Robert B Scharpf

Summary

Affiliation: Johns Hopkins Bloomberg School of Public Health
Country: USA

Publications

  1. pmc Cross-platform Comparison of Two Pancreatic Cancer Phenotypes
    Robert B Scharpf
    Departments of Oncology
    Cancer Inform 9:257-64. 2010
  2. pmc A multilevel model to address batch effects in copy number estimation using SNP arrays
    Robert B Scharpf
    Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Biostatistics 12:33-50. 2011
  3. ncbi request reprint When should one subtract background fluorescence in 2-color microarrays?
    Robert B Scharpf
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
    Biostatistics 8:695-707. 2007
  4. pmc A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk
    Samuel G Younkin
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
    BMC Genet 15:24. 2014
  5. pmc A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral clefts
    Samuel G Younkin
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore
    Birth Defects Res A Clin Mol Teratol 103:276-83. 2015
  6. pmc Pre-processing Agilent microarray data
    Marianna Zahurak
    Johns Hopkins University School of Medicine, Oncology Biostatistics, Baltimore, MD 21205, USA
    BMC Bioinformatics 8:142. 2007
  7. pmc Fast detection of de novo copy number variants from SNP arrays for case-parent trios
    Robert B Scharpf
    Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
    BMC Bioinformatics 13:330. 2012
  8. pmc R classes and methods for SNP array data
    Robert B Scharpf
    Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
    Methods Mol Biol 593:67-79. 2010
  9. pmc Identifying a Deletion Affecting Total Lung Capacity Among Subjects in the COPDGene Study Cohort
    Ferdouse Begum
    Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
    Genet Epidemiol 40:81-8. 2016
  10. pmc Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
    Robert B Scharpf
    550 N, Broadway, Suite 1101, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
    BMC Genet 15:81. 2014

Collaborators

Detail Information

Publications13

  1. pmc Cross-platform Comparison of Two Pancreatic Cancer Phenotypes
    Robert B Scharpf
    Departments of Oncology
    Cancer Inform 9:257-64. 2010
    ..Using this approach, we identify several transcripts from the integrative analysis whose over-or under-expression in pancreatic cancer cell lines was validated by qPCR...
  2. pmc A multilevel model to address batch effects in copy number estimation using SNP arrays
    Robert B Scharpf
    Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Biostatistics 12:33-50. 2011
    ..The software is open source and implemented in the R package crlmm at Bioconductor (http:www.bioconductor.org)...
  3. ncbi request reprint When should one subtract background fluorescence in 2-color microarrays?
    Robert B Scharpf
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
    Biostatistics 8:695-707. 2007
    ..Using these results, we develop recommendations for diagnostic visualizations that can help decisions about background subtraction...
  4. pmc A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk
    Samuel G Younkin
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA
    BMC Genet 15:24. 2014
    ..We compare de novo deletion frequencies in children of European ancestry with an isolated, non-syndromic oral cleft to frequencies in children of European ancestry from randomly sampled trios...
  5. pmc A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral clefts
    Samuel G Younkin
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore
    Birth Defects Res A Clin Mol Teratol 103:276-83. 2015
    ..Individual patients with multiple birth defects (including oral clefts) have been shown to carry small and large chromosomal deletions...
  6. pmc Pre-processing Agilent microarray data
    Marianna Zahurak
    Johns Hopkins University School of Medicine, Oncology Biostatistics, Baltimore, MD 21205, USA
    BMC Bioinformatics 8:142. 2007
    ..The larger goal is to define best study design and pre-processing practices for Agilent arrays, and we offer some suggestions...
  7. pmc Fast detection of de novo copy number variants from SNP arrays for case-parent trios
    Robert B Scharpf
    Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
    BMC Bioinformatics 13:330. 2012
    ..We evaluate these issues in a study of oral cleft case-parent trios...
  8. pmc R classes and methods for SNP array data
    Robert B Scharpf
    Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
    Methods Mol Biol 593:67-79. 2010
    ..This chapter highlights the advantages of adopting and extending Biobase class definitions through a working example of one implementation of classes for the analysis of high-throughput SNP arrays...
  9. pmc Identifying a Deletion Affecting Total Lung Capacity Among Subjects in the COPDGene Study Cohort
    Ferdouse Begum
    Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
    Genet Epidemiol 40:81-8. 2016
    ..Although the ARIC cohort did not have the phenotype of TLCCT , we found similar counts of CNV deletions and amplifications among AA and European subjects in this second cohort. ..
  10. pmc Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
    Robert B Scharpf
    550 N, Broadway, Suite 1101, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
    BMC Genet 15:81. 2014
    ..Whether copy number polymorphisms (CNPs) contribute to uric acid levels is unknown...
  11. pmc Tackling the widespread and critical impact of batch effects in high-throughput data
    Jeffrey T Leek
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205 2179, USA
    Nat Rev Genet 11:733-9. 2010
    ..We review experimental and computational approaches for doing so...
  12. ncbi request reprint SNPchip: R classes and methods for SNP array data
    Robert B Scharpf
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
    Bioinformatics 23:627-8. 2007
    ..bioconductor.org. SUPPLEMENTARY INFORMATION: The supplementary material as described in this article (case studies, installation guidelines and R code) is available from http://biostat.jhsph.edu/~iruczins/publications/sm/..
  13. ncbi request reprint Utility of whole blood hemostatometry using the clot signature analyzer for assessment of hemostasis in cardiac surgery
    Nauder Faraday
    Department of Anesthesiology, Johns Hopkins Medical Institutions, Baltimore, Maryland 21287, USA
    Anesthesiology 96:1115-22. 2002
    ..The Clot Signature Analyzer is a hemostatometer that measures global hemostasis in whole blood. The authors hypothesized that point-of-care hemostatometry could detect a clinical coagulopathic state in cardiac surgical patients...