Comparison of Genetic Algorithm and Particle Swarm Optimizer When Evolving a Recurrent Neural Network. - Matthew Settles; Brandon Rodebaugh; Terence Soule (GECCO, 2003)

Breeding swarms: a new approach to recurrent neural network training. - Matthew Settles; Paul Nathan; Terence Soule (GECCO, 2005)

Breeding swarms: a GA/PSO hybrid. - Matthew Settles; Terence Soule (GECCO, 2005)

OTUbase: an R infrastructure package for operational taxonomic unit data. - Daniel Beck; Matt Settles; James A. Foster (Bioinform., 2011)

mcaGUI: microbial community analysis R-Graphical User Interface (GUI). - Wade K. Copeland; Vandhana Krishnan; Daniel Beck; Matt Settles; James A. Foster; Kyu-Chul Cho; Mitch Day; Roxana Hickey; Ursel M. E. Schütte; Xia Zhou; Christopher J. Williams; Larry J. Forney; et al. (Bioinform., 2012)

Super deduper, fast PCR duplicate detection in fastq files. - Kristen R. Petersen; David A. Streett; Alida T. Gerritsen; Samuel S. Hunter; Matthew L. Settles (BCB, 2015)

expHTS: analysis of high throughput sequence data in an experimental framework. - David A. Streett; Kristen R. Petersen; Alida T. Gerritsen; Samuel S. Hunter; Matthew L. Settles (BCB, 2015)

SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing. - Ilya Y. Zhbannikov; Samuel S. Hunter; James A. Foster; Matthew L. Settles (BCB, 2017)

clonevdjseq: A workflow and bioinformatics management system for sequencing, archiving, and analysis of VDJ sequences from clonal libraries. - Keith Mitchell; Samuel Hunter; Lutz Froenicke; Karl Murray; Matthew Settles; James S. Trimmer (BMC Bioinform., 2025)