| Issue Date | Title | Author(s) |
| - | Progressive Mauve: Multiple alignment of genomes with gene flux and rearrangement | Darling, AE; Mau, B; Perna, NT |
| 2012-09-13 | An Integrated Pipeline for de Novo Assembly of Microbial Genomes | Tritt, A; Eisen, JA; Facciotti, MT; Darling, AE |
| 2011-10-05 | The rise and fall of breakpoint reuse depending on genome resolution | Attie, O; Darling, AE; Yancopoulos, S |
| 2013-01-01 | Draft genome sequence of an actinobacterium, Brachybacterium muris strain UCD-AY4 | Lo, JR; Lang, JM; Darling, AE; Eisen, JA; Coil, DA |
| 2017-12 | Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26. | Reid, CJ; Wyrsch, ER; Roy Chowdhury, P; Zingali, T; Liu, M; Darling, AE; Chapman, TA; Djordjevic, SP |
| 2017-12-01 | Porcine commensal escherichia coli: A reservoir for class 1 integrons associated with IS26 | Reid, CJ; Wyrsch, ER; Chowdhury, PR; Zingali, T; Liu, M; Darling, AE; Chapman, TA; Djordjevic, SP |
| 2016-01-01 | Bacterial communities vary between sinuses in chronic rhinosinusitis patients | Joss, TV; Burke, CM; Hudson, BJ; Darling, AE; Forer, M; Alber, DG; Charles, IG; Stow, NW |
| 2013-01-01 | Draft genome sequence of Dietzia sp. strain UCD-THP (phylum Actinobacteria) | Diep, AL; Lang, JM; Darling, AE; Eisen, JA; Coil, DA |
| 2009-08-01 | Reordering contigs of draft genomes using the Mauve Aligner | Rissman, AI; Mau, B; Biehl, BS; Darling, AE; Glasner, JD; Perna, NT |
| 2014-09-01 | A draft genome of Escherichia coli sequence type 127 strain 2009-46 | Darling, AE; McKinnon, J; Worden, P; Santos, J; Charles, IG; Chowdhury, PR; Djordjevic, SP |
