John Boyle

Summary

Affiliation: Institute for Systems Biology
Country: USA

Publications

  1. pmc Methods for visual mining of genomic and proteomic data atlases
    John Boyle
    Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98092, USA
    BMC Bioinformatics 13:58. 2012
  2. pmc Interfaces to PeptideAtlas: a case study of standard data access systems
    Sarah Killcoyne
    Institute for Systems Biology, Seattle, WA 98109, USA
    Brief Bioinform 13:615-26. 2012
  3. pmc SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments
    David B Burdick
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 11:377. 2010
  4. pmc EPEPT: a web service for enhanced P-value estimation in permutation tests
    Theo A Knijnenburg
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 12:411. 2011
  5. pmc Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
    Steven Lewis
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 13:324. 2012
  6. pmc Fastbreak: a tool for analysis and visualization of structural variations in genomic data
    Ryan Bressler
    Institute for System Biology, 401 Terry Avenue North, Seattle, WA, 98109 5234, USA
    EURASIP J Bioinform Syst Biol 2012:15. 2012
  7. ncbi Mining PeptideAtlas for biomarkers and therapeutics in human disease
    Sarah Killcoyne
    Institute for Systems Biology, 401 Terry Ave North, Seattle, WA 98109, USA
    Curr Pharm Des 18:748-54. 2012
  8. pmc Systems biology driven software design for the research enterprise
    John Boyle
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 9:295. 2008
  9. pmc Adaptable data management for systems biology investigations
    John Boyle
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 10:79. 2009
  10. pmc SAMQA: error classification and validation of high-throughput sequenced read data
    Thomas Robinson
    Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
    BMC Genomics 12:419. 2011

Collaborators

Detail Information

Publications13

  1. pmc Methods for visual mining of genomic and proteomic data atlases
    John Boyle
    Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98092, USA
    BMC Bioinformatics 13:58. 2012
    ..The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing...
  2. pmc Interfaces to PeptideAtlas: a case study of standard data access systems
    Sarah Killcoyne
    Institute for Systems Biology, Seattle, WA 98109, USA
    Brief Bioinform 13:615-26. 2012
    ..g. security versus speed). This means that an understanding of specific requirements and tradeoffs is necessary before selecting the access technology...
  3. pmc SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments
    David B Burdick
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 11:377. 2010
    ..However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires...
  4. pmc EPEPT: a web service for enhanced P-value estimation in permutation tests
    Theo A Knijnenburg
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 12:411. 2011
    ..This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values...
  5. pmc Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
    Steven Lewis
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 13:324. 2012
    ..Each mass spectrometer can generate data at an astonishingly high rate, and the scope of what is searched for is continually increasing. Therefore solutions for improving our ability to perform these searches are needed...
  6. pmc Fastbreak: a tool for analysis and visualization of structural variations in genomic data
    Ryan Bressler
    Institute for System Biology, 401 Terry Avenue North, Seattle, WA, 98109 5234, USA
    EURASIP J Bioinform Syst Biol 2012:15. 2012
    ..We introduce Fastbreak, a fast and scalable toolkit that enables the analysis and visualization of large amounts of data from projects such as The Cancer Genome Atlas...
  7. ncbi Mining PeptideAtlas for biomarkers and therapeutics in human disease
    Sarah Killcoyne
    Institute for Systems Biology, 401 Terry Ave North, Seattle, WA 98109, USA
    Curr Pharm Des 18:748-54. 2012
    ..Here we describe PeptideAtlas and associated methods for mining the data, as well as the software tools necessary to support large-scale integration and mining...
  8. pmc Systems biology driven software design for the research enterprise
    John Boyle
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 9:295. 2008
    ..As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools...
  9. pmc Adaptable data management for systems biology investigations
    John Boyle
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 10:79. 2009
    ..To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage...
  10. pmc SAMQA: error classification and validation of high-throughput sequenced read data
    Thomas Robinson
    Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA
    BMC Genomics 12:419. 2011
    ..These tests are necessary to ensure that data is of a minimum necessary standard for use in downstream analysis. In this paper we present the SAMQA tool to rapidly and robustly identify errors in population-scale sequence data...
  11. pmc Genome-wide analysis of effectors of peroxisome biogenesis
    Ramsey A Saleem
    Institute for Systems Biology, Seattle, Washington, USA
    PLoS ONE 5:e11953. 2010
    ..By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function...
  12. pmc mspecLINE: bridging knowledge of human disease with the proteome
    Jeremy Handcock
    Institute for Systems Biology, 1441 N 34th St, Seattle, WA 98103, USA
    BMC Med Genomics 3:7. 2010
    ..We used an established semantic distance measure that is based on the co-occurrence of disease and protein terms in the MEDLINE bibliographic database...
  13. doi Cytoscape: a community-based framework for network modeling
    Sarah Killcoyne
    Institute for Systems Biology, Seattle, WA, USA
    Methods Mol Biol 563:219-39. 2009
    ..It also describes the development of a plugin used to investigate a particular research question in systems biology and walks through an example analysis using Cytoscape...