The khmer software package: enabling efficient nucleotide sequence analysis. - Michael R. Crusoe; Hussien F. Alameldin; Sherine Awad; Elmar Boucher; Adam Caldwell; Reed Cartwright; Amanda Charbonneau; Bede Constantinides; Greg Edvenson; Scott A. Fay; Jacob Fenton; Thomas Fenzl; et al. (F1000Research, 2015)

PubTree: A Hierarchical Search Tool for the MEDLINE Database. - William Rowe; Paul D. Dobson; Bede Constantinides; Mark Platt (CoRR, 2017)

Kindel: indel-aware consensus for nucleotide sequence alignments. - Bede Constantinides; David L. Robertson (J. Open Source Softw., 2017)

ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads. - Martin Hunt; Jeremy Swann; Bede Constantinides; Philip Fowler; Zamin Iqbal (Bioinform., 2022)

Hostile: accurate decontamination of microbial host sequences. - Bede Constantinides; Martin Hunt; Derrick W. Crook (Bioinform., 2023)