Sushmita Roy

Summary

Affiliation: University of New Mexico
Country: USA

Publications

  1. ncbi Multivariate curve resolution of time course microarray data
    Peter D Wentzell
    Department of Chemistry, Dalhousie University, Halifax, NS B3H 4J3, Canada
    BMC Bioinformatics 7:343. 2006
  2. ncbi Scalable learning of large networks
    S Roy
    Department of Computer Science, University of New Mexico, NM, USA
    IET Syst Biol 3:404-13. 2009
  3. ncbi Exploiting amino acid composition for predicting protein-protein interactions
    Sushmita Roy
    Sushmita Roy Computer Science, University of New Mexico, Albuquerque, New Mexico, United States of America
    PLoS ONE 4:e7813. 2009
  4. ncbi Characterization of differentiated quiescent and nonquiescent cells in yeast stationary-phase cultures
    Anthony D Aragon
    Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    Mol Biol Cell 19:1271-80. 2008
  5. ncbi A hidden-state Markov model for cell population deconvolution
    Sushmita Roy
    Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA
    J Comput Biol 13:1749-74. 2006
  6. ncbi Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress
    Anthony D Aragon
    Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    Genome Biol 7:R9. 2006
  7. ncbi The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures
    George S Davidson
    Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
    Mol Biol Cell 22:988-98. 2011
  8. ncbi An automated, pressure-driven sampling device for harvesting from liquid cultures for genomic and biochemical analyses
    Anthony D Aragon
    Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    J Microbiol Methods 65:357-60. 2006
  9. ncbi A multiple network learning approach to capture system-wide condition-specific responses
    Sushmita Roy
    Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA
    Bioinformatics 27:1832-8. 2011
  10. ncbi Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes
    M Juanita Martinez
    Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    Mol Biol Cell 15:5295-305. 2004

Collaborators

Detail Information

Publications12

  1. ncbi Multivariate curve resolution of time course microarray data
    Peter D Wentzell
    Department of Chemistry, Dalhousie University, Halifax, NS B3H 4J3, Canada
    BMC Bioinformatics 7:343. 2006
    ..Moreover, implicit assumptions about the measurement errors often limit the application of these methods to log-transformed data, destroying linear structure in the untransformed expression data...
  2. ncbi Scalable learning of large networks
    S Roy
    Department of Computer Science, University of New Mexico, NM, USA
    IET Syst Biol 3:404-13. 2009
    ..Includes supplementary material]...
  3. ncbi Exploiting amino acid composition for predicting protein-protein interactions
    Sushmita Roy
    Sushmita Roy Computer Science, University of New Mexico, Albuquerque, New Mexico, United States of America
    PLoS ONE 4:e7813. 2009
    ..This simple feature, which is based on normalized counts of single or pairs of amino acids, is applicable to proteins from any sequenced organism and can be used to compensate for the lack of domain information...
  4. ncbi Characterization of differentiated quiescent and nonquiescent cells in yeast stationary-phase cultures
    Anthony D Aragon
    Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    Mol Biol Cell 19:1271-80. 2008
    ..These studies are relevant to chronological aging, cell cycle, and genome evolution, and they provide insight into complex responses that even simple organisms have to starvation...
  5. ncbi A hidden-state Markov model for cell population deconvolution
    Sushmita Roy
    Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA
    J Comput Biol 13:1749-74. 2006
    ....
  6. ncbi Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress
    Anthony D Aragon
    Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    Genome Biol 7:R9. 2006
    ..We asked whether cells in stationary phase cultures respond to additional stress at the level of transcript abundance...
  7. ncbi The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures
    George S Davidson
    Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
    Mol Biol Cell 22:988-98. 2011
    ....
  8. ncbi An automated, pressure-driven sampling device for harvesting from liquid cultures for genomic and biochemical analyses
    Anthony D Aragon
    Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    J Microbiol Methods 65:357-60. 2006
    ..Correlation between biological replicate time courses measured by microarrays was extremely high. The sampler enables sampling at intervals within the range of many important biological processes...
  9. ncbi A multiple network learning approach to capture system-wide condition-specific responses
    Sushmita Roy
    Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA
    Bioinformatics 27:1832-8. 2011
    ..Such approaches do not exploit the shared information across conditions during network learning...
  10. ncbi Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes
    M Juanita Martinez
    Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    Mol Biol Cell 15:5295-305. 2004
    ....
  11. ncbi A system for generating transcription regulatory networks with combinatorial control of transcription
    Sushmita Roy
    Department of Computer Science and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    Bioinformatics 24:1318-20. 2008
    ..AVAILABILITY: RENCO is a C++ command line program, available at http://sourceforge.net/projects/renco/..
  12. ncbi Aging and the Survival of Quiescent and Non-quiescent Cells in Yeast Stationary-Phase Cultures
    M Werner-Washburne
    Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
    Subcell Biochem 57:123-43. 2012
    ....