Alexey V Antonov

Summary

Country: Germany

Publications

  1. ncbi request reprint Mining protein lists from proteomics studies: applications for drug discovery
    Alexey V Antonov
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D 85764, Neuherberg, Germany 49 89 3187 2788 49 89 3187 3585
    Expert Opin Drug Discov 5:323-31. 2010
  2. pmc BioProfiling.de: analytical web portal for high-throughput cell biology
    Alexey V Antonov
    Helmholtz Zentrum Munchen, Institute for Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 39:W323-7. 2011
  3. pmc R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases
    Alexey V Antonov
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute for Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 38:W78-83. 2010
  4. doi request reprint TICL--a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics
    Alexey V Antonov
    Helmholtz Zentrum Munchen, Institute for Bioinformatics and Systems Biology, Neuherberg, Germany
    FEBS J 276:2084-94. 2009
  5. pmc A systematic approach to infer biological relevance and biases of gene network structures
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 34:e6. 2006
  6. pmc GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists
    Alexey V Antonov
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute for Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 37:W323-8. 2009
  7. doi request reprint PPI spider: a tool for the interpretation of proteomics data in the context of protein-protein interaction networks
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, Neuherberg, Germany
    Proteomics 9:2740-9. 2009
  8. ncbi request reprint BIOREL: the benchmark resource to estimate the relevance of the gene networks
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    FEBS Lett 580:844-8. 2006
  9. doi request reprint PLIPS, an automatically collected database of protein lists reported by proteomics studies
    Alexey V Antonov
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute for Bioinformatics and System Biology, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    J Proteome Res 8:1193-7. 2009
  10. pmc ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
    Alexey V Antonov
    Helmholtz Zentrum Munich, National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 36:W347-51. 2008

Detail Information

Publications17

  1. ncbi request reprint Mining protein lists from proteomics studies: applications for drug discovery
    Alexey V Antonov
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D 85764, Neuherberg, Germany 49 89 3187 2788 49 89 3187 3585
    Expert Opin Drug Discov 5:323-31. 2010
    ..Take home message: Reported protein lists represent a valuable resource which can be used for a variety of goals, ranging from biomarkers discovery to identification of novel therapeutic implications of known drugs...
  2. pmc BioProfiling.de: analytical web portal for high-throughput cell biology
    Alexey V Antonov
    Helmholtz Zentrum Munchen, Institute for Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 39:W323-7. 2011
    ..BioProfiling.de provides a user friendly dialog-driven web interface for several model organisms and supports most available gene identifiers. The web portal is freely available at http://www.BioProfiling.de/gene_list...
  3. pmc R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases
    Alexey V Antonov
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute for Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 38:W78-83. 2010
    ..R spider provides a user-friendly dialog-driven web interface for several model organisms and supports most available gene identifiers. R spider is freely available at http://mips.helmholtz-muenchen.de/proj/rspider...
  4. doi request reprint TICL--a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics
    Alexey V Antonov
    Helmholtz Zentrum Munchen, Institute for Bioinformatics and Systems Biology, Neuherberg, Germany
    FEBS J 276:2084-94. 2009
    ..The TICL web tool is freely accessible at http://mips.helmholtz-muenchen.de/proj/cmp...
  5. pmc A systematic approach to infer biological relevance and biases of gene network structures
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 34:e6. 2006
    ..By the analyses of real data we demonstrate that the potential application of BIOREL ranges from various benchmarking purposes to systematic analysis of the network biology...
  6. pmc GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists
    Alexey V Antonov
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute for Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 37:W323-8. 2009
    ..GeneSet2miRNA provides a user friendly dialog-driven web page submission available for several model organisms. GeneSet2miRNA is freely available at http://mips.helmholtz-muenchen.de/proj/gene2mir/...
  7. doi request reprint PPI spider: a tool for the interpretation of proteomics data in the context of protein-protein interaction networks
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, Neuherberg, Germany
    Proteomics 9:2740-9. 2009
    ..We reanalyzed them using PPI spider and demonstrated that in most cases PPI spider could provide statistically significant hypotheses that are helpful for understanding of the protein list...
  8. ncbi request reprint BIOREL: the benchmark resource to estimate the relevance of the gene networks
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    FEBS Lett 580:844-8. 2006
    ..Using BIOREL as the benchmark resource we compared the quality of experimental and theoretically predicted protein interaction data...
  9. doi request reprint PLIPS, an automatically collected database of protein lists reported by proteomics studies
    Alexey V Antonov
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute for Bioinformatics and System Biology, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    J Proteome Res 8:1193-7. 2009
    ..PLIPS is a freely available Web-based tool ( http://mips.helmholtz-muenchen.de/proj/plips )...
  10. pmc ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
    Alexey V Antonov
    Helmholtz Zentrum Munich, National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 36:W347-51. 2008
    ..In addition, the web service interface allows the submission of any kind of annotation data. ProfCom is freely available at http://webclu.bio.wzw.tum.de/profcom/...
  11. pmc KEGG spider: interpretation of genomics data in the context of the global gene metabolic network
    Alexey V Antonov
    GSF National Research Centre for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Genome Biol 9:R179. 2008
    ..Analyzing a number of experimentally derived gene lists, we demonstrate that KEGG spider provides deeper insights into metabolism variations in comparison to existing methods...
  12. ncbi request reprint MIPS bacterial genomes functional annotation benchmark dataset
    Igor V Tetko
    Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    Bioinformatics 21:2520-1. 2005
    ..Different program settings and incompatible protocols make a comparison of the analyzed methods difficult...
  13. ncbi request reprint Exploiting scale-free information from expression data for cancer classification
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Comput Biol Chem 29:288-93. 2005
    ..In proposed schema of data analyses only information on relative gene expression levels in each sample is exploited. Testing on publicly available datasets leads to superior classification results...
  14. ncbi request reprint Complex functionality of gene groups identified from high-throughput data
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    J Mol Biol 363:289-96. 2006
    ....
  15. ncbi request reprint A web portal for classification of expression data using maximal margin linear programming
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Bioinformatics 20:3284-5. 2004
    ..The input data format is the same as that used in most publicly available datasets. This makes the web resource particularly convenient for non-expert machine learning users working in the field of expression data analysis...
  16. doi request reprint Complex phylogenetic profiling reveals fundamental genotype-phenotype associations
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Neuherberg, Germany
    Comput Biol Chem 32:412-6. 2008
    ..Application of complex phylogenetic profiling to bacterial data and several well studied phenotypes reveals genotype-phenotype associations on the level of fundamental biochemical pathways...
  17. ncbi request reprint Optimization models for cancer classification: extracting gene interaction information from microarray expression data
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Bioinformatics 20:644-52. 2004
    ..Thus, they cannot be detected by simple classification approaches used previously. For these reasons, a classification procedure exploiting information related to changes in gene interactions is needed...