• Year 2019

    • Ma S, Attarwala I, Xie X-Q. SQSTM1/p62: a potential target for neurodegenerative disease. ACS Chem Neurosci 2019 Jan 18. doi: 10.1021/acschemneuro.8b00516.
    • Wang Y-q, Lin W-w, Wu N, Wang S, Chen M, Lin Z, Xie X-Q*, and Zhi-wei Feng*. Structural insight into the serotonin (5-HT) receptor family by molecular docking, molecular dynamics simulation and systems pharmacology analysis. Acta Pharmacologica Sinica, 2019, in press.
    • Man, V.; Truong, P.; Li, M.; Wang, J.; Van-Oanh, N.-T.; Derreumaux, P.; Nguyen, P. Molecular Mechanism of the Cell Membrane Pore Formation Induced by Bubble Stable Cavitation, J. Phys. Chem. B, 2019, 123, 71-78
    • Fan P, Wang N, Wang L*, and Xie XQ*. Autophagy and apoptosis specific knowledgebases-guided systems pharmacology drug research. Current Cancer Drug Targets 2019 Feb 6;doi:10.2174/1568009619666190206122149. [Epub ahead of print]. PMID:30727895
    • Wang H, Liu X, Tao Y, Ye W, Jin Q, Cohen JW, and Xing EP*. Automatic human-like mining and constructing reliable genetic association database with deep reinforcement learning, Proceedings of 24th Pacific Symposium on Biocomputing (PSB 2019). Publication is not a journal.
    • Wang H, Wu Z, and Xing EP*. Removing confounding factors associated weights in deep neural networks improves the prediction accuracy for healthcare applications, Proceedings of 24th Pacific Symposium on Biocomputing (PSB 2019). Publication is not a journal.

    Year 2018

    • Bertholomey ML, Stone K, Lam TT, Bang S, Wu W, Nairn AC, Taylor JR, Torregrossa MM*. Phosphoproteomic Analysis of the Amygdala Response to Adolescent Glucocorticoid Exposure Reveals G-Protein Coupled Receptor Kinase 2 as a Target for Reducing Motivation for Alcohol. Proteomes. 2018 Oct 12;6(4). pii: E41. doi: 10.3390/proteomes6040041. PMID:30322021 [Publication with FRP.]
    • Wu W*#, Bang S#, Bleecker ER, Castro M, Denlinger L, Erzurum SC, Fahy JV, Fitzpatrick AM, Gaston BM, Hastie AT, Israel E, Jarjour NN, Levy BD, Mauger DT, Meyers DA, Moore WC, Peters M, Phillips BR, Phipatanakul W, Sorkness RL, Wenzel SE* (# co-first authors). Multiview cluster analysis identifies variable corticosteroid response phenotypes in severe asthma”, Am J Resp Crit Care Med (accepted) [Publication with FRP.]
    • Zhou L*, Zhou S, Yang P, Tian Y, Feng Z, Xie XQ*, Liu Y*. Targeted inhibition of the type 2 cannabinoid receptor is a novel approach to reduce renal fibrosis.  Kidney Int. 2018 Oct;94(4):756-772. doi: 10.1016/j.kint.2018.05.023. Epub 2018 Aug 6. PMID:30093080.
    • Lee JY, Krieger J, Herguedas B, García-Nafría J, Dutta A, Shaikh SA, Greger IH*, Bahar I*. Druggability simulations and X-ray crystallography reveal a ligand-binding site in the GluA3 AMPA receptor N-terminal domain. Structure. 2018 Nov 3. pii: S0969-2126(18)30378-2. doi: 10.1016/j.str.2018.10.017. [Epub ahead of print] PMID: 30528594
    • Wang H, Lengerich BJ, Aragam B, Xing EP*. Precision Lasso: Accounting for Correlations and Linear Dependencies in High-Dimensional Genomic Data. Bioinformatics. 2018 Sep 1. doi: 10.1093/bioinformatics/bty750. PMID:30184048
    • van Dijk L, Giladi M, Refaeli B, Hiller R, Cheng MH, Bahar I*, Khananshvili D*. Key residues controlling bidirectional ion movements in Na+/Ca2+ exchanger. Cell Calcium. 2018 Dec;76:10-22. PMID:30248574
    • Wu X, Xie S, Wang L, Fan P, Ge S, Xie XQ, Wu W*. A computational strategy for finding novel targets and therapeutic compounds for opioid dependence. PLoS One. 2018 Nov 7;13(11):e0207027. doi: 10.1371/journal.pone.0207027. eCollection 2018. PMID:30403753 [Joint publication for Cores A and C.]
    • Hu Z, Wang L, Ma S, Kirisci L, Feng Z, Xue Y, Klunk WE, Kamboh MI, Sweet RA, Becker J, Lv Q, Lopez OL*, Xie XQ*. Synergism of antihypertensives and cholinesterase inhibitors in Alzheimer’s disease. Alzheimers Dement (NY). 2018 Oct 14;4:542-555. PMID:30386819
    • Wang, J; Ge, Y; Xie X-Q. Development and testing of druglike screening libraries.  J. Chem. Inf. Model., Article ASAP (DOI: 10.1021/acs.jcim.8b00537).
    • Man, V; He, X; Derreumaux, P; Ji, B; Xie X-Q; Nguyen, P; Wang, J. Effects of all-atom molecular mechanics force fields on Amyloid peptide assembly: the case of Aβ16-22 Dimer. J. Chem. Theor. Comput. (accepted) (Manuscript ID ct-2018-01107f.R1).
    • Wang, J; Cieplak, P; Luo, R; Duan, Y. Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization to Reproduce Ab Initio Anisotropy. J. Chem. Theor. Comput. (accepted) (Manuscript ID ct-2018-006033.R2)
    • He, X.; Man, V.; Ji, B.; Xie, X-Q; Wang, J.  Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3. J. Comput.-Aided Mol. Des. 2018, Article ASAP (DOI: 10.1007/s10822-018-0162-6)
    • Wang K, Steer E, Otero PA, Bateman N, Cheng MH, Scott A, Wu C, Bahar I, Shih Y-T, Hsueh Y-P, Chu CT* (2018) PINK1 interacts with VCP/p97 and activates PKA to promote NSFL1C/p47 phosphorylation and dendritic arborization in neurons. eNeuro, in press. PMID: pending
    • Pei F, Li H, Liu B*, and Bahar I*. Quantitative systems pharmacological analysis of drugs of abuse reveals the pleiotropy of their targets and the effector role of mTORC1. Frontiers in Pharmacology, accepted with minor revision, doi: 10.1101/470922. PMID: pending
    • Dominik, D.; Man, V.; Van-Oanh, N.-T.; Wang, J.; Kawasaki, T.; Derreumaux, P.; Nguyen, P. Breaking down cellulose fibrils with a mid-infrared laser, Cellulose, 2018, 25, 5553-5568.
    • 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

    Year 2017

    • 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.
    • 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.
    • 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.

    Year 2016

    Year 2015 and before

    • 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