Tracembler - software for in-silico chromosome walking in unassembled genomes. - Qunfeng Dong; Matthew D. Wilkerson; Volker Brendel (BMC Bioinform., 2007)

PlantGDB: a resource for comparative plant genomics. - Jon Duvick; Ann Fu; Usha Muppirala; Mukul Sabharwal; Matthew D. Wilkerson; Carolyn J. Lawrence; Carol Lushbough; Volker Brendel (Nucleic Acids Res., 2008)

Common introns within orthologous genes: software and application to plants. - Matthew D. Wilkerson; Yuanbin Ru; Volker Brendel (Briefings Bioinform., 2009)

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)

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)

MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes. - Anthony R. Soltis; Clifton L. Dalgard; Harvey B. Pollard; Matthew D. Wilkerson (BMC Bioinform., 2020)