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

Kaynak BT, Zhang S, Bahar I, Doruker P (2021) ClustENMD: Efficient sampling of biomolecular conformational space at atomic resolution. Bioinformatics. TRD1

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

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

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

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

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

Pei F, Shi Q, Zhang H, Bahar I (2021) Predicting Protein-Protein Interactions Using Symmetric Logistic Matrix Factorization. J Chem Inf Model. TRD1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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.

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

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

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

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

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

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

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

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

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

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; 117 (25) 14503-14511. TRD2

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Liao C, May V, Li J. (2019) Assessment of Conformational State Transitions of Class B GPCRs Using Molecular Dynamics. Methods Mol Biol. 1947:3-19. doi: 10.1007/978-1-4939-9121-1_1. PMID: 30969408 CSP

Han R, Bao Z, Zeng X, Niu T, Zhang F, Xu M, Gao X. (2019) A Joint Method for Marker-free Alignment of Tilt Series in Electron Tomography. Bioinformatics. 2019 Jul 15; 35(14):i249-i259. doi: 10.1093/bioinformatics/btz323. PMID: 31510669 TRD4

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

Majarian TD, Cao-Berg I, Ruan X, Murphy RF. (2019) CellOrganizer: Learning and Using Cell Geometries for Spatial Cell Simulations. Methods Mol Biol. 1945:251-264. doi: 10.1007/978-1-4939-9102-0_11. PMID: 30945250. TRD4

Liao C, May V, Li J. (2019) PAC1 Receptors: Shapeshifters in Motion. J Mol Neurosci. doi: 10.1007/s12031-018-1132-0. PMID: 30074173 CSP

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

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

Lorent JH, Levental KR, Ganesan L, Rivera-Longsworth G, Sezgin E, Doktorova M, Lyman E, Levental I. (2020) Plasma Membranes are Asymmetric in Lipid Unsaturation, Packing and Protein Shape.  Nat Chem Biol. 2020 Jun; 16(6):644-652. doi: 10.1038/s41589-020-0529-6. Epub 2020 May 4. PMID: 32367017 CSP

Tapia JJ, Saglam AS, Czech J, Kuczewski R, Bartol TM, Sejnowski TJ, Faeder JR. (2019) MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework. Methods Mol Biol. 1945:203-229.  doi: 10.1007/978-1-4939-9102-0_9. PMID: 30945248. TRD2 TRD3

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

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

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

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

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

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

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

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

Sorzano COS, Jiménez A, Mota J, Vilas JL, Maluenda D, Martínez M, Ramírez-Aportela E, Majtner T, Segura J, Sánchez-García R, Rancel Y, Del Caño L, Conesa P, Melero R, Jonic S, Vargas J, Cazals F, Freyberg Z, Krieger J, Bahar I, Marabini R, Carazo JM. (2019) Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallogr F Struct Biol Commun. 75(Pt 1):19-32. doi: 10.1107/S2053230X18015108. PMID: 30605122 TRD1

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

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

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

van Dijk L, Giladi M, Refaeli B, Hiller R, Cheng MH, Bahar I, Khananshvili D. (2018) Key residues controlling bidirectional ion movements in Na⁺/Ca²⁺ exchanger. Cell Calcium. 76:10-22. doi: 10.1016/j.ceca.2018.09.004. PMID: 30248574

Han L, Murphy RF, Ramanan D. (2018) Learning Generative Models of Tissue Organization with Supervised GANs. IEEE Winter Conf Appl Comput Vis. 2018:682-690. doi: 10.1109/WACV.2018.00080. PMID: 30177974 TRD4

Gupta S, Hainsworth L, Hogg JS, Lee REC, Faeder JR. (2018) Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology. Proc Euromicro Int Conf Parallel Distrib Netw Based Process. 2018:690-697. doi: 10.1109/PDP2018.2018.00114. PMID: 30175326.

Haas KT, Compans B, Letellier M, Bartol TM, Grillo-Bosch D, Sejnowski TJ, Sainlos M, Choquet D, Thoumine O, Hosy E. (2018) Pre-post synaptic alignment through neuroligin-1 tunes synaptic transmission efficiency. eLife. 7:. doi: 10.7554/eLife.31755. PMID: 30044218. TRD2

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

Antunes G, Simoes-de-Souza FM. (2018) AMPA receptor trafficking and its role in heterosynaptic plasticity. Sci Rep. 8(1):10349. doi: 10.1038/s41598-018-28581-w. PMID: 29985438

Debiec KT, Whitley MJ, Koharudin LMI, Chong LT, Gronenborn AM. (2018) Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein. Biophys J. 114(4):839-855. doi: 10.1016/j.bpj.2018.01.001. PMID: 29490245.

Jia S, Miedel MT, Ngo M, Hessenius R, Chen N, Wang P, Bahreini A, Li Z, Ding Z, Shun TY, Zuckerman DM, Taylor DL, Puhalla SL, Lee AV, Oesterreich S, Stern AM. (2018) Clinically Observed Estrogen Receptor Alpha Mutations within the Ligand-Binding Domain Confer Distinguishable Phenotypes. Oncology. 94(3):176-189. doi: 10.1159/000485510. PMID: 29306943.

Bromer C, Bartol TM, Bowden JB, Hubbard DD, Hanka DC, Gonzalez PV, Kuwajima M, Mendenhall JM, Parker PH, Abraham WC, Sejnowski TJ, Harris KM. (2018) Long-term potentiation expands information content of hippocampal dentate gyrus synapses. Proc Natl Acad Sci U S A. 115(10):E2410-E2418. doi: 10.1073/pnas.1716189115. PMID: 29463730. TRD2

Kaya C, Cheng MH, Block ER, Bartol TM, Sejnowski TJ, Sorkin A, Faeder JR, Bahar I. (2018) Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency. eNeuro. 5(1). pii: ENEURO.0298-17.2017. doi: 10.1523/ENEURO.0298-17.2017. eCollection 2018 Jan-Feb. PMID: 29430519. TRD1 TRD3

Zhao Y, Zeng X, Guo Q, Xu M. (2018) An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification. Bioinformatics. 34(13):i227-i236. doi: 10.1093/bioinformatics/bty267. PMID: 29949977.

Sauerwald N, Kingsford C. (2018) Quantifying the similarity of topological domains across normal and cancer human cell types. Bioinformatics. 34(13):i475-i483. doi: 10.1093/bioinformatics/bty265. PMID: 29949963. TRD1

Pino-Angeles A, Lazaridis T. (2018) Effects of Peptide Charge, Orientation, and Concentration on Melittin Transmembrane Pores. Biophys J. 114(12):2865-2874. doi: 10.1016/j.bpj.2018.05.006. PMID: 29925023.

Krieger J, Lee JY, Greger IH, Bahar I. (2018) Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions. Neurosci Lett. pii: S0304-3940(18)30132-0. doi: 10.1016/j.neulet.2018.02.050. PMID: 29481851. TRD1

Ponzoni L, Bahar I. (2018) Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci U S A. 115(16):4164-4169. doi: 10.1073/pnas.1715896115. PMID: 29610305. TRD1

Ponzoni L, Zhang S, Cheng MH, Bahar I. (2018) Shared dynamics of LeuT superfamily members and allosteric differentiation by structural irregularities and multimerization. Philos Trans R Soc Lond B Biol Sci. 373(1749). pii: 20170177. doi: 10.1098/rstb.2017.0177. PMID 29735731. TRD1

Ruiz-Martínez Á, Bartol TM, Sejnowski TJ, Tartakovsky DM. (2018) Efficient models of polymerization applied to FtsZ ring assembly in Escherichia coli. Proc Natl Acad Sci U S A. 115(19):4933-4938. doi: 10.1073/pnas.1719391115. PMID: 29686085. TRD2

Sparks S, Temel DB, Rout MP, Cowburn D. (2018) Deciphering the "Fuzzy" Interaction of FG Nucleoporins and Transport Factors Using Small-Angle Neutron Scattering. Structure. 26(3):477-484.e4. doi: 10.1016/j.str.2018.01.010. PMID: 29429880.

Ambler R, Ruan X, Murphy RF, Wulfing C. (2017) Systems Imaging of the immune synapse. Methods Mol Biol. TRD3 in press

Bahar I, Jernigan R, Dill K. (2017) Protein Actions: Principles & Modeling. New York, NY: Garland Science, Taylor & Francis Group ISBN: 9780815341772

Beaven AH, Maer AM, Sodt AJ, Rui H, Pastor RW, Andersen OS, Im W. (2017) Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation. Biophysical Journal. 112:1185-1197. doi: 10.1016/J.BPJ.2017.01.028.

Cheng MH, Garcia-Olivares J, Wasserman S, DiPietro J, Bahar I. (2017) Allosteric modulation of human dopamine transporter activity under conditions promoting its dimerization. The Journal of biological chemistry. 292:12471-12482. doi: 10.1074/jbc.M116.763565. PMID:28584050

Cheng MH, Torres-Salazar D, Gonzalez-Suarez AD, Amara SG, Bahar I. (2017) Substrate transport and anion permeation proceed through distinct pathways in glutamate transporters. eLife. 6:. doi: 10.7554/eLife.25850. PMID:28569666

Chong LT, Saglam AS, Zuckerman DM. (2017) Path-sampling strategies for simulating rare events in biomolecular systems. Current Opinion in Structural Biology. 43:88-94. doi: 10.1016/j.sbi.2016.11.019. PMID:27984811 TRD1

Gaieb Z, Morikis D. (2017) Conformational heterogeneity in CCR7 undergoes transitions to specific states upon ligand binding. Journal of Molecular Graphics and Modelling. 74:352-358. doi: 10.1016/J.JMGM.2017.04.012.

Gaieb Z, Morikis D. (2017) Detection of Side Chain Rearrangements Mediating the Motions of Transmembrane Helices in Molecular Dynamics Simulations of G Protein-Coupled Receptors. Computational and Structural Biotechnology Journal. 15:131-137. doi: 10.1016/J.CSBJ.2017.01.001.

Gretzmeier C, Eiselein S, Johnson GR, Engelke R, Nowag H, Zarei M, Kűttner V, Becker AC, Rigbolt KTG, Høyer-Hansen M, Andersen JS, Műnz C, Murphy RF, Dengjel J. (2017) Degradation of protein translation machinery by amino acid starvation-induced macroautophagy. Autophagy. TRD3 in press

Gur M, Cheng MH, Zomot E, Bahar I. (2017) Effect of Dimerization on the Dynamics of Neurotransmitter: Sodium Symporters. The Journal of Physical Chemistry B. acs.jpcb.6b09876. doi: 10.1021/acs.jpcb.6b09876. DBP1 TRD1

Huang YM, Raymundo MAV, Chen W, Chang CA. (2017) Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease. Biochemistry. 56:1311-1323. doi: 10.1021/acs.biochem.6b01112.

Johnson GR, Kangas JD, Dovzhekno A, Trojok R, Voigt K, Majarian TD, Palme K, Murphy RF. (2017) A Method for Characterizing Phenotypic Changes in Highly Variable Cell Populations and its Application to High Content Screening of Arabidopsis thaliana Protoplasts. Cytometry Part A. CSP12 TRD3 in press

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, Bayir H. (2017)Oxidized Arachidonic and Adrenic Phosphatidylethanolamines Navigate Cells to Ferroptosis NatureChem Biol13:81-90 PMID: 27842066

Li H, Sharma N, General IJ, Schreiber G, Bahar I. (2017)Dynamic Modulation of Binding Affinity as a Mechanism for Regulating Interferon Signaling. J Mol Biol429:2571-2589 PMID: 28648616

Li H, Chang YY, Lee JY, Bahar I, Yang LW. (2017)DynOmics: dynamics of structural proteome and beyondNucleic Acids Res45:W374–W380 PMID: 28472330

Liao C, Zhao X, Brewer M, May V, Li J. (2017) Conformational Transitions of the Pituitary Adenylate Cyclase-Activating Polypeptide Receptor, a Human Class B GPCR. Scientific Reports. 7:5427. doi: 10.1038/s41598-017-05815-x.

Liu B, Oltvai Z, Bayir H, Silverman G, Pak S, Perlmutter D, Bahar I. (2017) Quantitative Assessment Of Cell Fate Decision Between Autophagy And Apoptosis. bioRxiv. 129767. doi: 10.1101/129767.

Ma S, Cheng MH, Guthrie DA, Newman AH, Bahar I, Sorkin A. (2017)Targeting of dopamine transporter to filopodia requires an outward-facing conformation of the transporter. Sci Rep7:5399 PMID: 28710426

Mikulska-Ruminska K, Kulik AJ, Benadiba C, Bahar I, Dietler G, Nowak W. (2017)Nanomechanics of multidomain neuronal cell adhesion protein contactin revealed by single molecule AFM and SMD. Sci Rep7:8852 PMID: 28821864

Ramezani H, Akan OB. (2017) Importance of vesicle release stochasticity in neuro-spike communication. The Journal of Physical Chemistry B. 121:3343-3347. doi: 10.1109/EMBC.2017.8037572.

Rouviere E, Arnarez C, Yang L, Lyman E. (2017) Identification of Two New Cholesterol Interaction Sites on the A 2A Adenosine Receptor. Biophysical Journal. 113:2415-2424. doi: 10.1016/j.bpj.2017.09.027.

Sauerwald N, Zhang S, Kingsford C, Bahar I. (2017)Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplingsNucleic Acids Res45:3663-3673 PMID: 28334818

Sekar JAP, Tapia JJ, Faeder JR. (2017) Automated visualization of rule-based models. PLOS Computational Biology. 13:e1005857. doi: 10.1371/journal.pcbi.1005857.

Simakov N, Leonard DA, Smith JC, Wymore T, Szarecka A. (2017) A Distal Disulfide Bridge in OXA-1 $\beta$-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining $\Omega$ Loop. The Journal of Physical Chemistry B. 121:3285-3296. doi: 10.1021/acs.jpcb.6b07884.

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. (2017)Improved Total-Body Irradiation Survival by Delivery of Two Radiation Mitigators that Target Distinct Cell Death Pathways. Radiat Res DOI: 10.1667/RR14787.1 PMID: 29140165

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, Bayir H, Kagan VE. (2017)"Only a life lived for others is worth living:" Redox Signaling by Oxygenated Phospholipids in Cell Fate Decisions. Antioxid Redox Signal DOI:10.1089/ars.2017.7124 PMID: 28835115

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, Bayir H, Kagan VE. (2017)PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals. Cell 171:628-641 PMID: 29053969

Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y. (2017)Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis. EBioMedicine15:48-61 PMID: 28040451

Zuckerman DM, Chong LT. (2017) Weighted Ensemble Simulation: Review of Methodology, Applications, and Software. Annual Review of Biophysics. 46:43-57. doi: 10.1146/annurev-biophys-070816-033834.

Adelman JL, Ghezzi C, Bisignano P, Loo DDF, Choe S, Abramson J, Rosenberg JM, Wright EM, Grabe M. (2016) Stochastic steps in secondary active sugar transport. Proceedings of the National Academy of Sciences of the United States of America. 113:E3960-6. doi: 10.1073/pnas.1525378113. PMID:27325773

Anandakrishnan R, Zhang Z, Donovan-Maiye R, Zuckerman DM. (2016) Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process. Proceedings of the National Academy of Sciences of the United States of America. 113:11220-11225. doi: 10.1073/pnas.1608533113. PMID:27647911 TRD1

Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ. (2016) Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nature genetics. 48:117-25. doi: 10.1038/ng.3471. PMID:26691984

Chipot C, Comer J. (2016) Subdiffusion in Membrane Permeation of Small Molecules. Scientific reports. 6:35913. doi: 10.1038/srep35913. PMID:27805049

Debiec KT, Cerutti DS, Baker LR, Gronenborn AM, Case DA, Chong LT. (2016) Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model. Journal of chemical theory and computation. 12:3926-47. doi: 10.1021/acs.jctc.6b00567. PMID:27399642 CSP25

Dewan S, McCabe KJ, Regnier M, McCulloch AD, Lindert S. (2016) Molecular Effects of cTnC DCM Mutations on Calcium Sensitivity and Myofilament Activation-An Integrated Multiscale Modeling Study. The journal of physical chemistry. B. 120:8264-75. doi: 10.1021/acs.jpcb.6b01950. PMID:27133568

Dhakshnamoorthy B, Rohaim A, Rui H, Blachowicz L, Roux B. (2016) Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola. Nature communications. 7:12753. doi: 10.1038/ncomms12753. PMID:27678077

Donovan RM, Tapia JJ, Sullivan DP, Faeder JR, Murphy RF, Dittrich M, Zuckerman DM. (2016) Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. PLoS Computational Biology. 12:e1004611. doi: 10.1371/journal.pcbi.1004611. PMID:26845334 TRD2 TRD3

Faeder JR, Morel PA. (2016) Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments. Biophysical journal. 110:1681-3. doi: 10.1016/j.bpj.2016.03.025. PMID:27119628 CSP22 TRD2

Harris LA, Hogg JS, Tapia JJ, Sekar JAP, Gupta S, Korsunsky I, Arora A, Barua D, Sheehan RP, Faeder JR. (2016) BioNetGen 2.2: advances in rule-based modeling. Bioinformatics (Oxford, England). 32:3366-3368. doi: 10.1093/bioinformatics/btw469. PMID:27402907 TRD2

Jo S, Qi Y, Im W. (2016) Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins. Glycobiology. 26:19-29. doi: 10.1093/glycob/cwv083. PMID:26405106

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. (2016) Pore dilatation increases the bicarbonate permeability of CFTR, ANO1 and glycine receptor anion channels. The Journal of physiology. 594:2929-55. doi: 10.1113/JP271311. PMID:26663196 TRD1

Kagan VE, Mao G, Qu F, Angeli JPF, 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. (2016) Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nature Chemical Biology. 13:81-90. doi: 10.1038/nchembio.2238. PMID:27842066 TRD1

Kolouri S, Park SR, Rohde GK. (2016) The Radon Cumulative Distribution Transform and Its Application to Image Classification. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society. 25:920-34. doi: 10.1109/TIP.2015.2509419. PMID:26685245 CSP14 TRD3

Kolouri S, Tosun AB, Ozolek JA, Rohde GK. (2016) A continuous linear optimal transport approach for pattern analysis in image datasets. Pattern Recognition. 51:453-462. doi: 10.1016/j.patcog.2015.09.019. PMID:26858466 CSP14 TRD3

Lee WA, Bonin V, Reed M, Graham BJ, Hood G, Glattfelder K, Reid RC. (2016) Anatomy and function of an excitatory network in the visual cortex. Nature. 532:1-18. doi: 10.1038/nature17192. PMID:27018655 DBP5 TRD3

Li H, Chang YY, Yang LW, Bahar I. (2016) iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic acids research. 44:D415-22. doi: 10.1093/nar/gkv1236. PMID:26582920 TRD1

Li Y, Majarian TD, Naik AW, Johnson GR, Murphy RF. (2016) Point process models for localization and interdependence of punctate cellular structures. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 89:633-43. doi: 10.1002/cyto.a.22873. PMID:27327612 TRD3

Liu B, Liu Q, Yang L, Palaniappan SK, Bahar I, Thiagarajan PS, Ding JL. (2016) Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways. Science signaling. 9:ra70. doi: 10.1126/scisignal.aac9340. PMID:27405980 TRD1

Monje-Galvan V, Klauda JB. (2016) Peripheral membrane proteins: Tying the knot between experiment and computation. Biochimica et Biophysica Acta - Biomembranes. 1858:1584-1593. doi: 10.1016/j.bbamem.2016.02.018. PMID:26903211

Morel PA, Lee REC, Faeder JR. (2016) Demystifying the cytokine network: Mathematical models point the way. Cytokine. doi: 10.1016/j.cyto.2016.11.013. PMID:27919524 CSP22TRD2

Morgan JL, Berger DR, Wetzel AW, Lichtman JW. (2016) The Fuzzy Logic of Network Connectivity in Mouse Visual Thalamus. Cell. 165:192-206. doi: 10.1016/j.cell.2016.02.033. PMID:27015312 CSP10 TRD3

Murphy RF. (2016) Building cell models and simulations from microscope images. Methods (San Diego, Calif.). 96:33-9. doi: 10.1016/j.ymeth.2015.10.011. PMID:26484733 TRD3

Naik AW, Kangas JD, Sullivan DP, Murphy RF. (2016) Active machine learning-driven experimentation to determine compound effects on protein patterns. eLife. 5:e10047. doi: 10.7554/eLife.10047. PMID:26840049 TRD3

Perrin BS, Fu R, Cotten ML, Pastor RW. (2016) Simulations of Membrane-Disrupting Peptides II: AMP Piscidin 1 Favors Surface Defects over Pores. Biophysical journal. 111:1258-66. doi: 10.1016/j.bpj.2016.08.015. PMID:27653484

Perrin BS, Pastor RW. (2016) Simulations of Membrane-Disrupting Peptides I: Alamethicin Pore Stability and Spontaneous Insertion. Biophysical journal. 111:1248-57. doi: 10.1016/j.bpj.2016.08.014. PMID:27653483

Pino-Angeles A, Leveritt JM, Lazaridis T. (2016) Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family. PLoS Computational Biology. 12:e1004570. doi: 10.1371/journal.pcbi.1004570. PMID:26727376

Qi Y, Jo S, Im W. (2016) Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies. Glycobiology. 26:251-60. doi: 10.1093/glycob/cwv101. PMID:26537503

Raveh B, Karp JM, Sparks S, Dutta K, Rout MP, Sali A, Cowburn D. (2016) Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proceedings of the National Academy of Sciences of the United States of America. 113:E2489-97. doi: 10.1073/pnas.1522663113. PMID:27091992

Roybal KT, Buck TE, Ruan X, Cho BH, Clark DJ, Ambler R, Tunbridge HM, Zhang J, Verkade P, Wűlfing C, Murphy RF. (2016) Computational spatiotemporal analysis identifies WAVE2 and cofilin as joint regulators of costimulation-mediated T cell actin dynamics. Science Signaling. 9:1-13. doi: 10.1126/scisignal.aad4149. PMID:27095595 DBP4 TRD3

Rui H, Artigas P, Roux B. (2016) The selectivity of the Na(+)/K(+)-pump is controlled by binding site protonation and self-correcting occlusion. eLife. 5:. doi: 10.7554/eLife.16616. PMID:27490484

Schiffer JM, Feher VA, Malmstrom RD, Sida R, Amaro RE. (2016) Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A. Biophysical journal. 111:1631-1640. doi: 10.1016/j.bpj.2016.08.041. PMID:27760351

Sodt AJ, Venable RM, Lyman E, Pastor RW. (2016) Nonadditive Compositional Curvature Energetics of Lipid Bilayers. Physical review letters. 117:138104. doi: 10.1103/PhysRevLett.117.138104. PMID:27715135

Suárez E, Adelman JL, Zuckerman DM. (2016) Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models. Journal of chemical theory and computation. 12:3473-81. doi: 10.1021/acs.jctc.6b00339. PMID:27340835 TRD1

Suárez E, Pratt AJ, Chong LT, Zuckerman DM. (2016) Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses. Protein Science. 25:67-78. doi: 10.1002/pro.2738. PMID:26131764 CSP25 TRD1

Wetzel A, Bakal J, Dittrich M. (2016) A Virtual File System for On-Demand Processing of Multidimensional Datasets. Protein science : a publication of the Protein Society. 25:1-5. doi: 10.1145/2949550.2949656. PMID:26131764 TRD3

Williams AH, O'Donnell C, Sejnowski TJ, O'Leary T. (2016) Dendritic trafficking faces physiologically critical speed-precision tradeoffs. eLife. 5:. doi: 10.7554/eLife.20556. PMID:28034367 TRD2

Yuan S, Peng Q, Palczewski K, Vogel H, Filipek S. (2016) Mechanistic Studies on the Stereoselectivity of the Serotonin 5-HT sub1A/sub Receptor. Angewandte Chemie International Edition. 55:8661-8665. doi: 10.1002/anie.201603766.

Yuan S, Peng Q, Palczewski K, Vogel H, Filipek S. (2016) Mechanistic Studies on the Stereoselectivity of the Serotonin 5-HT1A Receptor. Angewandte Chemie (International ed. in English). 55:8661-5. doi: 10.1002/anie.201603766. PMID:27244650

Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ. (2015) Systematic identification of significantly mutated regions reveals a rich landscape of functional molecular alterations across cancer genomes. bioRxiv. 48:020875. doi: 10.1101/020875. PMID:26691984 TRD1

Bahar I, Cheng MH, Lee JY, Kaya C, Zhang S. (2015) Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions. Biophysical Journal. 109:1101-1109. doi: 10.1016/j.bpj.2015.06.004. PMID:26143655 TRD1

Bakan , Kapralov , Bayir H, Hu F, Kagan VE, Bahar I. (2015) Inhibition of Peroxidase Activity of Cytochrome c: De Novo Compound Discovery and Validation. Molecular Pharmacology. 88:421-7. doi: 10.1124/mol.115.097816. PMID:26078313 TRD1

Bartol TM, Bromer C, Kinney J, Chirillo MA, Bourne JN, Harris KM, Sejnowski TJ. (2015) Nanoconnectomic upper bound on the variability of synaptic plasticity. eLife. 4:e10778. doi: 10.7554/eLife.10778. PMID:26618907 CSP6 DBP2 TRD2

Bartol TM, Keller DX, Kinney JP, Bajaj CL, Harris KM, Sejnowski TJ, Kennedy MB. (2015) Computational reconstitution of spine calcium transients from individual proteins. Frontiers in Synaptic Neuroscience. 7:17. doi: 10.3389/fnsyn.2015.00017. PMID:26500546 CSP6 DBP2 TRD2

Castillo JP, Rui H, Basilio D, Das A, Roux B, Latorre R, Bezanilla F, Holmgren M. (2015) Mechanism of potassium ion uptake by the Na+/K+-ATPase. Nature Communications. 6:7622. doi: 10.1038/ncomms8622. PMID:26205423

Cheng MH, Bahar I. (2015) Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter. Structure. 23:2171-2181. doi: 10.1016/j.str.2015.09.001. PMID:26481814 DBP1 TRD1

Cheng MH, Block E, Hu F, Cobanoglu MC, Sorkin A, Bahar I. (2015) Insights into the modulation of dopamine transporter function by amphetamine, orphenadrine and cocaine binding. Frontiers in Neurology. 6:134. doi: 10.3389/fneur.2015.00134. PMID:26106364 DBP3 TRD1

Cheng X, Jo S, Qi Y, Marassi FM, Im W. (2015) Solid-state NMR-restrained ensemble dynamics of a membrane protein in explicit membranes. Biophysical Journal. 108:1954-1962. doi: 10.1016/j.bpj.2015.03.012. PMID:25902435

Chylek LA, Harris LA, Faeder JR, Hlavacek WS. (2015) Modeling for (physical) biologists: an introduction to the rule-based approach. Physical biology. 12:045007. doi: 10.1088/1478-3975/12/4/045007. PMID:26178138

Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I. (2015) BalestraWeb: Efficient online evaluation of drug-target interactions. Bioinformatics. 31:131-133. doi: 10.1093/bioinformatics/btu599. PMID:25192741 TRD1

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R. (2015) The center for causal discovery of biomedical knowledge from big data. Journal of the American Medical Informatics Association. 22:1132-1136. doi: 10.1093/jamia/ocv059. PMID:26138794 TRD1

Duan M, Liu H, Li M, Huo S. (2015) Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562. The Journal of Chemical Physics. 143:135101. doi: 10.1063/1.4931921. PMID:26450332

Dutta A, Krieger J, Lee JY, Garcia-Nafria J, Greger IH, Bahar I. (2015) Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences. Structure. 23:1692-1704. doi: 10.1016/j.str.2015.07.002. PMID:26256538 CSP2 TRD1

Freites JA, Tobias DJ. (2015) Voltage Sensing in Membranes: From Macroscopic Currents to Molecular Motions. Journal of Membrane Biology. 248:419-430. doi: 10.1007/s00232-015-9805-x. PMID:25972106

Galindo-Murillo R, Roe DR, Cheatham TE. (2015) Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochimica et Biophysica Acta - General Subjects. 1850:1041-1058. doi: 10.1016/j.bbagen.2014.09.007. PMID:25219455

Gill RL, Castaing JP, Hsin J, Tan IS, Wang X, Huang KC, Tian F, Ramamurthi KS. (2015) Structural basis for the geometry-driven localization of a small protein. Proceedings of the National Academy of Sciences. 112:E1908-E1915. doi: 10.1073/pnas.1423868112. PMID:25825747

Gur M, Zomot E, Cheng MH, Bahar I. (2015) Energy landscape of LeuT from molecular simulations. Journal of Chemical Physics. 143:243134. doi: 10.1063/1.4936133. PMID:26723619 TRD1

Haliloglu T, Bahar I. (2015) Adaptability of protein structures to enable functional interactions and evolutionary implications. Current Opinion in Structural Biology. 35:17-23. doi: 10.1016/j.sbi.2015.07.007. PMID:26254902 TRD1

Hawse WF, Sheehan RP, Miskov-Zivanov N, Menk AV, Kane LP, Faeder JR, Morel PA. (2015) Cutting Edge: Differential Regulation of PTEN by TCR, Akt, and FoxO1 Controls CD4+ T Cell Fate Decisions. Journal of immunology (Baltimore, Md. : 1950). 194:4615-9. doi: 10.4049/jimmunol.1402554. PMID:25855357 CSP22 TRD2

Hlavacek LAC, Harris LA, Faeder JR, S W. (2015) Modeling for (physical) biologists: an introduction to the rule-based approach. Physical Biology. 12:45007. doi: 10.1088/1478-3975/12/4/045007. PMID:26178138 CSP5 TRD2

Hu D, Gur M, Zhou Z, Gamper A, Hung MC, Fujita N, Lan L, Bahar I, Wan Y. (2015) Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis. Nature communications. 6:8419. doi: 10.1038/ncomms9419. PMID:26420673 TRD1

Hussain F, Langmead CJ, Mi Q, Dutta-Moscato J, Vodovotz Y, Jha SK. (2015) Automated parameter estimation for biological models using Bayesian statistical model checking. BMC Bioinformatics. 16:S8. doi: 10.1186/1471-2105-16-S17-S8. PMID:26679759

Jo S, Qi Y, Im W. (2015) Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins. Glycobiology. 26:19-29. doi: 10.1093/glycob/cwv083. PMID:1000201519

Johnson GR, Li J, Shariff A, Rohde GK, Murphy RF. (2015) Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules. PLoS Computational Biology. 11:e1004614. doi: 10.1371/journal.pcbi.1004614. PMID:26624011 CSP14 TRD3

Johnson GR, Buck TE, Sullivan DP, Rohde GK, Murphy RF. (2015) Joint modeling of cell and nuclear shape variation. Molecular biology of the cell. 26:4046-56. doi: 10.1091/mbc.E15-06-0370. PMID:26354424 TRD3

Johnson GR, Li J, Shariff A, Rohde GK, Murphy RF. (2015) Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules. PLoS computational biology. 11:e1004614. doi: 10.1371/journal.pcbi.1004614. PMID:26624011

Johnson T, Bartol T, Sejnowski T, Mjolsness E. (2015) Model reduction for stochastic CaMKII reaction kinetics in synapses by graph-constrained correlation dynamics. Physical biology. 12:045005. doi: 10.1088/1478-3975/12/4/045005. PMID:26086598 TRD2

Kamisetty H, Ghosh B, Langmead CJ, Bailey-Kellogg C. (2015) Learning Sequence Determinants of Protein:Protein Interaction Specificity with Sparse Graphical Models. Journal of Computational Biology. 22:474-486. doi: 10.1089/cmb.2014.0289. PMID:25973864 CSP3 TRD1

Keskin O, Dyson HJ, Bahar I. (2015) Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions. Biophysical Journal. 109:E01-E102. doi: 10.1016/j.bpj.2015.08.005. PMID:26244747 TRD1

Kolouri S, Park SR, Rohde GK. (2015) The Radon cumulative distribution transform and its application to image classification. arXiv preprint arXiv:1511.03206. 25:1-14. doi: 10.1109/TIP.2015.2509419. PMID:26685245 CSP14 TRD3

Krieger J, Bahar I, Greger IH. (2015) Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains. Biophysical Journal. 109:1136-1148. doi: 10.1016/j.bpj.2015.06.061. PMID:26255587 CSP2 CSP3 TRD1

Lee HS, Qi Y, Im W. (2015) Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study. Scientific Reports. 5:8926. doi: 10.1038/srep08926. PMID:25748215

Lee S, Bhattacharya S, Tate CG, Grisshammer R, Vaidehi N. (2015) Structural dynamics and thermostabilization of neurotensin receptor 1. Journal of Physical Chemistry B. 119:4917-4928. doi: 10.1021/jp510735f. PMID:25807267

Leveritt JM, Pino-Angeles A, Lazaridis T. (2015) The Structure of a Melittin-Stabilized Pore. Biophysical Journal. 108:2424-2426. doi: 10.1016/j.bpj.2015.04.006. PMID:25992720

Li Q, Shen R, Treger JS, Wanderling SS, Milewski W, Siwowska K, Bezanilla F, Perozo E. (2015) Resting state of the human proton channel dimer in a lipid bilayer. Pnas. 112:1515043112-. doi: 10.1073/pnas.1515043112. PMID:26443860

Luo F, Dittrich M, Cho S, Stiles JR, Meriney SD. (2015) Transmitter release is evoked with low probability predominately by calcium flux through single channel openings at the frog neuromuscular junction. Journal of Neurophysiology. 113:jn.00879.2014. doi: 10.1152/jn.00879.2014. PMID:25652927 CSP4 TRD2

Ma J, Kelly L, Ingram J, Price TJ, Meriney SD, Dittrich M. (2015) New insights into short-term synaptic facilitation at the frog neuromuscular junction. Journal of Neurophysiology. 113:71-87. doi: 10.1152/jn.00198.2014. PMID:25210157 CSP4 TRD2

Malmstrom RD, Kornev AP, Taylor SS, Amaro RE. (2015) Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nature communications. 6:7588. doi: 10.1038/ncomms8588. PMID:26145448

Mao W, Kaya C, Dutta A, Horovitz A, Bahar I. (2015) Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. Bioinformatics. 31:1929-1937. doi: 10.1093/bioinformatics/btv103. PMID:25697822 CSP1 TRD1

Martin DR, Matyushov DV. (2015) Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bcinf1/inf complex. Journal of Chemical Physics. 142:161101. doi: 10.1063/1.4919222. PMID:25933744

Martin DR, Matyushov D. (2015) Photosynthetic Diode: Electron Transport Rectification by Wetting the Quinone Cofactor. Physical Chemistry Chemical Physics. 17:22523-8. doi: 10.1039/c5cp03397g. PMID:26171665

Mitchell JM, Clasman JR, June CM, Kaitany KCJ, LaFleur JR, Taracila MA, Klinger NV, Bonomo RA, Wymore T, Szarecka A, Powers RA, Leonard DA. (2015) Structural Basis of Activity against Aztreonam and Extended Spectrum Cephalosporins for Two Carbapenem-Hydrolyzing Class D ??-Lactamases from Acinetobacter baumannii. Biochemistry. 54:1976-1987. doi: 10.1021/bi501547k. PMID:25710192

Monje-Galvan V, Klauda JB. (2015) Peripheral membrane proteins: Tying the knot between experiment and computation. Biochimica et Biophysica Acta - Biomembranes. 1858:1584-93. doi: 10.1016/j.bbamem.2016.02.018. PMID:26903211

Mouchlis VD, Bucher D, McCammon JA, Dennis E. (2015) Membranes serve as allosteric activators of phospholipase A$\backslash$n 2$\backslash$n , enabling it to extract, bind, and hydrolyze phospholipid substrates. Proceedings of the National Academy of Sciences. 112:E516-E525. doi: 10.1073/pnas.1424651112. PMID:25624474

Qi Y, Jo S, Im W. (2015) Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies. Glycobiology. 26:251-260. doi: 10.1093/glycob/cwv101. PMID:26537503

Rohde GK. (2015) Computational analysis of cell images. Cytometry Part A. 87:294-295. doi: 10.1002/cyto.a.22653. PMID:25808302 TRD3

Slack RL, Spiriti J, Ahn J, Parniak MA, Zuckerman DM, Ishima R. (2015) Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase. Proteins. 83:1526-38. doi: 10.1002/prot.24843. PMID:26061827 TRD1

Sodt AJ, Pastor RW, Lyman E. (2015) Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin. Biophysical Journal. 109:948-955. doi: 10.1016/j.bpj.2015.07.036. PMID:26331252

Spiriti J, Zuckerman DM. (2015) Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits. Journal of Chemical Physics. 143:243159. doi: 10.1063/1.4938479. PMID:26723644 TRD1

Tosun AB, Yergiyev O, Kolouri S, Silverman JF, Rohde GK. (2015) Detection of malignant mesothelioma using nuclear structure of mesothelial cells in effusion cytology specimens. Cytometry Part A. 87:326-333. doi: 10.1002/cyto.a.22602. PMID:25598227

Wu EL, Qi Y, Park S, Mallajosyula SS, Mackerell AD, Klauda JB, Im W. (2015) Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophysical Journal. 109:2090-2100. doi: 10.1016/j.bpj.2015.10.009. PMID:26588568

Xiao F, Hrabe J, Hrabetova S. (2015) Anomalous extracellular diffusion in rat cerebellum. Biophysical Journal. 108:2384-2395. doi: 10.1016/j.bpj.2015.02.034. PMID:25954895

Zomot E, Gur M, Bahar I. (2015) Microseconds simulations reveal a new sodium-binding site and the mechanism of sodium-coupled substrate uptake by LeuT. Journal of Biological Chemistry. 290:544-555. doi: 10.1074/jbc.M114.617555. PMID:25381247 DBP1 TRD1

Zwier MC, Adelman JL, Kaus JW, Pratt AJ, Wong KF, Rego NB, Su??rez E, Lettieri S, Wang DW, Grabe M, Zuckerman DM, Chong LT. (2015) WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis. Journal of Chemical Theory and Computation. 11:800-809. doi: 10.1021/ct5010615. PMID:26392815 CSP25TRD1

Adelman JL, Sheng Y, Choe S, Abramson J, Wright EM, Rosenberg JM, Grabe M. (2014) Structural determinants of water permeation through the sodium-galactose transporter vSGLT. Biophysical Journal. 106:1280-1289. doi: 10.1016/j.bpj.2014.01.006. PMID:24655503

Bahar I. (2014) Coupling between neurotransmitter translocation and protonation state of a titratable residue during Na+-coupled transport. Biophysical Journal. 106:2547-2548. doi: 10.1016/j.bpj.2014.05.011. PMID:24940770 TRD1

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I. (2014) Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinformatics (Oxford, England). 30:2681-3. doi: 10.1093/bioinformatics/btu336. PMID:24849577 TRD1

Baker MK, Abrams CF. (2014) Dynamics of lipids, cholesterol, and transmembrane ??-helices from microsecond molecular dynamics simulations. Journal of Physical Chemistry B. 118:13590-13600. doi: 10.1021/jp507027t. PMID:25380392

Cheng MH, Bahar I. (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle. PLoS Computational Biology. 10:e1003879. doi: 10.1371/journal.pcbi.1003879. PMID:25299050 TRD1

Choudhary OP, Paz A, Adelman JL, Colletier JP, Abramson J, Grabe M. (2014) Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1. Nature structural & molecular biology. 21:626-32. doi: 10.1038/nsmb.2841. PMID:24908397

Chu CT, Bayir H, Kagan VE. (2014) LC3 binds externalized cardiolipin on injured mitochondria to signal mitophagy in neurons: Implications for Parkinson disease. Autophagy. 10:376-378. doi: 10.4161/auto.27191. PMID:24351649

Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS. (2014) Rule-based modeling: A computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 6:13-36. doi: 10.1002/wsbm.1245. PMID:24123887 CSP5 TRD2

Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B. (2014) Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model. PLoS Computational Biology. 10:e1003521. doi: 10.1371/journal.pcbi.1003521. PMID:24699246 CSP2 TRD1

Debiec KT, Gronenborn AM, Chong LT. (2014) Evaluating the strength of salt bridges: A comparison of current biomolecular force fields. Journal of Physical Chemistry B. 118:6561-6569. doi: 10.1021/jp500958r. PMID:24702709 CSP25

Edwards J, Daniel E, Kinney J, Bartol T, Sejnowski T, Johnston D, Harris K, Bajaj C. (2014) VolRoverN: Enhancing surface and volumetric reconstruction for realistic dynamical simulation of cellular and subcellular function. Neuroinformatics. 12:277-289. doi: 10.1007/s12021-013-9205-2. PMID:24100964 CSP6 TRD2

Eyal E, Lum G, Bahar I. (2014) The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics. 31:1487-1489. doi: 10.1093/bioinformatics/btu847. PMID:25568280 TRD1

General IJ, Liu Y, Blackburn ME, Mao W, Gierasch LM, Bahar I. (2014) ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones. PLoS Computational Biology. 10:e1003624. doi: 10.1371/journal.pcbi.1003624. PMID:24831085 CSP1 TRD1

Hogg JS, Harris LA, Stover LJ, Nair NS, Faeder JR. (2014) Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems. PLoS Computational Biology. 10:e1003544. doi: 10.1371/journal.pcbi.1003544. PMID:24699269 TRD2

Hong C, Tieleman DP, Wang Y. (2014) Microsecond Molecular Dynamics Simulations of Lipid Mixing. Langmuir. 30:11993-12001. doi: 10.1021/la502363b. PMID:25237736

Hussain F, Jha SK, Jha S, Langmead CJ. (2014) Parameter discovery in stochastic biological models using simulated annealing and statistical model checking. International Journal of Bioinformatics Research & Applications. 10:519-539. doi: http://dx.doi.org/10.1504/IJBRA.2014.062998. PMID:24989866

Jiang J, Bakan A, Kapralov AA, {Ishara Silva} K, Huang Z, Amoscato AA, Peterson J, {Krishna Garapati} V, Saxena S, Bayir H, Atkinson J, Bahar I, Kagan VE. (2014) Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: Mitochondria-targeted imidazole-substituted fatty acids. Free Radical Biology and Medicine. 71:221-230. doi: 10.1016/j.freeradbiomed.2014.02.029. PMID:24631490 TRD1

Kamisetty H, Ghosh B, Langmead CJ, Bailey-Kellogg C. (2014) Learning sequence determinants of protein: Protein interaction specificity with sparse graphical models. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 129-143. doi: 10.1007/978-3-319-05269-4_10. PMID:25414914 CSP3TRD1

Korotchenko VN, Saydmohammed M, Vollmer LL, Bakan A, Sheetz K, Debiec KT, Greene KA, Agliori CS, Bahar I, Day BW, Vogt A, Tsang M. (2014) In vivo structure-activity relationship studies support allosteric targeting of a dual specificity phosphatase. ChemBioChem. 15:1436-1445. doi: 10.1002/cbic.201402000. PMID:24909879 TRD1

Langmead CJ. (2014) Generative models of conformational dynamics. Advances in Experimental Medicine and Biology. 805:87-105. doi: 10.1007/978-3-319-02970-2_4. PMID:24446358TRD1

Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar I. (2014) Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies. Scientific reports. 4:6245. doi: 10.1038/srep06245. PMID:25175563 TRD1

Lui VWY, Peyser ND, Ng PKS, Hritz J, Zeng Y, Lu Y, Li H, Wang L, Gilbert BR, General IJ, Bahar I, Ju Z, Wang Z, Pendleton KP, Xiao X, Du Y, Vries JK, Hammerman PS, Garraway L, Mills GB, Johnson DE, Grandis JR. (2014) 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. doi: 10.1073/pnas.1319551111. PMID:24395800 TRD1

McClendon CL, Kornev AP, Gilson MK, Taylor SS. (2014) Dynamic architecture of a protein kinase. Proceedings of the National Academy of Sciences of the United States of America. 111:E4623-31. doi: 10.1073/pnas.1418402111. PMID:25319261

O'Reilly LP, Long OS, Cobanoglu MC, Benson JA, Luke CJ, Miedel MT, Hale P, Perlmutter DH, Bahar I, Silverman GA, Pak SC. (2014) A genome-wide RNAi screen identifies potential drug targets in a C. elegans model of α-1-antitrypsin deficiency. Human molecular genetics. 23:5123-5132. doi: 10.1093/hmg/ddu236. PMID:24838285 TRD1

Rui H, Root KT, Lee J, Glover KJ, Im W. (2014) Probing the U-shaped conformation of caveolin-1 in a bilayer. Biophysical Journal. 106:1371-1380. doi: 10.1016/j.bpj.2014.02.005. PMID:24655512

Sodt AJ, Sandar ML, Gawrisch K, Pastor RW, Lyman E. (2014) The molecular structure of the liquid-ordered phase of lipid bilayers. Journal of the American Chemical Society. 136:725-732. doi: 10.1021/ja4105667. PMID:24345334

Spiriti J, Zuckerman DM. (2014) Tunable coarse graining for Monte Carlo simulations of proteins via smoothed energy tables: Direct and exchange simulations. Journal of Chemical Theory and Computation. 10:5161-5177. doi: 10.1021/ct500622z. PMID:25400525 TRD1

Stefan MI, Bartol TM, Sejnowski TJ, Kennedy MB. (2014) Multi-state Modeling of Biomolecules. PLoS Computational Biology. 10:e1003844. doi: 10.1371/journal.pcbi.1003844. PMID:25254957 DBP2 TRD2

Suárez E, Lettieri S, Zwier MC, Stringer CA, Subramanian SR, Chong LT, Zuckerman DM. (2014) Simultaneous computation of dynamical and equilibrium information using a weighted ensemble of trajectories. Journal of Chemical Theory and Computation. 10:2658-2667. doi: 10.1021/ct401065r. PMID:25246856 CSP25 TRD1

Venable RM, Sodt AJ, Rogaski B, Rui H, Hatcher E, MacKerell AD, Pastor RW, Klauda JB. (2014) CHARMM all-atom additive force field for sphingomyelin: Elucidation of hydrogen bonding and of positive curvature. Biophysical Journal. 107:134-145. doi: 10.1016/j.bpj.2014.05.034. PMID:24988348

Wang CY, Miller TF. (2014) Allosteric response and substrate sensitivity in peptide binding of the signal recognition particle. Journal of Biological Chemistry. 289:30868-30879. doi: 10.1074/jbc.M114.584912. PMID:25237192

Wenskovitch JE, Harris LA, Tapia JJ, Faeder JR, Marai GE. (2014) MOSBIE: a tool for comparison and analysis of rule-based biochemical models. BMC bioinformatics. 15:316. doi: 10.1186/1471-2105-15-316. PMID:25253680 TRD2

Wodarz D. (2014) Modeling T cell responses to antigenic challenge. Journal of Pharmacokinetics and Pharmacodynamics. 41:415-429. doi: 10.1007/s10928-014-9387-8. PMID:25269610

Wymore T, Field MJ, Langan P, Smith JC, Parks JM. (2014) Hydrolysis of DFP and the nerve agent (S)-sarin by DFPase proceeds along two different reaction pathways: Implications for engineering bioscavengers. Journal of Physical Chemistry B. 118:4479-4489. doi: 10.1021/jp410422c. PMID:24720808

Cheng MH, Bahar I. (2013) Coupled global and local changes direct substrate translocation by neurotransmitter-sodium symporter ortholog LeuT. Biophysical Journal. 105:630-639. doi: 10.1016/j.bpj.2013.06.032. PMID:23931311 TRD1

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, Borisenko G, Huang Z, Gusdon AM, Cheikhi A, Steer EK, Wang R, Baty C, Watkins S, Bahar I, Bayır H, Kagan VE. (2013) Cardiolipin externalization to the outer mitochondrial membrane acts as an elimination signal for mitophagy in neuronal cells. Nature cell biology. 15:1197-205. doi: 10.1038/ncb2837. PMID:24036476 TRD1

Coelho LP, Kangas JD, Naik AW, Osuna-Highley E, Glory-Afshar E, Fuhrman M, Simha R, Berget PB, Jarvik JW, Murphy RF. (2013) Determining the subcellular location of new proteins from microscope images using local features. Bioinformatics. 29:2343-2349. doi: 10.1093/bioinformatics/btt392. PMID:23836142 TRD3

Dittrich M, Pattillo JM, King JD, Cho S, Stiles JR, Meriney SD. (2013) An excess-calcium-binding-site model predicts neurotransmitter release at the neuromuscular junction. Biophysical Journal. 104:2751-2763. doi: 10.1016/j.bpj.2013.05.023. PMID:23790384 CSP4 TRD2

Donovan RM, Sedgewick AJ, Faeder JR, Zuckerman DM. (2013) Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories. Journal of Chemical Physics. 139:115105. doi: 10.1063/1.4821167. PMID:24070313 TRD2

Gur M, Zomot E, Bahar I. (2013) Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions. Journal of Chemical Physics. 139:121912. doi: 10.1063/1.4816375. PMID:24089724 TRD1

Gur M, Madura JD, Bahar I. (2013) Global transitions of proteins explored by a multiscale hybrid methodology: Application to adenylate kinase. Biophysical Journal. 105:1643-1652. doi: 10.1016/j.bpj.2013.07.058. PMID:24094405 TRD1

Kunze MBA, Wright DW, Werbeck ND, Kirkpatrick J, Coveney PV, Hansen DF. (2013) Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8. Journal of the American Chemical Society. 135:17862-17868. doi: 10.1021/ja408184x. PMID:2417145

Meriney SD, Dittrich M. (2013) Organization and function of transmitter release sites at the neuromuscular junction. The Journal of physiology. 591:3159-65. doi: 10.1113/jphysiol.2012.248625. PMID:23613535 CSP4 TRD2

Mowrey D, Cheng MH, Liu LT, Willenbring D, Lu X, Wymore T, Xu Y, Tang P. (2013) Asymmetric ligand binding facilitates conformational transitions in pentameric ligand-gated ion channels. Journal of the American Chemical Society. 135:2172-2180. doi: 10.1021/ja307275v. PMID:23339564

Naik AW, Kangas JD, Langmead CJ, Murphy RF. (2013) Efficient modeling and active learning discovery of biological responses. PLoS ONE. 8:e83996. doi: 10.1371/journal.pone.0083996. PMID:24358322 TRD3

Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR. (2013) Special section dedicated to The Sixth q-bio Conference: meeting report and. Phys. Biol. 10:030301. doi: 10.1088/1478-3975/10/3/030301. PMID:23735417 CSP5 TRD2

Price I, Ermentrout B, Zamora R, Wang B, Azhar N, Mi Q, Constantine G, Faeder JR, Luckhart S, Vodovotz Y. (2013) In vivo, in vitro, and in silico studies suggest a conserved immune module that regulates malaria parasite transmission from mammals to mosquitoes. Journal of Theoretical Biology. 334:173-186. doi: 10.1016/j.jtbi.2013.05.028. PMID:23764028

Roybal KT, Sinai P, Verkade P, Murphy RF, Wűlfing C. (2013) The actin-driven spatiotemporal organization of T-cell signaling at the system scale. Immunological Reviews. 256:133-147. doi: 10.1111/imr.12103. PMID:24117818 DBP4 TRD3

Stadler C, Rexhepaj E, Singan VR, Murphy RF, Pepperkok R, Uhlén M, Simpson JC, Lundberg E. (2013) Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells. Nature methods. 10:315-23. doi: 10.1038/nmeth.2377. PMID:23435261 TRD3

Tarr TB, Dittrich M, Meriney SD. (2013) Are unreliable release mechanisms conserved from NMJ to CNS?. Trends in Neurosciences. 36:14-22. doi: 10.1016/j.tins.2012.09.009. PMID:23102681 CSP4 TRD2

Wang W, Slepčev D, Basu S, Ozolek JA, Rohde GK. (2013) A linear optimal transportation framework for quantifying and visualizing variations in sets of images. International Journal of Computer Vision. 101:254-269. doi: 10.1007/s11263-012-0566-z. PMID:23729991

Weber S, Fernández-Cachón ML, Nascimento JM, Knauer S, Offermann B, Murphy RF, Boerries M, Busch H. (2013) Label-Free Detection of Neuronal Differentiation in Cell Populations Using High-Throughput Live-Cell Imaging of PC12 Cells. PLoS ONE. 8:e56690. doi: 10.1371/journal.pone.0056690. PMID:23451069 TRD3

Zomot E, Bahar I. (2013) Intracellular gating in an inward-facing state of aspartate transporter GltPh is regulated by the movements of the helical hairpin HP2. Journal of Biological Chemistry. 288:8231-8237. doi: 10.1074/jbc.M112.438432. PMID:23386619 DBP1 TRD1

Bakan A, Nevins N, Lakdawala AS, Bahar I. (2012) Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules. Journal of Chemical Theory and Computation. 8:2435-2447. doi: 10.1021/ct300117j. PMID:22798729 TRD1

Bhatt D, Bahar I. (2012) An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates. Journal of Chemical Physics. 137:104101. doi: 10.1063/1.4748278. PMID:22979844 TRD1

Buck TE, Li J, Rohde GK, Murphy RF. (2012) Toward the virtual cell: Automated approaches to building models of subcellular organization "learned" from microscopy images. BioEssays. 34:791-799. doi: 10.1002/bies.201200032. PMID:22777818 TRD3

Cho BH, Cao-Berg I, Bakal JA, Murphy RF. (2012) OMERO.searcher: content-based image search for microscope images. Nature Methods. 9:633-634. doi: 10.1038/nmeth.2086. PMID:22743762 TRD3

Dutta A, Shrivastava IH, Sukumaran M, Greger IH, Bahar I. (2012) Comparative dynamics of NMDA- and AMPA-glutamate receptor n-terminal domains. Structure. 20:1838-1849. doi: 10.1016/j.str.2012.08.012. PMID:22959625 TRD1

Eliceiri KW, Berthold MR, Goldberg IG, Ibanez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Swedlow JR, Tomancak P, Carpenter AE. (2012) Biological imaging software tools. Nat Methods. 9:697-710. doi: 10.1038/nmeth.2084. PMID:22743775 TRD3

Isin B, Tirupula KC, Oltvai ZN, Klein-Seetharaman J, Bahar I. (2012) Identification of motions in membrane proteins by elastic network models and their experimental validation. Methods in molecular biology (Clifton, N.J.). 914:285-317. doi: 10.1007/978-1-62703-023-6_17. PMID:22976035 TRD1

Kurkcuoglu Z, Bakan A, Kocaman D, Bahar I, Doruker P. (2012) Coupling between Catalytic Loop Motions and Enzyme Global Dynamics. PLoS Computational Biology. 8:e1002705. doi: 10.1371/journal.pcbi.1002705. PMID:23028297 TRD1

Lezon TR, Bahar I. (2012) Constraints imposed by the membrane selectively guide the alternating access dynamics of the glutamate transporter Glt Ph. Biophysical Journal. 102:1331-1340. doi: 10.1016/j.bpj.2012.02.028. PMID:22455916 TRD1

Li J, Newberg JY, Uhlén M, Lundberg E, Murphy RF. (2012) Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas. PLoS ONE. 7:e50514. doi: 10.1371/journal.pone.0050514. PMID:23226299 TRD3

Li J, Shariff A, Wiking M, Lundberg E, Rohde GK, Murphy RF. (2012) Estimating Microtubule Distributions from 2D Immunofluorescence Microscopy Images Reveals Differences among Human Cultured Cell Lines. PLoS ONE. 7:e50292. doi: 10.1371/journal.pone.0050292. PMID:23209697 TRD3

Li J, Xiong L, Schneider J, Murphy RF. (2012) Protein subcellular location pattern classification in cellular images using latent discriminative models. Bioinformatics. 28:i32-9. doi: 10.1093/bioinformatics/bts230. PMID:22689776 TRD3

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, {De Koning} APJ, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjólander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. (2012) The interface of protein structure, protein biophysics, and molecular evolution. Protein Science. 21:769-785. doi: 10.1002/pro.2071. PMID:22528593 TRD1

Liu L, Byeon IJL, Bahar I, Gronenborn AM. (2012) 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. doi: 10.1021/ja210118w. PMID:22296296 TRD1

Liu Y, Bahar I. (2012) Sequence evolution correlates with structural dynamics. Molecular Biology and Evolution. 29:2253-2263. doi: 10.1093/molbev/mss097. PMID:22427707 TRD1

Murphy RF. (2012) CellOrganizer: Image-Derived Models of Subcellular Organization and Protein Distribution. Methods in Cell Biology. 110:179-193. doi: 10.1016/B978-0-12-388403-9.00007-2. PMID:22482949 TRD3