JULIA VLADIMIROVNA PONOMARENKO

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies
    Sergey Kozhenkov
    San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    BMC Syst Biol 5:7. 2011
  2. ncbi BiologicalNetworks 2.0--an integrative view of genome biology data
    Sergey Kozhenkov
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    BMC Bioinformatics 11:610. 2010
  3. ncbi Curation of complex, context-dependent immunological data
    Randi Vita
    La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, California, USA
    BMC Bioinformatics 7:341. 2006
  4. ncbi IEDB-3D: structural data within the immune epitope database
    Julia Ponomarenko
    San Diego Supercomputer Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, CA 92093, USA
    Nucleic Acids Res 39:D1164-70. 2011
  5. ncbi Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology
    Julia V Ponomarenko
    San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093 0537, USA
    Proteins 58:855-65. 2005
  6. ncbi ElliPro: a new structure-based tool for the prediction of antibody epitopes
    Julia Ponomarenko
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    BMC Bioinformatics 9:514. 2008
  7. ncbi Antibody-protein interactions: benchmark datasets and prediction tools evaluation
    Julia V Ponomarenko
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    BMC Struct Biol 7:64. 2007
  8. ncbi Semantic integration of data on transcriptional regulation
    Michael Baitaluk
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Bioinformatics 26:1651-61. 2010
  9. ncbi Immune epitope database analysis resource (IEDB-AR)
    Qing Zhang
    Immune Epitope Database and Analysis Resource IEDB AR, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
    Nucleic Acids Res 36:W513-8. 2008
  10. ncbi Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population
    Jason A Greenbaum
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 106:20365-70. 2009

Research Grants

  1. Transcription Factor-DNA Interactions: Structural Classification and Prediction
    Julia Ponomarenko; Fiscal Year: 2009
  2. Transcription Factor-DNA Interactions: Structural Classification and Prediction
    JULIA VLADIMIROVNA PONOMARENKO; Fiscal Year: 2010
  3. Transcription Factor-DNA Interactions: Structural Classification and Prediction
    JULIA VLADIMIROVNA PONOMARENKO; Fiscal Year: 2010

Collaborators

Detail Information

Publications10

  1. ncbi BiologicalNetworks--tools enabling the integration of multi-scale data for the host-pathogen studies
    Sergey Kozhenkov
    San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    BMC Syst Biol 5:7. 2011
    ....
  2. ncbi BiologicalNetworks 2.0--an integrative view of genome biology data
    Sergey Kozhenkov
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    BMC Bioinformatics 11:610. 2010
    ..Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems...
  3. ncbi Curation of complex, context-dependent immunological data
    Randi Vita
    La Jolla Institute for Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, California, USA
    BMC Bioinformatics 7:341. 2006
    ..The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data http://www.immuneepitope.org...
  4. ncbi IEDB-3D: structural data within the immune epitope database
    Julia Ponomarenko
    San Diego Supercomputer Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, CA 92093, USA
    Nucleic Acids Res 39:D1164-70. 2011
    ..The query results can be downloaded in Microsoft Excel format, or the entire database, together with structural data both curated and calculated, can be downloaded in either XML or MySQL formats...
  5. ncbi Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology
    Julia V Ponomarenko
    San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093 0537, USA
    Proteins 58:855-65. 2005
    ..The effect of superfolds (folds with many functions) is considered and, by comparison to the Structural Classification of Proteins (SCOP), the individual effects of family, superfamily, and fold...
  6. ncbi ElliPro: a new structure-based tool for the prediction of antibody epitopes
    Julia Ponomarenko
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    BMC Bioinformatics 9:514. 2008
    ..The aim of this work was to implement that method as a web-tool and evaluate its performance on discontinuous epitopes known from the structures of antibody-protein complexes...
  7. ncbi Antibody-protein interactions: benchmark datasets and prediction tools evaluation
    Julia V Ponomarenko
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
    BMC Struct Biol 7:64. 2007
    ..As the number of structures of antibody-protein complexes grows, further interest in prediction methods using 3D structure is anticipated. This work aims to establish a benchmark for 3D structure-based epitope prediction methods...
  8. ncbi Semantic integration of data on transcriptional regulation
    Michael Baitaluk
    San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
    Bioinformatics 26:1651-61. 2010
    ..However, there are no resources to integrate these data automatically or to provide a 'one-stop shop' experience for users seeking information essential for deciphering and modeling gene regulatory networks...
  9. ncbi Immune epitope database analysis resource (IEDB-AR)
    Qing Zhang
    Immune Epitope Database and Analysis Resource IEDB AR, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
    Nucleic Acids Res 36:W513-8. 2008
    ..New functionalities have been added to most of the previously implemented tools, and a total of eight new tools were added, including two B-cell epitope prediction tools, four T-cell epitope prediction tools and two analysis tools...
  10. ncbi Pre-existing immunity against swine-origin H1N1 influenza viruses in the general human population
    Jason A Greenbaum
    Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
    Proc Natl Acad Sci U S A 106:20365-70. 2009
    ..These results are consistent with reports about disease incidence, severity, and mortality rates associated with human S-OIV...

Research Grants4

  1. Transcription Factor-DNA Interactions: Structural Classification and Prediction
    Julia Ponomarenko; Fiscal Year: 2009
    ..This information is significant for designing drugs for treatment of diseases associated with inadequate gene regulation. ..
  2. Transcription Factor-DNA Interactions: Structural Classification and Prediction
    JULIA VLADIMIROVNA PONOMARENKO; Fiscal Year: 2010
    ..This information is significant for designing drugs for treatment of diseases associated with inadequate gene regulation. ..
  3. Transcription Factor-DNA Interactions: Structural Classification and Prediction
    JULIA VLADIMIROVNA PONOMARENKO; Fiscal Year: 2010
    ..This information is significant for designing drugs for treatment of diseases associated with inadequate gene regulation. ..