Anagha Joshi

Summary

Publications

  1. pmc Characterizing regulatory path motifs in integrated networks using perturbational data
    Anagha Joshi
    Department of Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
    Genome Biol 11:R32. 2010
  2. doi Reverse-engineering transcriptional modules from gene expression data
    Tom Michoel
    Department of Plant Systems Biology, VIB, Gent, Belgium
    Ann N Y Acad Sci 1158:36-43. 2009
  3. doi Module networks revisited: computational assessment and prioritization of model predictions
    Anagha Joshi
    Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, B 9052 Gent, Belgium
    Bioinformatics 25:490-6. 2009
  4. pmc Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
    Tom Michoel
    Department of Plant Systems Biology, VIB, Technologiepark 927, B 9052 Gent, Belgium
    BMC Syst Biol 3:49. 2009
  5. doi Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development
    Vanessa Vermeirssen
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    Mol Biosyst 5:1817-30. 2009
  6. pmc Module network inference from a cancer gene expression data set identifies microRNA regulated modules
    Eric Bonnet
    Department of Plant Systems Biology, VIB, Gent, Belgium
    PLoS ONE 5:e10162. 2010
  7. pmc Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast
    Anagha Joshi
    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust MRC Building Hills Road, Cambridge CB2 0XY, UK
    Nucleic Acids Res 39:9108-17. 2011
  8. pmc Validating module network learning algorithms using simulated data
    Tom Michoel
    Bioinformatics and Evolutionary Genomics, Department of Plant Systems Biology, VIB Ghent University, Ghent, Belgium
    BMC Bioinformatics 8:S5. 2007
  9. ncbi Analysis of a Gibbs sampler method for model-based clustering of gene expression data
    Anagha Joshi
    Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
    Bioinformatics 24:176-83. 2008

Detail Information

Publications9

  1. pmc Characterizing regulatory path motifs in integrated networks using perturbational data
    Anagha Joshi
    Department of Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
    Genome Biol 11:R32. 2010
    ..A case study in Saccharomyces cerevisiae identifies eight regulatory path motifs and demonstrates their biological significance...
  2. doi Reverse-engineering transcriptional modules from gene expression data
    Tom Michoel
    Department of Plant Systems Biology, VIB, Gent, Belgium
    Ann N Y Acad Sci 1158:36-43. 2009
    ..We show that the inferred probabilistic models extend beyond the dataset used to learn the models...
  3. doi Module networks revisited: computational assessment and prioritization of model predictions
    Anagha Joshi
    Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, B 9052 Gent, Belgium
    Bioinformatics 25:490-6. 2009
    ..As time progresses, computational power increases but well-established inference methods often remain locked in their initial suboptimal solution...
  4. pmc Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
    Tom Michoel
    Department of Plant Systems Biology, VIB, Technologiepark 927, B 9052 Gent, Belgium
    BMC Syst Biol 3:49. 2009
    ..To date, there has been no systematic comparison of the relative strengths and weaknesses of both types of methods...
  5. doi Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development
    Vanessa Vermeirssen
    Department of Plant Systems Biology, VIB, B 9052 Ghent, Belgium
    Mol Biosyst 5:1817-30. 2009
    ..In conclusion, through reverse-engineering of C. elegans expression data, we obtained transcription regulatory networks that can provide further insight into metazoan development...
  6. pmc Module network inference from a cancer gene expression data set identifies microRNA regulated modules
    Eric Bonnet
    Department of Plant Systems Biology, VIB, Gent, Belgium
    PLoS ONE 5:e10162. 2010
    ..However, defining the place and function of miRNAs in complex regulatory networks is not straightforward. Systems approaches, like the inference of a module network from expression data, can help to achieve this goal...
  7. pmc Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast
    Anagha Joshi
    Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust MRC Building Hills Road, Cambridge CB2 0XY, UK
    Nucleic Acids Res 39:9108-17. 2011
    ....
  8. pmc Validating module network learning algorithms using simulated data
    Tom Michoel
    Bioinformatics and Evolutionary Genomics, Department of Plant Systems Biology, VIB Ghent University, Ghent, Belgium
    BMC Bioinformatics 8:S5. 2007
    ..Additionally, we assess the effect of various parameters, such as the size of the data set and the amount of noise, on the inference performance...
  9. ncbi Analysis of a Gibbs sampler method for model-based clustering of gene expression data
    Anagha Joshi
    Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
    Bioinformatics 24:176-83. 2008
    ..An in-depth analysis can reveal important insights about the performance of the algorithm, the expected quality of the output clusters, and the possibilities for extracting more relevant information out of a particular data set...