Adam B Olshen

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Parent-specific copy number in paired tumor-normal studies using circular binary segmentation
    Adam B Olshen
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
    Bioinformatics 27:2038-46. 2011
  2. pmc Copy number and gene expression differences between African American and Caucasian American prostate cancer
    Amy E Rose
    Department of Urology, New York University School of Medicine, New York, New York 10016, USA
    J Transl Med 8:70. 2010
  3. pmc Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Bioinformatics 27:1698-9. 2011
  4. pmc Pattern discovery and cancer gene identification in integrated cancer genomic data
    Qianxing Mo
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 110:4245-50. 2013
  5. ncbi request reprint A faster circular binary segmentation algorithm for the analysis of array CGH data
    E S Venkatraman
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Bioinformatics 23:657-63. 2007
  6. pmc A classification model for distinguishing copy number variants from cancer-related alterations
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BMC Bioinformatics 11:297. 2010
  7. pmc Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI
    Nima Nabavizadeh
    Department of Radiation Oncology, University of California, San Francisco Comprehensive Cancer Center, 1600 Divisadero Street H1031, San Francisco, CA 94143 1708, USA
    Integr Biol (Camb) 3:490-6. 2011
  8. pmc Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
    Ronglai Shen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Bioinformatics 25:2906-12. 2009
  9. pmc Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis
    Aditi Bhattacharya
    Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
    Clin Cancer Res 17:7024-34. 2011
  10. ncbi request reprint Circular binary segmentation for the analysis of array-based DNA copy number data
    Adam B Olshen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Biostatistics 5:557-72. 2004

Collaborators

Detail Information

Publications10

  1. pmc Parent-specific copy number in paired tumor-normal studies using circular binary segmentation
    Adam B Olshen
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
    Bioinformatics 27:2038-46. 2011
    ..The raw data from such experiments are two-dimensional, but are unphased. Consequently, inference based on them necessitates development of new analytic methods...
  2. pmc Copy number and gene expression differences between African American and Caucasian American prostate cancer
    Amy E Rose
    Department of Urology, New York University School of Medicine, New York, New York 10016, USA
    J Transl Med 8:70. 2010
    ....
  3. pmc Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Bioinformatics 27:1698-9. 2011
    ..For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results...
  4. pmc Pattern discovery and cancer gene identification in integrated cancer genomic data
    Qianxing Mo
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 110:4245-50. 2013
    ..Application of the cancer genome atlas colorectal cancer data reveals distinct integrated tumor subtypes, suggesting different genetic pathways in colon cancer progression...
  5. ncbi request reprint A faster circular binary segmentation algorithm for the analysis of array CGH data
    E S Venkatraman
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Bioinformatics 23:657-63. 2007
    ..This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm...
  6. pmc A classification model for distinguishing copy number variants from cancer-related alterations
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BMC Bioinformatics 11:297. 2010
    ..In order to identify important cancer genes CNAs and CNVs must be distinguished. Although the Database of Genomic Variants (DGV) contains a list of all known CNVs, there is no standard methodology to use the database effectively...
  7. pmc Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI
    Nima Nabavizadeh
    Department of Radiation Oncology, University of California, San Francisco Comprehensive Cancer Center, 1600 Divisadero Street H1031, San Francisco, CA 94143 1708, USA
    Integr Biol (Camb) 3:490-6. 2011
    ..Identification of a cancer-associated stroma may be further developed to help guide local therapy to reduce recurrence and morbidity in breast cancer patients...
  8. pmc Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
    Ronglai Shen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Bioinformatics 25:2906-12. 2009
    ..A more statistically powerful approach would incorporate all data types simultaneously and generate a single integrated cluster assignment...
  9. pmc Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis
    Aditi Bhattacharya
    Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
    Clin Cancer Res 17:7024-34. 2011
    ..Thus, the objective of this study was to clarify the role of genomic aberrations in oral cancer progression and metastasis...
  10. ncbi request reprint Circular binary segmentation for the analysis of array-based DNA copy number data
    Adam B Olshen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Biostatistics 5:557-72. 2004
    ..The method is evaluated by simulation and is demonstrated on cell line data with known copy number alterations and on a breast cancer cell line data set...