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John Boyle

2013
Boyle J.  2013.  There and back again. Nature biotechnology. 31:13-5.
2012
Bressler R, Lin J, Eakin A, Robinson T, Kreisberg R, Rovira H, Knijnenburg T, Boyle J, Shmulevich I.  2012.  Fastbreak: a tool for analysis and visualization of structural variations in genomic data. EURASIP journal on bioinformatics & systems biology. 2012:15.
Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.  2012.  Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. BMC bioinformatics. 13:324.
Killcoyne S, Handcock J, Robinson T, Deutsch EW, Boyle J.  2012.  Interfaces to PeptideAtlas: a case study of standard data access systems. Briefings in bioinformatics. 13:615-26.
Boyle J, Kreisberg R, Bressler R, Killcoyne S.  2012.  Methods for visual mining of genomic and proteomic data atlases. BMC bioinformatics. 13:58.
Killcoyne S, Deutsch EW, Boyle J.  2012.  Mining PeptideAtlas for Biomarkers and Therapeutics in Human Disease. Current pharmaceutical design.
2011
Knijnenburg TA, Lin J, Rovira H, Boyle J, Shmulevich I.  2011.  EPEPT: A web service for enhanced P-value estimation in permutation tests. BMC bioinformatics. 12:411.
Robinson T, Killcoyne S, Bressler R, Boyle J.  2011.  SAMQA: error classification and validation of high-throughput sequenced read data. BMC genomics. 12:419.
2010
Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemisto A, Boyle J, Rachubinski RA et al..  2010.  Genome-wide analysis of effectors of peroxisome biogenesis. PLoS OnePLoS ONE. 5
Handcock J, Deutsch EW, Boyle J.  2010.  mspecLINE: bridging knowledge of human disease with the proteome. BMC Med Genomics. 3:7.
Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD.  2010.  QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. J Am Soc Mass Spectrom. 21:1417-22.
Burdick DB, Cavnor CC, Handcock J, Killcoyne S, Lin J, Marzolf B, Ramsey SA, Rovira H, Bressler R, Shmulevich I et al..  2010.  SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. BMC Bioinformatics. 11:377.
2009
Boyle J, Rovira H, Cavnor C, Burdick D, Killcoyne S, Shmulevich I.  2009.  Adaptable data management for systems biology investigations. BMC Bioinformatics. 10:79.
Killcoyne S, Carter GW, Smith J, Boyle J.  2009.  Cytoscape: a community-based framework for network modeling. Methods Mol Biol. 563:219-39.
Killcoyne S, Boyle J.  2009.  Managing Chaos: Lessons Learned Developing Software in the Life Sciences. IEEE Design & Test. 11:20-29.
2008
Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O'Donnell R, Rachubinski RA, Aitchison JD.  2008.  Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis. J Cell Biol. 181:281-92.
Boyle J, Cavnor C, Killcoyne S, Shmulevich I.  2008.  Systems biology driven software design for the research enterprise. BMC Bioinformatics. 9:295.
2006
Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT et al..  2006.  Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell. 24:785-96.

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