shrivastava IH, Liu C, Dutta A, Bakan A, Bahar I. (2020) Allostery as Structure-Encoded Collective Dynamics: Significance in Drug Design. Structural Biology in Drug Discovery: Methods, Techniques, and Practices. Eds Jean-Paul Renaud. Chapter 6, p125-141, John Wiley & Sons, NY TRD1
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Rodnin MV, Vasquez-Montes V, Nepal B, Ladokhin AS, Lazaridis T. (2020) Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers. J Membr Biol 253(3):287-298. CSP
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Ponzoni L, Penaherrera DA, Oltvai Z, and Bahar I. (2020) Rhapsody: Predicting the pathogenicity of human missense variants. Bioinformatics 36 (10): 3084–3092. PMID: 32101277 PMCID: PMC7214033 TRD1
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Zhou Z, Zhou H, Ponzoni L, Luo A, Zhu R, He M, Huang Y, Guan KL, Bahar I, Liu Z, Wan Y. (2020) EIF3H Orchestrates Hippo Pathway-mediated Oncogenesis via Catalytic Control of YAP Stability. Cancer Research, 2020 Apr 8;canres.3718.2019 doi:10.1158/0008-5472.can-19-3718. PMID: 32269044 TRD1
- Ruan, X., Johnson GR, Bierschenk I, Nitschke R, Boerries M, Busch H, Murphy RF. (2020) Image-derived Models of Cell Organization Changes During Differentiation and Drug Treatments. Mol Biol Cell. 2020 Mar 19; 31(7):655-666. doi: 10.1091/mbc.E19-02-0080. PMID: 31774723 TRD4
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Gupta S, Lee REC, Faeder JR. (2020) Parallel Tempering with Lasso for Model Reduction in Systems Biology. PLoS Comput Biol. 2020 Mar 9; 16(3):e1007669. doi: 10.1371/journal.pcbi.1007669. eCollection 2020 Mar. PMID: 32150537 PMCID: 7082068 TRD3
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Sepehri A, PeBenito L, Pino-Angeles A, Lazaridis T. (2020) What Makes a Good Pore Former: A Study of Synthetic Melittin Derivatives. Biophys J. 118(8):1901-1913. CSP
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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, Artyukhova MA, Ponomareva LA, Timashev PS, Domingues RM, Stoyanovsky DA, Greenberger JS, Mallampalli RK, Bahar I, Gabrilovich DI, Bayır H, Kagan VE. (2020) Redox lipid reprogramming commands susceptibility of macrophages and microglia to ferroptotic death. Nat Chem Biol. 2020 Mar; 16(3):278-290. doi: 10.1038/s41589-019-0462-8. Epub 2020 Feb 17. PMID: 32080625 TRD1
- Shi, J, Zeng X, Jiang R, Jiang T, Xu M. (2020) A Simulated Annealing Approach for Resolution Guided Homogeneous Cryo-electron Microscopy Image selection. Quant. Biol., 2020. 8(1): p. 51-63. https://doi.org/10.1007/s40484-019-0191-8. TRD4
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Li H, Pei F, Taylor DL, Bahar I. (2020) QuartataWeb: An Integrated Chemical-protein Interaction Prediction and Pathway Inference Server for Polyphamalogical and Chemogenomics Analysis. https://doi.org/10.1093/bioinformatics/btaa210 Bioinformatics, btaa210. TRD1
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Morgan JL, Lichtman JW. (2020) An Individual Interneuron Participates in Many Kinds of Inhibition and Innervates Much of the Mouse Visual Thalamus. Neuron 106(3):468-481. CSP
- Xu YY, Shen HB, Murphy RF. (2020) Learning Complex Subcellular Distribution Patterns of Proteins via Analysis of Immunohistochemistry Images. Bioinformatics. 2020 Mar 1; 36(6):1908-1914. doi: 10.1093/bioinformatics/btz844. PMID: 31722369 TRD4
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Sauerwald N, Singhal A, and Kingsford C. (2020) Analysis of the structural variability of topologically associated domains as revealed by Hi-C. NAR genomics and bioinformatics 2020 Mar; 2(1):lqz008. doi: 10.1093/nargab/lqz008. Epub 2019 Sep 30. PMID: 31687663 TRD1
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Jullié D, Stoeber M, Sibarita JB, Zieger HL, Bartol TM, Arttamangkul S, Sejnowski TJ, Hosy E, von Zastrow M. (2020) A Discrete Presynaptic Vesicle Cycle for Neuromodulator Receptors. Neuron. 2020 Feb 19; 105(4):663-677.e8. doi: 10.1016/j.neuron.2019.11.016. Epub 2019 Dec 11. PMID: 31837915 PMCID: 7035187 TRD2
- Lu Y, Zeng X, Tian X, Shi X, Wang H, Zheng X, Liu X, Zhao X, Gao X, Xu M. (2020) Spark-based Parallel Calculation of 3D Fourier Shell correlation for macromolecule structure Local Resolution Estimation. The 18th Asia Pacific Bioinformatics Conference, (conference paper) TRD4
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Kim YJ, Jun IH, Shin DH, Yoon JG, Piao H, Jung JS, Park HW, Cheng MH, Bahar I, Whitcomb DC, and Lee MG. (2020) Regulation of CFTR Bicarbonate Channel Activity by WNK1: Implications for Pancreatitis and CFTR-Related Disorders. Cellular and Molecular Gastroenterology and Hepatology. 9 (1), 79-103. PMID: 31561038 TRD1
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Lugo-Martinez J, Dengjel J, Bar-Joseph Z, Murphy RF. Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. 2019. p. 144-153. (conference paper) TRD4
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Zhang S, Chen F, Bahar I. (2020) Differences in the Intrinsic Spatial Dynamics of the Chromatin Contribute to Cell Differentiation. Nucleic Acids Res. 48:1131-1145. PMID: 31828312 PMCID: 7026660 TRD1
- Lee JY, Krieger JM, Li H & Bahar I. (2020) Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations. Protein Sci, 2020 Jan; 29(1):76-86. TRD1
2019
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Cheng J, Wang S, Lin W, Wu N, Wang Y, Chen M, Xie XQ, Feng Z. (2019) Computational Systems Pharmacology-Target Mapping for Fentanyl-Laced Cocaine Overdose. ACS Chem Neurosci 10(8):3486-3499. CSP
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Spiriti J, Subramanian SR, Palli R, Wu M, Zuckerman DM. (2019) Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α. PLoS One 14(4):e0215694. TRD1 CSP
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Pei F, Li H, Liu B, Bahar I. (2019) Quantitative Systems Pharmacological Analysis of Drugs of Abuse Reveals the Pleiotropy of Their Targets and the Effector Role of mTORC1. Front Pharmacol 10:191 TRD1
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Mikulska-Ruminska K, Shrivastava I, Krieger J, Zhang S, Li H, Bayır H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. (2019) Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. J Chem Inf Model 59(5):2496-2508. TRD1 CSP
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Xu M, Singla J, Tocheva EI, Chang YW, Stevens RC, Jensen GJ, Alber F. (2019) De Novo Structural Pattern Mining in Cellular Electron Cryotomograms. Stucture 27(4):679-691. CSP
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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. (2019) Allostery in Its Many Disguises: From Theory to Applications. Structure 27(4):566-578. TRD1 CSP
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Arif-Tiwari H, Twiss CO, Lin FC, Funk JT, Vedantham S, Martin DR, Kalb BT. (2019) Improved Detection of Pelvic Organ Prolapse: Comparative Utility of Defecography Phase Sequence to Nondefecography Valsalva Maneuvers in Dynamic Pelvic Floor Magnetic Resonance Imaging. Curr Probl Diagn Radiol. 48(4):342-347. CSP
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Stoyanovsky DA, Tyurina YY, Shrivastava I, Bahar I, Tyurin VA, Protchenko O, Jadhav S, Bolevich SB, Kozlov AV, Vladimirov YA, Shvedova AA, Philpott CC, Bayir H, Kagan VE. Iron catalysis of lipid peroxidation in ferroptosis: Regulated enzymatic or random free radical reaction? (2019) Free Radic Biol Med 133:153-161. TRD1 CSP
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Ruiz-Martínez Á, Bartol TM, Sejnowski TJ, Tartakovsky DM. (2019) Stochastic Self-Tuning Hybrid Algorithm for Reaction-diffusion Systems. J Chem Phys. 2019 Dec 28; 151(24):244117. doi: 10.1063/1.5125022. PMID: 31893874 TRD2
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Pharris MC, Patel NM, VanDyk TG, Bartol TM, Sejnowski TJ, Kennedy MB, Stefan MI, Kinzer-Ursem TL (2019) A multi-state model of the CaMKII dodecamer suggests a Role for calmodulin in Maintenance of Autophosphorylation. PLoS Comput Biol. 2019 Dec 23; 15(12):e1006941. doi: 10.1371/journal.pcbi.1006941. eCollection 2019 Dec. PMID: 31869343 PMCID: PMC6957207 TRD2
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Garcia GC, Bartol TM, Phan S, Bushong EA, Perkins G, Sejnowski TJ, Ellisman MH, Skupin A. (2019) Mitochondrial Morphology Provides a Mechanism for Energy Buffering at Synapses. Sci Rep. 2019 Dec 4; 9(1):18306. doi: 10.1038/s41598-019-54159-1. PMID: 31797946 PMCID: PMC6893035 TRD2
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Belovich AN, Aguilar JI, Mabry SJ, Cheng MH, Zanella D, Hamilton PJ, Stanislowski DJ, Shekar A, Foster JD, Bahar I, Matthies HJG, Galli A. (2019) A network of phosphatidylinositol (4,5)-bisphosphate (PIP2) binding sites on the dopamine transporter regulates amphetamine behavior in Drosophila Melanogaster. Mol Psychiatry. 2019 Dec 3. doi: 10.1038/s41380-019-0620-0. [Online ahead of print] PMID: 31796894 TRD1
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Cheng MH, Ponzoni L., Sorkina T., Lee JY, Zhang S., Sorkin A. & Bahar I. (2019) Trimerization of dopamine transporter triggered by AIM-100 binding: Underlying molecular mechanisms and effect of mutations. Neuropharmocology, 161:15. PMID: 31228486 TRD1
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Chi J, Li H, Zhou Z, Izquierdo-Ferrer J, Xue Y, Wavelet CM, Schiltz GE, Zhang B, Cristofanilli M, Lu X, Bahar I, Wan Y. (2019) A Novel Strategy to Block Mitotic Progression for Targeted Therapy. EBioMedicine 49:40-54 PMID:31669221 PMCID: 6945239 TRD1
- Clark DJ, McMillan LE, Tan SL, Bellomo G, Massoue C, Thompson H, Mykhaylechko L, Alibhai D, Ruan X, Singleton KL, Du M, Hedges A, Schwartzberg PL, Verkade P, Murphy RF, Wülfing C. (2019) Transient Protein Accumulation at the Center of the T cell Antigen-presenting Cell Interface Drives Efficient IL-2 Secretion. Elife. 2019 Oct 30; 8:e45789. doi: 10.7554/eLife.45789. PMID: 31663508 TRD4
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Zhang S, Li H, Krieger JM, Bahar I. (2019) Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity. Mol Biol Evol. 2019 Sep 1; 36(9):2053-2068. doi: 10.1093/molbev/msz102. PMID: 31028708 TRD1
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Lü Y, Zeng X, Zhao X, Li S, Li H, Gao X, Xu Min. (2019) Fine-grained Alignment of Cryo-electron Subtomograms Based on MPI Parallel Optimization. BMC Bioinformatics. 2019 Aug 28;20(1):443. doi: 10.1186/s12859-019-3003-2. PMID: 31455212 PMCID: PMC6712796 TRD4
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Cugno A, Bartol TM, Sejnowski TJ, Iyengar R, Rangamani P. (2019) Geometric Principles of Second Messenger Dynamics in Dendritic Spines. Sci Rep. 2019 Aug 12; 9(1):11676. doi: 10.1038/s41598-019-48028-0. PMID: 31406140 PMCID: PMC6691135 TRD2
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Bell M, Bartol TM, Sejnowski TJ, Rangamani P. (2019) Addendum: Dendritic Spine Geometry and Spine Apparatus Organization Govern the Spatiotemporal Dynamics of Calcium. J Gen Physiol. 2019 Sep 2; 151(9):2221-2222. doi: 10.1085/jgp.20181226107312019a. Epub 2019 Aug 2. PMID: 31375548 PMCID: 6719410 TRD2
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Bell M, Bartol TM, Sejnowski TJ, Rangamani P. (2019) Dendritic Spine Geometry and Spine Apparatus Organization Govern the Spatiotemporal Dynamics of Calcium. J Gen Physiol. 2019 Aug 5; 151(8):1017-1034. doi: 10.1085/jgp.201812261. Epub 2019 Jul 19. PMID: 31324651 PMCID: PMC6683673 TRD2
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Zhou Z, Feng Z, Hu D, Yang P, Gur M, Bahar I, Cristofanilli M, Gradishar WJ, Xie XQ, Wan Y. (2019) A novel small-molecule antagonizes PRMT5-mediated KLF4 methylation for targeted therapy. EBioMedicine, 2019 Jun; 44:98-111. doi: 10.1016/j.ebiom.2019.05.011. PMID: 31101597 TRD1
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Cheng MH, Bahar I. (2019) Monoamine transporters: structure, intrinsic dynamics and allosteric regulation. Nat Struct Mol Biol. 2019 Jul; 26(7):545-556. doi: 10.1038/s41594-019-0253-7. Epub 2019 Jul 3. PMID: 31270469 TRD1
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Ernst OK, Bartol TM, Sejnowski TJ, Mjolsness E. (2019) Learning Moment Closure in Reaction-diffusion Systems with Spatial Dynamic Boltzmann Distributions. Phys Rev E. 2019 Jun; 99(6-1):063315. doi: 10.1103/PhysRevE.99.063315. PMID: 31330605 TRD2
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Lin YT, Feng S, Hlavacek WS. (2019) Scaling Methods for Accelerating Kinetic Monte Carlo Simulations of Chemical Reaction Networks. J Chem Phys. 2019 Jun 28; 150(24):244101. doi: 10.1063/1.5096774. PMID: 31255063 CSP
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Li R, Zeng X, Sigmund SE, Lin R, Zhou B, Liu C, Wang K, Jiang R, Freyberg Z, Lv H, Xu M. (2019) Automatic localization and identification of mitochondria in cellular electron cryo-tomography using faster-RCNN. BMC Bioinformatics. 20(Suppl 3):132. doi: 10.1186/s12859-019-2650-7. PMID: 30925860
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Taylor DL, Gough A, Schurdak ME, Vernetti L, Chennubhotla CS, Lefever D, Pei F, Faeder JR, Lezon TR, Stern AM, Bahar I. (2019) Harnessing Human Microphysiology Systems as Key Experimental Models for Quantitative Systems Pharmacology. Handb Exp Pharmacol. 2019; 260:327-367. doi: 10.1007/164_2019_239. PMID: 31201557 TRD1 TRD3
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Zhang B, Li F, Chen Z, Shrivastava IH, Gasanoff ES, Dagda RK. (2019) Naja mossambica mossambica Cobra Cardiotoxin Targets Mitochondria to Disrupt Mitochondrial Membrane Structure and Function. Toxins (Basel). 11(3). doi: 10.3390/toxins11030152. PMID: 30857180
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Wang KZQ, Steer E, Otero PA, Bateman NW, Cheng MH, Scott AL, Wu C, Bahar I, Shih YT, Hsueh YP, Chu CT. (2019) PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons. eNeuro. 5(6). doi: 10.1523/ENEURO.0466-18.2018. PMID: 30783609
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Park SJ, Lee J, Qi Y, Kern NR, Lee HS, Jo S, Joung I, Joo K, Lee J, Im W. (2019) CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates. Glycobiology. 29(4):320-331. doi: 10.1093/glycob/cwz003. PMID: 30689864
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Majarian TD, Murphy RF, Lakdawala SS. (2019) Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization. PLoS Comput Biol. 15(1):e1006199. doi: 10.1371/journal.pcbi.1006199. PMID: 30689627 TRD4
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McGraw C, Yang L, Levental I, Lyman E, Robinson AS. (2019) Membrane cholesterol depletion reduces downstream signaling activity of the adenosine A2A receptor. Biochim Biophys Acta Biomembr. 1861(4):760-767. doi: 10.1016/j.bbamem.2019.01.001. PMID: 30629951
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Ruan X, Murphy RF. (2019) Evaluation of methods for generative modeling of cell and nuclear shape. Bioinformatics. doi: 10.1093/bioinformatics/bty983. PMID: 30535313 TRD4
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Shahul Hameed UF, Liao C, Radhakrishnan AK, Huser F, Aljedani SS, Zhao X, Momin AA, Melo FA, Guo X, Brooks C, Li Y, Cui X, Gao X, Ladbury JE, Jaremko Ł, Jaremko M, Li J, Arold ST. (2019) H-NS uses an autoinhibitory conformational switch for environment-controlled gene silencing. Nucleic Acids Res. Mar 18;47(5):2666-2680. doi: 10.1093/nar/gky1299. PMID: 30597093
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Rui H, Das A, Nakamoto R, Roux B. (2018) Proton Countertransport and Coupled Gating in the Sarcoplasmic Reticulum Calcium Pump. J Mol Biol. 430(24):5050-5065. doi: 10.1016/j.jmb.2018.10.014. PMID: 30539761
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Lee JY, Krieger J, Herguedas B, García-Nafría J, Dutta A, Shaikh SA, Greger IH, Bahar I. (2018) Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain. Structure. 27(2):241-252.e3. doi: 10.1016/j.str.2018.10.017. PMID: 30528594. TRD1
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Ernst OK, Bartol T, Sejnowski T, Mjolsness E. (2018) Learning dynamic Boltzmann distributions as reduced models of spatial chemical kinetics. J Chem Phys. 149(3):034107. doi: 10.1063/1.5026403. PMID: 30037235 TRD2
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