Database Issues for Data Visualization: Interaction, User Interfaces, and Presentation. - John Boyle; Stephen G. Eick; Matthias L. Hemmje; Daniel A. Keim; John Peter Lee; Eric E. Sumner Jr. (Workshop on Database Issues for Data Visualization, 1993)

Design of a 3D User Interface to a Database. - John Boyle; John E. Fothergill; Peter M. D. Gray (Workshop on Database Issues for Data Visualization, 1993)

The Design of 3D metaphors for Database Visualisation. - John Boyle; Peter M. D. Gray (VDB, 1995)

From WIMPS to 3D: The Development of AMAZE. - John Boyle; Scott Leishman; Peter M. D. Gray (J. Vis. Lang. Comput., 1996)

SeqExpress: desktop analysis and visualization tool for gene expression experiments. - John Boyle (Bioinform., 2004)

Gene-Expression Omnibus integration and clustering Tools in SeqExpress. - John Boyle (Bioinform., 2005)

Systems biology driven software design for the research enterprise. - John Boyle; Christopher C. Cavnor; Sarah A. Killcoyne; Ilya Shmulevich (BMC Bioinform., 2008)

Adaptable data management for systems biology investigations. - John Boyle; Hector Rovira; Christopher C. Cavnor; David B. Burdick; Sarah A. Killcoyne; Ilya Shmulevich (BMC Bioinform., 2009)

Managing Chaos: Lessons Learned Developing Software in the Life Sciences. - Sarah A. Killcoyne; John Boyle (Comput. Sci. Eng., 2009)

Howdah - A Flexible Pipeline Framework for Analyzing Genomic Data. - Steven Lewis; Sheila Reynolds; Hector Rovira; Mike O'Leary; Sarah A. Killcoyne; Ilya Shmulevich; John Boyle (CloudCom, 2010)

An Integration Architecture Designed to Deal with the Issues of Biological Scope, Scale and Complexity. - Hector Rovira; Sarah A. Killcoyne; Ilya Shmulevich; John Boyle (DILS, 2010)

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. - David B. Burdick; Christopher C. Cavnor; Jeremy Handcock; Sarah A. Killcoyne; Jake Lin; Bruz Marzolf; Stephen A. Ramsey; Hector Rovira; Ryan Bressler; Ilya Shmulevich; John Boyle (BMC Bioinform., 2010)

EPEPT: A web service for enhanced P-value estimation in permutation tests. - Theo A. Knijnenburg; Jake Lin; Hector Rovira; John Boyle; Ilya Shmulevich (BMC Bioinform., 2011)

Interfaces to PeptideAtlas: a case study of standard data access systems. - Sarah A. Killcoyne; Jeremy Handcock; Thomas Robinson; Eric W. Deutsch; John Boyle (Briefings Bioinform., 2012)

Methods for visual mining of genomic and proteomic data atlases. - John Boyle; Richard Kreisberg; Ryan Bressler; Sarah A. Killcoyne (BMC Bioinform., 2012)

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. - Steven Lewis; Attila Csordas; Sarah A. Killcoyne; Henning Hermjakob; Michael R. Hoopmann; Robert L. Moritz; Eric W. Deutsch; John Boyle (BMC Bioinform., 2012)

Fastbreak: a tool for analysis and visualization of structural variations in genomic data. - Ryan Bressler; Jake Lin; Andrea Eakin; Thomas Robinson; Richard Kreisberg; Hector Rovira; Theo A. Knijnenburg; John Boyle; Ilya Shmulevich (EURASIP J. Bioinform. Syst. Biol., 2012)

Secure Data Processing in the Cloud. - Zoltán Ádám Mann; Eliot E. Salant; Mike Surridge; Dhouha Ayed; John Boyle; Maritta Heisel; Andreas Metzger; Paul Mundt (ESOCC Workshops, 2017)

Improving the learning of chemical-protein interactions from literature using transfer learning and specialized word embeddings. - Peter Corbett; John Boyle (Database J. Biol. Databases Curation, 2018)

Chemlistem: chemical named entity recognition using recurrent neural networks. - Peter Corbett; John Boyle (J. Cheminformatics, 2018)