Research Topics
| John BoyleSummaryAffiliation: Institute for Systems Biology Country: USA Publications
Research Grants
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Detail Information
Publications
Systems biology driven software design for the research enterpriseJohn 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...- Adaptable data management for systems biology investigationsJohn 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... - SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experimentsDavid 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... - EPEPT: a web service for enhanced P-value estimation in permutation testsTheo 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... - SAMQA: error classification and validation of high-throughput sequenced read dataThomas 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... - Mining PeptideAtlas for biomarkers and therapeutics in human diseaseSarah 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... - Cytoscape: a community-based framework for network modelingSarah 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... - mspecLINE: bridging knowledge of human disease with the proteomeJeremy 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... - Genome-wide analysis of effectors of peroxisome biogenesisRamsey 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... - Gene-Expression Omnibus integration and clustering tools in SeqExpressJohn Boyle
Bioinformatics 21:2550-1. 2005..com and runs under Windows. A server-based version is available and is required for the GEO integration. SeqExpress is not affiliated with any academic institution, funding body or commercial organization and is free to use by all... - SeqExpress: desktop analysis and visualization tool for gene expression experimentsJohn Boyle
Holbeck, George Street, Cambridge CB4 1AJ, UK
Bioinformatics 20:1649-50. 2004..If R is installed then the application can use this to provide further analysis. AVAILABILITY: SeqExpress is available at: http://www.seqexpress.com..
Research Grants
- Providing Peptide Atlas Based Services through the caGRID infrastructureJohn Boyle; Fiscal Year: 2009..The information within the PeptideAtlas is of a high quality, is well annotated and is well organized. ..
- Providing Peptide Atlas Based Services through the caGRID infrastructureJohn Boyle; Fiscal Year: 2010..The information within the PeptideAtlas is of a high quality, is well annotated and is well organized. ..
- Development of Trans Proteomics Pipeline, an Analysis Suite for Mass SpectrometryEric Deutsch; Fiscal Year: 2010....