Ismael A Vergara

Summary

Publications

  1. pmc CooVar: co-occurring variant analyzer
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, B, C, V5A 1S6, Canada
    BMC Res Notes 5:615. 2012
  2. pmc StAR: a simple tool for the statistical comparison of ROC curves
    Ismael A Vergara
    Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Alameda 340, Santiago, Chile
    BMC Bioinformatics 9:265. 2008
  3. pmc OrthoClusterDB: an online platform for synteny blocks
    Man Ping Ng
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
    BMC Bioinformatics 10:192. 2009
  4. pmc RNA-seq analysis of the C. briggsae transcriptome
    Bora Uyar
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
    Genome Res 22:1567-80. 2012
  5. pmc Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
    BMC Genomics 11:516. 2010
  6. pmc Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
    BMC Genomics 15:255. 2014
  7. doi request reprint Using OrthoCluster for the detection of synteny blocks among multiple genomes
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
    Curr Protoc Bioinformatics . 2009
  8. ncbi request reprint A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations
    Evandro Ferrada
    Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Alameda 340, Santiago, Chile
    Cell Biochem Biophys 49:111-24. 2007
  9. pmc Quantitative trait locus (QTL) mapping reveals a role for unstudied genes in Aspergillus virulence
    Julian K Christians
    Department of Biological Sciences and Simon Fraser University, Burnaby, British Columbia, Canada
    PLoS ONE 6:e19325. 2011
  10. pmc Polymorphic segmental duplication in the nematode Caenorhabditis elegans
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
    BMC Genomics 10:329. 2009

Detail Information

Publications12

  1. pmc CooVar: co-occurring variant analyzer
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, B, C, V5A 1S6, Canada
    BMC Res Notes 5:615. 2012
    ....
  2. pmc StAR: a simple tool for the statistical comparison of ROC curves
    Ismael A Vergara
    Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Alameda 340, Santiago, Chile
    BMC Bioinformatics 9:265. 2008
    ..This constitutes the typical scenario for the optimization of parameters when developing new classifiers and also for their performance validation through the comparison to previous art...
  3. pmc OrthoClusterDB: an online platform for synteny blocks
    Man Ping Ng
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
    BMC Bioinformatics 10:192. 2009
    ....
  4. pmc RNA-seq analysis of the C. briggsae transcriptome
    Bora Uyar
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
    Genome Res 22:1567-80. 2012
    ..briggsae reference genome that can be readily corrected. The revised C. briggsae genome annotation represents a solid platform for comparative genomics analysis and evolutionary studies of Caenorhabditis species...
  5. pmc Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
    BMC Genomics 11:516. 2010
    ..In this work, we have demonstrated the application of OrthoCluster in identifying synteny blocks between the genomes of Caenorhabditis elegans and Caenorhabditis briggsae, two closely related hermaphrodite nematodes...
  6. pmc Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
    BMC Genomics 15:255. 2014
    ..Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species...
  7. doi request reprint Using OrthoCluster for the detection of synteny blocks among multiple genomes
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
    Curr Protoc Bioinformatics . 2009
    ..OrthoClusterDB provides a Web interface for running OrthoCluster with user-defined datasets and parameters, as well as for browsing and downloading precomputed synteny blocks for different groups of genomes...
  8. ncbi request reprint A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations
    Evandro Ferrada
    Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Alameda 340, Santiago, Chile
    Cell Biochem Biophys 49:111-24. 2007
    ..Some external knowledge-based energy functions that are widely used in model assessment performed poorly, indicating that the benchmark of models and the specific discrimination task tested in this work constitutes a difficult challenge...
  9. pmc Quantitative trait locus (QTL) mapping reveals a role for unstudied genes in Aspergillus virulence
    Julian K Christians
    Department of Biological Sciences and Simon Fraser University, Burnaby, British Columbia, Canada
    PLoS ONE 6:e19325. 2011
    ..This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation...
  10. pmc Polymorphic segmental duplication in the nematode Caenorhabditis elegans
    Ismael A Vergara
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
    BMC Genomics 10:329. 2009
    ..elegans genome has been scrutinized and the last gaps were filled in November 2002, which present a unique opportunity for examining genome-wide segmental duplications...
  11. ncbi request reprint Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile
    Ismael A Vergara
    Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Alameda 340, Santiago, Chile
    Forensic Sci Int Genet 6:e83-5. 2012
    ..This is the first report of allele frequencies for the thirteen STRs loci defined in the CODIS system from the Chilean population...
  12. pmc Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression
    Fernando Faunes
    Center for Cell Regulation and Pathology and Center for Aging and Regeneration, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Alameda 340, Santiago, 8331150, Chile
    Genome Biol 10:R15. 2009
    ..In order to identify novel transcripts involved in dorso-ventral patterning, we compared dorsal and ventral transcriptomes of Xenopus tropicalis at the gastrula stage using serial analysis of gene expression (SAGE)...