Year 2015 and before

  • Feng, Z.; Pearce, L. V.; Xu, X.; Yang, X.; Yang, P.; Blumberg, P. M.; Xie, Xa.-Q. Structural Insight into Tetrameric hTRPV1 from Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Virtual Screening and Bioassay Validations. J. Chem. Inf. Model. 2015.
  • Feng, Z.; Ma, S.; Hu, G.; Xie, X.-Q. Allosteric Binding Site and Activation Mechanism of Class C G-Protein Coupled Receptors: Metabotropic Glutamate Receptor Family. AAPS J. 2015, 1-17.
  • Feng, Z.; Pearce, L. V.; Xu, X.; Yang, X.; Yang, P.; Blumberg, P. M.; Xie, X.-Q. Structural Insight into Tetrameric hTRPV1 from Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Virtual Screening and Bioassay Validations. J. Chem. Inf. Model. 2015.
  • Feng, Z.; Ma, S.; Hu, G.; Xie, X.-Q. Allosteric Binding Site and Activation Mechanism of Class C G-Protein Coupled Receptors: Metabotropic Glutamate Receptor Family. AAPS J. 2015, 1-17.
  • Rentian Feng, Qin Tong, Zhaojun Xie, Haizi Cheng, Lirong Wang, Suzanne Lentzsch, G.David Roodman and Xiang-Qun Xie. Targeting cannabinoid receptor-2 pathway by phenylacetylamide suppresses the proliferation of human myeloma cells through mitotic dysregulation and cytoskeleton disruption. Molecular Carcinogenesis, DOI: 10.1002/mc.22251 16 JAN 2015
  • Feng, Zhiwei, Stanton Kochanek, David Close, LiRong Wang, Ajay Srinivasan, Abdulrahman A. Almehizia, Prema Iyer, Xiang-Qun Xie, Paul A. Johnston, and Barry Gold. “Design and activity of AP endonuclease-1 inhibitors.” Journal of Chemical Biology (2015): 1-15.
  • Yingdai Gao, Peng Yang, Hongmei Shen, Hui Yu, Xianmin Song, Liyan Zhang, Peng Zhang, Haizi Cheng, Zhaojun Xie, Sha Hao, Yahui Ding, Lirong Wang, Haibin Liu, Yanxin Li, Hui Cheng, Weimin Miao, Weiping Yuan, Youzhong Yuan, Tao Cheng, Xiang-Qun Xie* “Small-molecule inhibitors targeting INK4 protein p18 INK4C enhance ex vivo expansion of haematopoietic stem cells” Nature Communications. 02/2015; 6. DOI: 10.1038/ncomms7328
  • Feng, Z., Ma, S., Hu, G., & Xie, X. Q. (2015). Allosteric binding site and activation mechanism of class C G-protein coupled receptors: metabotropic glutamate receptor family. The AAPS journal, 17(3), 737-753.
  • Xiang-Qun Xie,* Lirong Wang, Haibin Liu, Qin Ouyang, Cheng Fang, and Weiwei Su.(2014) Chemogenomics knowledgebased polypharmacology analyses of drug abuse related G-protein coupled receptors and their ligands. Front Pharmacol. doi:  10.3389/fphar.2014.00003
  • Ji, Kai-Long, Ping Zhang, Xiao-Nian Li, Juan Guo, Hua-Bin Hu, Chun-Fen Xiao, Xiang-Qun Xie, and You-Kai Xu. “Cytotoxic limonoids from Trichilia americana leaves.” Phytochemistry 118 (2015): 61-67.
  • Myint, K. Z., & Xie, X. Q. (2015). Ligand Biological Activity Predictions Using Fingerprint-Based Artificial Neural Networks (FANN-QSAR). In Artificial Neural Networks (pp. 149-164). Springer New York.
  • Teramachi, J.; Silbermann, R.; Yang, P.; Zhao, W.; Mohammad, K. S.; Guo, J.; Anderson, J. L.; Zhou, D.; Feng, R.; Myint, K. Z.; Maertz, N.; Beumer, J. H.; Eiseman, J. L.; Windle, J. J.; Xie, X. Q.; Roodman, G. D.; Kurihara, N., Blocking the ZZ domain of sequestosome1/p62 suppresses myeloma growth and osteoclast formation in vitro and induces dramatic bone formation in myeloma-bearing bones in vivo. Leukemia 2015.
  • Silbermann, R., Zhou, D., Teramachi, J., Xie, X. Q., Roodman, G. D., & Kurihara, N. (2014). The p62-ZZ Domain Inhibitor XRK3F2 Alters Myeloma-Induced Suppression of Osteoblast Differentiation and Is Highly Cytotoxic to Myeloma Cells in Combination with Bortezomib. Blood, 124(21), 2083-2083.
  • Zeng, D., Ouyang, Q., Cai, Z., Xie, X. Q., & Anderson, C. J. (2014). New cross-bridged cyclam derivative CB-TE1K1P, an improved bifunctional chelator for copper radionuclides. Chemical Communications, 50(1), 43-45.
  • Zhang, S., Jia, N., Shao, P., Tong, Q., Xie, X. Q., & Bai, M. (2014). Target-Selective Phototherapy Using a Ligand-Based Photosensitizer for Type 2 Cannabinoid Receptor. Chemistry & biology, 21(3), 338-344.
  • Wang, L., & Xie, X. Q. (2014). Computational target fishing: what should chemogenomics researchers expect for the future of in silico drug design and discovery?. Future medicinal chemistry, 6(3), 247-249.
  • Liu, H., Wang, L., Su, W., & Xie, X. Q. (2014). Advances in recent patent and clinical trial drug development for Alzheimer’s disease. Pharmaceutical patent analyst, 3(4), 429-447.
  • Feng, R., Milcarek, C. A., & Xie, X. Q. (2014). Antagonism of cannabinoid receptor 2 pathway suppresses IL-6-induced immunoglobulin IgM secretion.BMC Pharmacology and Toxicology, 15(1), 30.
  • Feng, Z.; Alqarni, M. H.; Yang, P.; Tong, Q.; Chowdhury, A.; Wang, L.; Xie, X.-Q. Modeling, Molecular Dynamics Simulation and Mutation Validation for Structure of Cannabinoid Receptor 2 Based on Known Crystal Structures of GPCRs. J. Chem. Inf. Model. 2014, 54, 2483-2499.
  • Qin Ouyang, Lirong Wang, Ying Mu, Xiang-Qun Xie, “Modeling skin sensitization potential of mechanistically hard-to-be-classified aniline and phenol compounds with quantum mechanistic properties”. BMC pharmacology & toxicology 12/2014; 15(1):76. DOI: 10.1186/2050-6511-15-76
  • Lirong Wang, Chao Ma, Peter Wipf, Haibin Liu, Weiwei Su, Xiang-Qun Xie. TargetHunter: An In Silico Target Identification Tool for Predicting Therapeutic Potential of Small Organic Molecules Based on Chemogenomic Database. AAPS J. 2013 Apr; 15(2): 395–406. Published online 2013 Jan 5. doi: 10.1208/s12248-012-9449-z
  • 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.
  • Zomot E, Gur M, Bahar I. Microseconds Simulations Reveal a New Sodium-Binding Site and the Mechanism of Sodium-Coupled Substrate Uptake by LeuT. J Biol Chem. 2015;290(1):544-55. doi: 10.1074/jbc.M114.617555. PubMed PMID: 25381247; PMCID: PMC4281755.
  • 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.
  • 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.
  • Kolar M, Liu H, Xing EP. Graph Estimation from Multi-Attribute Data. Journal of Machine Learning Research. 2014;15(May):1713-50. PubMed PMID: 25620892; PMCID: PMC4303188.
  • Feng Z, Hu G, Ma S, Xie X-Q. Computational Advances for the Development of Allosteric Modulators and Bitopic Ligands in G Protein-Coupled Receptors. AAPS J. 2015;17(5):1080-95; PMCID: PMC4540734.
  • Chang X, Yang Y, Xing E, Yu Y. Complex event detection using semantic saliency and nearly-isotonic SVM. InInternational Conference on Machine Learning 2015 Jun 1 (pp. 1348-1357).
  • Alqarni M, Myint KZ, Tong Q, Yang P, Bartlow P, Wang L, Feng R, Xie X-Q. Examining the Critical Roles of Human CB2 Receptor Residues Valine 3.32 (113) and Leucine 5.41 (192) in Ligand Recognition and Downstream Signaling Activities. Biochem Biophys Res Commun. 2014;452(3):334-9; PMCID: PMC4465889.
  • Zheng X, Yu Y, Xing EP. Linear time samplers for supervised topic models using compositional proposals. InProceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 2015 Aug 10 (pp. 1523-1532). ACM