Computational Systems Biology and Bioinformatics Lab


 

2016

  • S. H. Chiu, L. Xie (2016) "Toward high-throughput predictive modeling of protein binding/unbinding kinetics". BioRxiv, doi: http://dx.doi.org/10.1101/024513. [PDF] JCIM, in revision
  • Z. Zhao, L. Xie, L. Xie, P. E. Bourne (2016) "Delineation of polypharmacology across the human structural kinome using a functional site interaction fingerprint approach ". J Med Chem. DOI: 10.1021/acs.jmedchem.5b02041 [PDF]
  • G. I. Allen, Amoroso N. Amoroso, Anghel G. Anghel et al. (2016) "Crowdsourced estimation of cognitive decline and resilience in Alzermer’s disease ". Alzheimer’s & Dementia, in press.
  • J. Lhota, L. Xie (2016) "Protein fold recognition using an improved single source k diverse shortest paths algorithm ". Proteins, [Epub ahead of print] [PDF]
  • T. Hart, S. Diber, W. Han, H. Xu, Z. Zhao, L Xie (2016) "Toward repurposing metformin as a precision anti-cancer therapy using structural systems pharmacology ". Sci Rep. , 6:20441 [PDF]
  • T. Hart, L Xie (2016) "Providing data science support for systems pharmacology and its implications to drug discovery ". Expert Opin Drug Discov., 11(3):241-256 [PDF]
  • Z. Zhao, C. Martin, R. Fan, P. E. Bourne, L Xie (2016) "Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology ". BMC Bioinformatics, 17(1):90 [PDF]
  • Y. Zhang, L. Xie, L. Xie & P. E.Bourne (2016) "The Plasmodium falciparum Drugome and its Polypharmacological Implications" BioRxiv doi: http://biorxiv.org/content/early/2016/03/05/042481. [PDF]

2015

  • L. Xie and P. E. Bourne (2015) "Developing multi-target therapeutics to fine-tune the evolutionary dynamics of the cancer ecosystem". Front. Pharmacol. 6:209. doi: 10.3389/fphar.2015.00209 [PDF]
  • L.-C. L. Tsai, L. Xie, K. Dore, L. Xie, J. C. Del Rio, C. C. King, G. MartinezAriza, C. Hulme, R. Malinow, P. E. Bourne, A. C. Newton (2015) "Zeta inhibitory peptide disrupts electrostatic interactions that maintain atypical protein kinase C in its active conformation on the scaffold p62". J. Biol. Chem, 290(36):21845-56. [PDF]
  • J. Lhota, R. Hauptman, T. Hart, C. Ng, L. Xie (2015) "A new method to improve network topological similarity search: applied to fold recognition", Bioinformatics, 31(13):2106-14. [PDF]
  • Y. Liu, H. Tong, L. Xie, Y. Tang (2015) "Supervised Link Prediction Using Random Walks ". Social Media Processing, 568:pp107-118 [PDF]

2014

  • L. Xie, X. Ge, H. Tan, L. Xie, Y. Zhang, T. Hart, X. Yan, P. E. Bourne (2014) "Toward Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine". PLoS Comp Biol, 10(5):e1003554. [PDF]
  • C. Ng, Y. Zhang, P. E. Bourne & L. Xie (2014) "Anti-infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach", Pacific Symposium on Biocomputing, 19:136-47. [PDF]
  • T. Evangelidis, L. Xie (2014) "An integrated workflow for proteome-wide off-target identification and polypharmacology drug design". Tsinghua Science and Technology, 19(3):275-284. [PDF]

2013

  • R. Chang, L. Xie, P.E. Bourne, B. Palsson (2013) "Antibacterial Mechanisms Identified Through Structural Systems Pharmacology". BMC Syst. Biol. 7:102 [PDF]
  • H. Tan, X. Ge, L. Xie (2013) "Structural Systems Pharmacology: a New Frontier in Discovering Novel Drug Targets". Curr Drug Targets, 14:952-956. [Link]
  • L. Xie, C. Ng, T. Ali, V. Valencia, B.L. Ferreira, V. Xue, M. Tanweer, D. Zhou, G. Haddad, P. E. Bourne, L. Xie.(2013) "Multiscale Modeling of the Causal Functional Roles of nsSNPs in a Genome-Wide Association Study: Application to Hypoxia". BMC Genomics 14(S3):S9 [PDF]
  • S. L. Epstein, X. Yun, L. Xie L (2013) "Multi-Agent, Multi-Case-Based Reasoning". Lecture Notes in Computer Science, Vol7969: 74-88 [Link]
  • G. Daniel, S.L. Kinnings, L. Xie, L. Xie, Y. Zhang, P. E. Bourne, and Y. Gil (2013) "Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome". PLoS One 8(11):e80278 [PDF]


2012

  • L. Xie, S.L. Kinnings, L. Xie and P.E. Bourne (2012) Predicting the Polypharmacology of Drugs: Identifying New Uses Through Cheminformatics, Structural Informatics and Molecular Modeling-based Approaches in Drug Repurposing M. Barrett and D. Frail (Eds.) Chap. 7, 163-194, Wiley and Sons.
  • S.J. Ho Sui, R. Lo, R. Fernandes, M.DG.Caulfield, J. Lerman, L. Xie, P.E. Bourne, D.L.Baillie and F.S.L.Brinkman (2012) "Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence". Int. J. of Antimicrobial Agents 40(3):246-251 [PDF].
  • L. Xie, L. Xie, S. L. Kinnings, and P.E. Bourne (2012) "Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs". Annu. Rev. Pharmacol. Toxicol. 52: 361-379 [PDF].


2011

  • L. Xie, T. Evangelidis, L. Xie and P.E. Bourne (2011) "Drug Discovery Using Chemical Systems Biology: Weak inhibition of multiple kinases may contribute to the anti-cancer effect of Nelfinavir". PLoS Comp. Biol. 7(4) e1002037 [PDF].
    (Comments: Science 2011 332(6030) 648-649 [Link])
  • L. Xie, L. Xie and P.E. Bourne (2011) "Structure-based Systems Biology for Analyzing Off-target Binding". Curr. Opinions in Struct. Biol. 21(2):189-199 [PDF].
  • S.L. Kinnings, N. Liu, P.J. Tonge, R.M. Jackson, L. Xie and P.E.Bourne (2011) "A Machine Learning Based Method to Improve Docking Scoring Functions and its Application to Drug Repurposing". J. Chem. Info. Model. 51(2):408-419 [PDF].

2010

  • S.L. Kinnings, L. Xie, K.H.Fung, R.M. Jackson, L. Xie and P.E. Bourne (2010) "The Mycbacterium tuberculosis druggome and its Pharmaceutical Implications". Plos Comp. Biol. 6(11): e1000976 [PDF]
  • R.L Chang, L. Xie, L. Xie, P.E. Bourne B.O. Palsson (2010) "Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model". Plos Comp. Biol. 6(9): e1000938 [PDF]
  • J. Ren, L. Xie, W. Li, P. E. Bourne (2010) "SMAP-WS: A Parallel Web Service for Structural Proteome-Wide Ligand Binding Site Comparison.". Nucleic Acids Res., 38(Suppl):W441-4 [PDF]
  • J. D. Durrant, R. E. Amaro, L. Xie, M. D. Urbaniak, M. A. J. Ferguson, A. Haapalainen, Z. Chen, A. M. Di Guilmi, F. Wunder, P. E. Bourne, J. A. McCammon (2010) "A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology". PLoS Comp. Biol., 6(1):e1000648 [PDF]

2009

  • S. Kinnings, N. Liu, N. Buchmeier, P.J. Tonge, L. Xie and P.E. Bourne (2009) "Drug discovery using chemical systems biology: repositioning the safe medicine Comtan to treat multi-drug and extensively drug resistant tuberculosis". PLoS Comp. Biol., 5(7):e1000423 [PDF]
  • L. Xie, J. Li, L. Xie and P.E. Bourne (2009) "Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors". PLoS Comp. Biol., 5(5):e1000387 [PDF]
  • L. Xie, L. Xie and P.E. Bourne (2009) "A unified statistical model to support local sequence order independent similarity searching for ligand binding sites and its application to genome-based drug discovery". Bioinformatics, 25(12):i305-i312 [PDF]

2008

  • L. Xie and P.E. Bourne (2008) "Detecting Evolutionary Relationships Across Existing Fold Space, Using Sequence Order Independent Profile-profile Alignments". PNAS, 105(14):5441 [PDF]

2007

  • L. Xie, J. Wang and P.E. Bourne (2007) "In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Esterogen Receptor Modulators". PLoS Comp. Biol., 3(11):e217 [PDF].
  • L. Xie, and P.E. Bourne (2007) "A Robust and Efficient Algorithm for the Shape Description of Protein Structures and Its Application in Predicting Ligand Binding Sites". BMC Bioinformatics, 8(Suppl 4):S9 [PDF].

2006

  • A. Kouranov, L. Xie, J. de la Cruz, L. Chen, J. Westbrook, P.E. Bourne, H.M. Berman (2006) "The RCSB PDB information portal for structural genomic". Nucleic Acids Res., 34(Database issue):D302-305 [PDF].

2005

  • L. Xie and P.E. Bourne (2005) "Functional coverage of the human genome by existing structures, structural genomics targets, and homology models". PLoS Comp. Biol., 1(3):e31 [PDF].
  • N. Deshpande, K.J. Addess, W.F. Bluhm, J.C. Merino-Ott, W. Townsend-Merino, Q. Zhang, C. Knezevich, L. Xie, L. Chen, Z. Feng, R.K. Green, J.L. Flippen-Anderson, J. Westbrook, H.M. Berman, P.E. Bourne (2005) " The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema". Nucleic Acids Res., 33(Database issue):D233-237 [PDF].

2003

  • C.L. Tang, L. Xie, I.Y. Koh, S. Posy, E. Alexov, B. Honig (2003) "On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles". J. Mol. Biol., 334(5):1043-1062.
  • D. Petrey, Z. Xiang, C.L. Tang, L. Xie, M. Gimpelev, T. Mitros, C.S. Soto, S. Goldsmith-Fischman, A. Kernytsky, A. Schlessinger, I.Y. Koh, E. Alexov, B. Honig (2003) " Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling". Proteins, 53(S6):430-435.