ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. - Matthew D. Wilkerson; D. Neil Hayes (Bioinform., 2010)

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. - Christopher R. Cabanski; Keary Cavin; Chris Bizon; Matthew D. Wilkerson; Joel S. Parker; Kirk C. Wilhelmsen; Charles M. Perou; J. S. Marron; D. Neil Hayes (BMC Bioinform., 2012)

Multiple Response Regression for Gaussian Mixture Models with Known Labels. - Wonyul Lee; Ying Du; Wei Sun; David Neil Hayes; Yufeng Liu (Stat. Anal. Data Min., 2012)

ABRA: improved coding indel detection via assembly-based realignment. - Lisle E. Mose; Matthew D. Wilkerson; D. Neil Hayes; Charles M. Perou; Joel S. Parker (Bioinform., 2014)

Large-margin classification with multiple decision rules. - Patrick K. Kimes; David Neil Hayes; J. S. Marron; Yufeng Liu (Stat. Anal. Data Min., 2016)

DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference. - Vonn Walter; Hyo Young Choi; Xiaobei Zhao; Yan Gao; Jeremiah Holt; D. Neil Hayes (Bioinform., 2022)