Core A

Core B

  • 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: e25850.PMID: 28569666. (* equally contributed)
  • Cheng MH, Garcia-Olivares J, Wasserman S, DiPietro J, Bahar I. (2017) Allosteric modulation of human dopamine transporter activity under conditions promoting its dimerization.  J. Biol. Chem; in press.
  • Lee J. Y., Feng Z., Xie X.-Q. , and Bahar I. (2017) Allosteric modulation of intact γ-secretase collective dynamics. Biophys. J. in revision.
  • 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 Biol; in press PMID:28648616.
  • Li H, Chang Y-Y, Lee JY, Bahar I and Yang L-W. (2017) DynOmics: Dynamics of Structural Proteome and Beyond. Nucleic Acids Res. 45: W374-W380; PMID: 28472330.
  • 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 Rep. 7: 5399; PMID:28710426.
  • Cheng, MH*, Garcia-Olivares, J*, Wasserman, S, DiPietro, J & Bahar, I. (2017) Allosteric modulation of human dopamine transporter activity under conditions promoting its dimerization. J. Biol. Chem 292:12471-12482; PMID: 28584050.
  • Gur M, Cheng MH, Zomot E, Bahar I. (2017) Effect of dimerization on the dynamics of neurotransmitter: sodium symporters. J. Phys. Chem. B 121: 3657–3666. PMID: 28118712.
  • Li H, Chang YY, Yang LW, Bahar I (2016) iGNM 2.0: the Gaussian network model database for bimolecular structural dynamics Nucleic Acids Res 44: D415-422 PMID: 26582920.
  • Kurkcuoglu Z, Bahar I, Doruker P (2016) ClustENM: ENM-based sampling of essential conformational space at full atomic resolution. J. Chem. Theory Comput. 12:4549-62; PMID: 27494295.
  • Jun I*, Cheng MH*, Sim E*, Jung J, Suh BL, Kim Y, Son H, Park K, Kim CH, Yoon J-H, Whitcomb DC, Bahar I, Lee MG (2016) Pore Dilation Increases the Bicarbonate Permeability of CFTR, ANO1, and Glycine Receptor Anion Channels. Journal of Physiology 594: 2929-55; PMID:26663196.
  • Cheng MH, Bahar I (2015) Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter. Structure 23: 2171-81; PMID: 26106364.
  • Gur M, Zomot E, Cheng MH, Bahar I (2015) Energy landscape of LeuT from molecular simulations. J Chem Phys 143: 243134; PMID: 26723619.
  • Keskin O, Dyson HJ, Bahar I (2015) Biomolecular Systems Interactions, Dynamics, and Allostery. Reflections and New Directions. Biophys J 109: E01-2; PMID: 26377787.
  • Krieger J, Bahar I, Greger IH (2015) Structure, Dynamics, and Allosteric Potential of Ionotropic Glutamate Receptor N-Terminal Domains. Biophys J 109: 1136-48; PMID: 26255587.
  • 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; PMID: 26256538.
  • Haliloglu T, Bahar I (2015) Adaptability of protein structures to enable functional interactions and evolutionary implications. Current Opinion in Structural Biology 35: 17-23; PMID: 26254902.
  • Bahar I, Cheng MH, Lee JY, Kaya C, Zhang S (2015) Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions. Biophys J 109: 1101-9; PMID: 26143655.
  • 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; Front Neurol 6: 134; PMID: 26106364.
  • Eyal E, Lum G, Bahar I (2015) The Anisotropic Network Model web server at 2015 (ANM 2.0). Bioinformatics 2015: 1-3; PMID: 25568280.
  • Cheng MH, Bahar I (2014) Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle. PLoS Comput Biol 10: e1003879; PMID: 25299050.
  • Cobanoglu MC, Oltvai ZN, Taylor DL, Bahar I (2014) BalestraWeb: Efficient, online evaluation of drug-target interactions. Bioinformatics 31:131-3; PMID: 25192741.
  • Bahar I (2014) Coupling between Neurotransmitter Translocation and Protonation State of a Titratable Residue during Na(+)-Coupled Transport. Biophys J 106: 2547-8 PMID: 24940770.
  • 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 30: 2681-3; PMID: 24849577.
  • 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 Comput Biol 10: e1003521 PMID: 24699246.

Core C

  • Lee, S, Lozano, A., Kambadur, P., and Xing EP “An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations.” Journal of Computational Biology 2016, 23(5): 372-389.
  • Lee S, Kong S, Xing EP. “A Network-driven Approach for Genome-wide Association Mapping.” Bioinformatics 2016, 32(12):i164-i173. doi: 10.1093/bioinformatics/btw270.
  • Bang, S. and Wu, W. “Naive-Bayes Ensemble: A New Approach to Classifying Unlabeled Multi-Class Asthma Subjects.” The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016).
  • Xu, X. Chai, H. Muthakana, X. Liang, G. Yang, T. Zeev-Ben-Mordehai and E. P. Xing, “Deep learning based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms.” The Twenty-fifth International Conference on Intelligence Systems for Molecular Biology (ISMB 2017). Bioinformatics (2017) in press.
  • Haohan Wang, Benjamin J. Lengerich, Bryon Aragam and Eric P. Xing, “Precision Lasso: Accounting for Correlations and Linear Dependencies in High-Dimensional Genomic Data” Submitted.
  • Marchetti-Bowick, J. Yin, J. Howrylak and E. P. Xing, A time-varying group sparse additive model for genome-wide association studies of dynamic complex traits, Bioinformatics 2016, 32 (19):btw347.
  • Bryon Aragam and Eric P. Xing, “A convergent algorithm for learning genome-scale Bayesian networks from high-dimensional data” Submitted.
  • S. Lee, A. Lozano, P. Kambadur, and E. P. Xing, An Efficient Nonlinear Regression Approach for Genome-Wide Detection of Marginal and Interacting Genetic Variations, to appear in the 19th International Conference on Research in Computational Molecular Biology (RECOMB 2015)
  • S. Lee, J. K. Kim, X. Zheng, Q. Ho, G. A. Gibson, and E. P. Xing, On Model Parallelization and Scheduling Strategies for Distributed Machine Learning, Advances in Neural Information Processing Systems 28 (eds. Corinna Cortes and Neil Lawrence), MIT Press, 2014. (NIPS 2014).
  • Wu, W.*, Bleecker, E., Moore, W., Busse, W. W., Jarjour, N., Castro, M., Chung, K. F., Calhoun, W. J., Erzurum, S., Gaston, B., Israel, E., Curran-Everett, D., Wenzel, S. E.* (2014) “Unsupervised phenotyping of Severe Asthma Research Program participants using expanded lung data.” Journal of Allergy and Clinical Immunology 133(5):1280-1288. NIHMS562128. (PMCID: PMC4038417).
  • E. P. Xing, R. Curtis, G. Schoenherr, S. Lee, J. Yin, K. Puniyani, W. Wu, P. Kinnaird, GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap, PLoS One, Volume 9, Issue 6, e97524, 2014.