Orly Alter

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Singular value decomposition for genome-wide expression data processing and modeling
    O Alter
    Departments of Genetics and Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 97:10101-6. 2000
  2. pmc Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms
    Orly Alter
    Department of Genetics, Stanford University, Stanford, CA 94305
    Proc Natl Acad Sci U S A 100:3351-6. 2003
  3. pmc Variation in gene expression patterns in follicular lymphoma and the response to rituximab
    Sean P Bohen
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:1926-30. 2003
  4. ncbi request reprint Genomic signal processing: from matrix algebra to genetic networks
    Orly Alter
    Department of Biomedical Engineering, Institute for Cellular and Molecular Biology and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, USA
    Methods Mol Biol 377:17-60. 2007
  5. pmc Singular value decomposition of genome-scale mRNA lengths distribution reveals asymmetry in RNA gel electrophoresis band broadening
    Orly Alter
    Department of Biomedical Engineering, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 103:11828-33. 2006
  6. pmc A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies
    Larsson Omberg
    Department of Biomedical Engineering, and Institutes for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 104:18371-6. 2007
  7. pmc Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription
    Orly Alter
    Department of Biomedical Engineering and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 101:16577-82. 2004
  8. pmc Discovery of principles of nature from mathematical modeling of DNA microarray data
    Orly Alter
    Department of Biomedical Engineering, Institute for Cellular and Molecular Biology and Institute for Computational Engineering and Sciences, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 103:16063-4. 2006
  9. ncbi request reprint Molecular characterisation of soft tissue tumours: a gene expression study
    Torsten O Nielsen
    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
    Lancet 359:1301-7. 2002
  10. pmc Reconstructing the pathways of a cellular system from genome-scale signals by using matrix and tensor computations
    Orly Alter
    Department of Biomedical Engineering and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 102:17559-64. 2005

Collaborators

Detail Information

Publications10

  1. pmc Singular value decomposition for genome-wide expression data processing and modeling
    O Alter
    Departments of Genetics and Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 97:10101-6. 2000
    ....
  2. pmc Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms
    Orly Alter
    Department of Genetics, Stanford University, Stanford, CA 94305
    Proc Natl Acad Sci U S A 100:3351-6. 2003
    ..This framework enables comparative reconstruction and classification of the genes and arrays of both data sets. We illustrate this framework with a comparison of yeast and human cell-cycle expression data sets...
  3. pmc Variation in gene expression patterns in follicular lymphoma and the response to rituximab
    Sean P Bohen
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 100:1926-30. 2003
    ..These findings suggest the possibility that the response of follicular lymphoma to rituximab treatment may be predicted from the gene expression pattern of tumors...
  4. ncbi request reprint Genomic signal processing: from matrix algebra to genetic networks
    Orly Alter
    Department of Biomedical Engineering, Institute for Cellular and Molecular Biology and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX, USA
    Methods Mol Biol 377:17-60. 2007
    ..These models may become the foundation of a future in which biological systems are modeled as physical systems are today...
  5. pmc Singular value decomposition of genome-scale mRNA lengths distribution reveals asymmetry in RNA gel electrophoresis band broadening
    Orly Alter
    Department of Biomedical Engineering, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 103:11828-33. 2006
    ..We show that the asymmetry in the profiles of the genes might be due to a previously unknown asymmetry in the gel electrophoresis thermal broadening of a moving, rather than a stationary, band of RNA molecules...
  6. pmc A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies
    Larsson Omberg
    Department of Biomedical Engineering, and Institutes for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 104:18371-6. 2007
    ..A genome-scale correlation between DNA replication initiation and RNA transcription, which is equivalent to a recently discovered correlation and might be due to a previously unknown mechanism of regulation, is independently uncovered...
  7. pmc Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription
    Orly Alter
    Department of Biomedical Engineering and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 101:16577-82. 2004
    ..Novel correlation between DNA replication initiation and RNA transcription during the yeast cell cycle, which might be due to a previously unknown mechanism of regulation, is predicted...
  8. pmc Discovery of principles of nature from mathematical modeling of DNA microarray data
    Orly Alter
    Department of Biomedical Engineering, Institute for Cellular and Molecular Biology and Institute for Computational Engineering and Sciences, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 103:16063-4. 2006
  9. ncbi request reprint Molecular characterisation of soft tissue tumours: a gene expression study
    Torsten O Nielsen
    Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
    Lancet 359:1301-7. 2002
    ..We aimed to start molecular characterisation of these rare neoplasms and to do a genome-wide search for new diagnostic markers...
  10. pmc Reconstructing the pathways of a cellular system from genome-scale signals by using matrix and tensor computations
    Orly Alter
    Department of Biomedical Engineering and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
    Proc Natl Acad Sci U S A 102:17559-64. 2005
    ..e., pathway-dependent, relations among genes. We illustrate the EVD, pseudoinverse projection, and HOEVD of genome-scale networks with analyses of yeast DNA microarray data...