• Xue Y, Feng ZW, Li XY, Hu ZH, Xu Q, Wang Z, Cheng JH, Shi HT, Wang QB, Wu HY, Xie X.-Q. The efficacy and safety of cilostazol as an alternative to aspirin in Chinese patients with aspirin intolerance after coronary stent implantation: a combined clinical study and computational system pharmacology analysis. Acta Pharmacologica Sinica. 2018 Feb;39(2):205. PMID: 28933424 PMCID: PMC5800472
  • Cha-Molstad H, Lee SH, Kim JG, Sung KW, Hwang J, Shim SM, Ganipisetti S, McGuire T, Mook-Jung I, Ciechanover A, Xie XQ, Kim BY, Kwon YT. Regulation of autophagic proteolysis by the N-recognin SQSTM1/p62 of the N-end rule pathway. 2018 Jan 29:1-3. doi: 10.1080/15548627.2017.1415190. [Epub ahead of print] PMID:29261001
  • Chen S, Feng Z, Wang Y, Ma S, Hu Z, Yang P, Chai Y, Xie, X.-Q*. Discovery of Novel Ligands for TNF-α and TNF Receptor-1 through Structure-Based Virtual Screening and Biological Assay. J Chem Inf Model. 2017 Apr 19. PMID: 28422491
  • Bian Y, Feng Z, Yang P, Xie, X.-Q*. Integrated In Silico Fragment-Based Drug Design: Case Study with Allosteric Modulators on Metabotropic Glutamate Receptor 5. AAPS J. 2017 Jul;19(4):1235-1248.
  • Cha-Molstad H, Yu JE, Feng Z, Lee SH, Kim JG, Yang P, Han B, Sung KW, Yoo YD, Hwang J, McGuire T, Shim SM, Song HD, Ganipisetti S, Wang N, Jang JM, Lee MJ, Kim SJ, Lee KH, Hong JT, Ciechanover A, Mook-Jung I, Kim KP, Xie, X.-Q*, Kwon YT*, Kim BY*. p62/SQSTM1/Sequestosome-1 is an N-recognin of the N-end rule pathway which modulates autophagosome biogenesis. Nature Communications 8, Article number: 102 (2017).
  • Wang N, Wang L, Xie X.-Q. ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research. J Chem Inf Model. 2017 Nov 27;57(11):2686-2698. doi: 10.1021/acs.jcim.7b00277. Epub 2017 Oct 26. PMID:29016123
  • Sauerwald N, Zhang S, Kingsford C, Bahar I. Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings. Nucleic acids research. 2017 Apr 20;45(7):3663-73. PubMed PMID: 28334818; PubMed Central PMCID: PMC5397156.
  • 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.
  • Wang H, Aragam B, Xing EP. Variable Selection in Heterogeneous Datasets: A Truncated-rank Sparse Linear Mixed Model with Applications to Genome-wide Association Studies. KDD : proceedings. International Conference on Knowledge Discovery & Data Mining. bioRxiv. 2017 Jan 1:228106.
  • 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.
  • Xie X-Q, Wang L, Wang J, Xie Z, Yang P, Ouyang Q. Neuropathology of Drug Addictions and Substance Misuse. San Diego, CA. Elsevier Inc.;. Chapter 19, In silico chemogenomics knowledgebase and computational system neuropharmacology approach for cannabinoid drug research.
  • Wang L, Xie X-Q. Cancer genomics: opportunities for medicinal chemistry? Future medicinal chemistry. 2016;8(4):357-359. doi:10.4155/fmc.16.1. PubMed PMID: 26976526; PubMed Central PMCID: PMC4847433.
  • Hu J, Feng Z, Ma S, Zhang Y, Tong Q, Alqarni MH, Gou X, Xie X-Q. Difference and influence of inactive and active states of cannabinoid receptor subtype CB2: from conformation to drug discovery. Journal of chemical information and modeling. 2016 May 26;56(6):1152-63. PubMed PMID: 27186994; PubMed Central PMCID: PMC5395206.
  • Feng Z, Pearce LV, Zhang Y, Xing C, Herold BK, Ma S, Hu Z, Turcios NA, Yang P, Tong Q, McCall AK. Multi-functional diarylurea small molecule inhibitors of TRPV1 with therapeutic potential for neuroinflammation. The AAPS journal. 2016 Jul 1;18(4):898-913. PubMed PMID: 27000851; PubMed Central PMCID: PMC5333490.
  • Xu X, Ma S, Feng Z, Hu G, Wang L, Xie, X.-Q*. Chemogenomics knowledgebase and systems pharmacology for hallucinogen target identification-Salvinorin A as a case study. J Mol Graph Model. 2016 Nov;70:284-295. PMID: 27810775
  • Zhang H, Ma S, Feng Z, Wang D, Li C, Cao Y, Chen X, Liu A, Zhu Z, Zhang J, Zhang G, Chai Y, Wang L, Xie, X.-Q*. Cardiovascular Disease Chemogenomics Knowledgebase-guided Target Identification and Drug Synergy Mechanism Study of an Herbal Formula. Sci Rep. 2016 Sep 28;6:33963. PMID: 27678063
  • Zhang Y, Wang L, Feng Z, Cheng H, McGuire TF, Ding Y, Cheng T, Gao Y, Xie, X.-Q*. StemCellCKB: An Integrated Stem Cell-Specific Chemogenomics KnowledgeBase for Target Identification and Systems-Pharmacology Research. J Chem Inf Model. 2016 Oct 24;56(10):1995-2004. PMID: 27643925
  • Hu J, Hu Z, Zhang Y, Gou X, Mu Y, Wang L, Xie, X.-Q*. Metal binding mediated conformational change of XPA protein: a potential cytotoxic mechanism of nickel in the nucleotide excision repair. J Mol Model. 2016 Jul;22(7):156. PMID: 27307058
  • Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y. Regulation of XIAP turnover reveals a role for USP11 in promotion of tumorigenesis. EBioMedicine. 2017 Feb 1;15:48-61.PubMed PMID: 28040451; PubMed Central PMCID: PMC5233825.
  • Stern AM, Schurdak ME, Bahar I, Berg JM, Taylor DL. A perspective on implementing a quantitative systems pharmacology platform for drug discovery and the advancement of personalized medicine. Journal of biomolecular screening. 2016 Jul;21(6):521-34. PubMed PMID: 26962875; PubMed Central PMCID: PMC4917453.
  • Liu B, Liu Q, Yang L, Palaniappan SK, Bahar I, Thiagarajan PS, Ding JL. Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways. Sci. Signal.. 2016 Jul 12;9(436):ra70-. PubMed PMID: 27405980; PubMed Central PMCID: PMC5087126.
  • 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.
  • 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).
  • 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.
  • 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, In press.
  • 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.
  • 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.

Manuscripts submitted