Yanli Wang

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc PubChem's BioAssay Database
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D400-12. 2012
  2. pmc An overview of the PubChem BioAssay resource
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D255-66. 2010
  3. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D13-25. 2012
  4. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D38-51. 2011
  5. pmc PubChem: a public information system for analyzing bioactivities of small molecules
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:W623-33. 2009
  6. pmc FSelector: a Ruby gem for feature selection
    Tiejun Cheng
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 28:2851-2. 2012
  7. pmc Structure-based virtual screening for drug discovery: a problem-centric review
    Tiejun Cheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    AAPS J 14:133-41. 2012
  8. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D5-16. 2010
  9. pmc Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection
    Tiejun Cheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Chem Inf Model 51:229-36. 2011
  10. doi request reprint PubChem BioAssay: 2014 update
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 42:D1075-82. 2014

Collaborators

Detail Information

Publications24

  1. pmc PubChem's BioAssay Database
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D400-12. 2012
    ..In this work, we provide an update for the PubChem BioAssay resource, including information content growth, data model extension and new developments of data submission, retrieval, analysis and download tools...
  2. pmc An overview of the PubChem BioAssay resource
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D255-66. 2010
    ..In this work, we describe the PubChem BioAssay database, including data model, bioassay deposition and utilities that PubChem provides for searching, downloading and analyzing the biological activity information contained therein...
  3. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 40:D13-25. 2012
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  4. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 39:D38-51. 2011
    ..Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  5. pmc PubChem: a public information system for analyzing bioactivities of small molecules
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 37:W623-33. 2009
    ..Most of the tools described in this work can be directly accessed at http://pubchem.ncbi.nlm.nih.gov/assay/. URLs for accessing other tools described in this work are specified individually...
  6. pmc FSelector: a Ruby gem for feature selection
    Tiejun Cheng
    Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 28:2851-2. 2012
    ..FSelector also provides many useful auxiliary tools, including normalization, discretization and missing data imputation...
  7. pmc Structure-based virtual screening for drug discovery: a problem-centric review
    Tiejun Cheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    AAPS J 14:133-41. 2012
    ....
  8. pmc Database resources of the National Center for Biotechnology Information
    Eric W Sayers
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Nucleic Acids Res 38:D5-16. 2010
    ..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov...
  9. pmc Binary classification of aqueous solubility using support vector machines with reduction and recombination feature selection
    Tiejun Cheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
    J Chem Inf Model 51:229-36. 2011
    ..Moreover, our work may be used for comparative evaluation of solubility classification studies ascribe to the use of completely public resources...
  10. doi request reprint PubChem BioAssay: 2014 update
    Yanli Wang
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 42:D1075-82. 2014
    ....
  11. pmc Pharmacophore and 3D-QSAR characterization of 6-arylquinazolin-4-amines as Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A) inhibitors
    Yongmei Pan
    National Center for Biotechnology Information, National Library of Medicine, National Institution of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA
    J Chem Inf Model 53:938-47. 2013
    ....
  12. pmc Multi-conformation 3D QSAR study of benzenesulfonyl-pyrazol-ester compounds and their analogs as cathepsin B inhibitors
    Zhigang Zhou
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health Bethesda, MD 20894, USA
    J Mol Graph Model 30:135-47. 2011
    ..The multi-conformation method to build 3D QSAR is very effective approach to obtain satisfactory models with high correlation with experimental results and high prediction power for unknown compounds...
  13. pmc A novel method for mining highly imbalanced high-throughput screening data in PubChem
    Qingliang Li
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 25:3310-6. 2009
    ....
  14. pmc PubChem as a public resource for drug discovery
    Qingliang Li
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Drug Discov Today 15:1052-7. 2010
    ..As a public resource, PubChem lowers the barrier for researchers to advance the development of chemical tools for modulating biological processes and drug candidates for disease treatments...
  15. pmc QSAR models for predicting cathepsin B inhibition by small molecules--continuous and binary QSAR models to classify cathepsin B inhibition activities of small molecules
    Zhigang Zhou
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    J Mol Graph Model 28:714-27. 2010
    ....
  16. pmc Identifying compound-target associations by combining bioactivity profile similarity search and public databases mining
    Tiejun Cheng
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
    J Chem Inf Model 51:2440-8. 2011
    ..Furthermore, BASS identified a significant fraction of structurally diverse compounds with similar bioactivities, indicating its feasibility of "scaffold hopping" in searching novel molecules against the target of interest...
  17. doi request reprint Pathway analysis for drug repositioning based on public database mining
    Yongmei Pan
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
    J Chem Inf Model 54:407-18. 2014
    ....
  18. pmc The Text-mining based PubChem Bioassay neighboring analysis
    Lianyi Han
    National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    BMC Bioinformatics 11:549. 2010
    ..In this work, we propose a text-mining based approach for bioassay neighboring analysis from the unstructured text descriptions contained in the PubChem BioAssay database...
  19. pmc Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules
    Tiejun Cheng
    National Center for Biotechnology Information, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Bioinformatics 26:2881-8. 2010
    ....
  20. pmc A survey of across-target bioactivity results of small molecules in PubChem
    Lianyi Han
    National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
    Bioinformatics 25:2251-5. 2009
    ..This work enables one to select target specific inhibitors, identify promiscuous compounds and better understand the biological mechanisms of target-small molecule interactions...
  21. pmc Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem
    Lianyi Han
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Bioinformatics 9:401. 2008
    ..Computational approaches for the analysis of HTS results face great challenges due to the large quantity of information and significant amounts of erroneous data produced...
  22. pmc An efficient algorithm coupled with synthetic minority over-sampling technique to classify imbalanced PubChem BioAssay data
    Ming Hao
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Anal Chim Acta 806:117-27. 2014
    ..Therefore, we hope that the proposed combinatorial algorithm based on GLMBoost and SMOTE could be extensively used to tackle the imbalanced classification problem. ..
  23. pmc Computational analysis of the cathepsin B inhibitors activities through LR-MMPBSA binding affinity calculation based on docked complex
    Zhigang Zhou
    National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, Bethesda, Maryland 20894, USA
    J Comput Chem 30:2165-75. 2009
    ..Our results also show that the results based on protein dimer show better correlations with experimental activity when compared to results based on monomer in the in silico calculations...
  24. pmc Improving protein structure similarity searches using domain boundaries based on conserved sequence information
    Kenneth Evan Thompson
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    BMC Struct Biol 9:33. 2009
    ....