A New Approach to Gene Prediction Using the Self-Organizing Map. - Shaun Mahony; Terry J. Smith; James O. McInerney; Aaron Golden (CSB, 2003)

Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models. - Shaun Mahony; James O. McInerney; Terry J. Smith; Aaron Golden (BMC Bioinform., 2004)

Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. - Shaun Mahony; Aaron Golden; Terry J. Smith; Panayiotis V. Benos (ISMB (Supplement of Bioinformatics), 2005)

Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences. - Shaun Mahony; David Hendrix; Terry J. Smith; Aaron Golden (Artif. Intell. Rev., 2005)

Transcription factor binding site identification using the self-organizing map. - Shaun Mahony; David Hendrix; Aaron Golden; Terry J. Smith; Daniel S. Rokhsar (Bioinform., 2005)

Gene Prediction in Metagenomic Libraries Using the Self Organising Map and High Performance Computing Techniques. - Nigel McCoy; Shaun Mahony; Aaron Golden (GCCB, 2006)

Self-organizing neural networks to support the discovery of DNA-binding motifs. - Shaun Mahony; Panayiotis V. Benos; Terry J. Smith; Aaron Golden (Neural Networks, 2006)

Thermodynamically constrained steady state solution space of the E. coli metabolic network. - Ronan M. T. Fleming; Aaron Golden; Heinz-Peter Nasheuer (BMC Syst. Biol., 2007)

BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server. - Paul Geeleher; Dermot Morris; John P. Hinde; Aaron Golden (Bioinform., 2009)

Opendda: a Novel High-Performance Computational Framework for the Discrete Dipole Approximation. - James Mc Donald; Aaron Golden; S. Gerard Jennings (Int. J. High Perform. Comput. Appl., 2009)

The Einstein Genome Gateway using WASP - A High Throughput Multi-Layered Life Sciences Portal for XSEDE. - Aaron Golden; Andrew S. McLellan; Robert A. Dubin; Qiang Jing; Pilib Ó Broin; David Moskowitz; Zhengdong Zhang; Masako Suzuki; Joseph Hargitai; R. Brent Calder; John M. Greally (HealthGrid, 2012)

'Spring through the gateway': deploying genomic workflows with XSEDE. - David Rhee; Joseph Hargitai; R. Brent Calder; Pilib Ó Broin; Kevin R. Shieh; Aaron Golden (XSEDE, 2013)

Gene-set analysis is severely biased when applied to genome-wide methylation data. - Paul Geeleher; Lori Hartnett; Laurance J. Egan; Aaron Golden; Raja Affendi Raja Ali; Cathal Seoighe (Bioinform., 2013)

Using SAGA and the Open Science Grid to Search for Aptamers. - Kevin R. Shieh; Pilib Ó Broin; David Rhee; Matthew Levy; Aaron Golden (XSEDE, 2014)

toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research. - David B. Rhee; Matthew McKnight Croken; Kevin R. Shieh; Julie M. Sullivan; Gos Micklem; Kami Kim; Aaron Golden (Database J. Biol. Databases Curation, 2015)

Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach. - Pilib Ó Broin; Terry J. Smith; Aaron Golden (BMC Bioinform., 2015)

Understanding the Systems Biology of Pathogen Virulence Using Semantic Methodologies. - David Rhee; Kevin R. Shieh; Julie M. Sullivan; Gos Micklem; Kami Kim; Aaron Golden (ICSC, 2016)

AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX. - Kevin R. Shieh; Christina Kratschmer; Keith E. Maier; John M. Greally; Matthew Levy; Aaron Golden (Bioinform., 2020)