ASAP, a systematic annotation package for community analysis of genomes. - Jeremy D. Glasner; Paul Liss; Guy Plunkett III; Aaron E. Darling; Tejasvini Prasad; Michael Rusch; Alexis Byrnes; Michael K. Gilson; Bryan S. Biehl; Frederick R. Blattner; Nicole T. Perna (Nucleic Acids Res., 2003)

Multiple Alignment of Rearranged Genomes. - Aaron E. Darling; Bob Mau; Mark Craven; Nicole T. Perna (CSB, 2004)

Identifying Evolutionarily Conserved Segments Among Multiple Divergent and Rearranged Genomes. - Bob Mau; Aaron E. Darling; Nicole T. Perna (Comparative Genomics, 2004)

GRIL: genome rearrangement and inversion locator. - Aaron E. Darling; Bob Mau; Frederick R. Blattner; Nicole T. Perna (Bioinform., 2004)

Procrastination Leads to Efficient Filtration for Local Multiple Alignment. - Aaron E. Darling; Todd J. Treangen; Louxin Zhang; Carla Kuiken; Xavier Messeguer; Nicole T. Perna (WABI, 2006)

ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. - Jeremy D. Glasner; Michael Rusch; Paul Liss; Guy Plunkett III; Eric L. Cabot; Aaron E. Darling; Bradley D. Anderson; Paul Infield-Harm; Michael C. Gilson; Nicole T. Perna (Nucleic Acids Res., 2006)

Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats. - Todd J. Treangen; Aaron E. Darling; Mark A. Ragan; Xavier Messeguer (ISBRA, 2008)

Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. - Jeremy D. Glasner; Guy Plunkett III; Bradley D. Anderson; David J. Baumler; Bryan S. Biehl; Valerie Burland; Eric L. Cabot; Aaron E. Darling; Bob Mau; Eric C. Neeno-Eckwall; David Pot; Yu Qiu; et al. (Nucleic Acids Res., 2008)

Seevolution: visualizing chromosome evolution. - Andrés Esteban-Marcos; Aaron E. Darling; Mark A. Ragan (Bioinform., 2009)

Reordering contigs of draft genomes using the Mauve Aligner. - Anna I. Rissman; Bob Mau; Bryan S. Biehl; Aaron E. Darling; Jeremy D. Glasner; Nicole T. Perna (Bioinform., 2009)

A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats. - Todd J. Treangen; Aaron E. Darling; Guillaume Achaz; Mark A. Ragan; Xavier Messeguer; Eduardo P. C. Rocha (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Mauve Assembly Metrics. - Aaron E. Darling; Andrew J. Tritt; Jonathan A. Eisen; Marc T. Facciotti (Bioinform., 2011)

The rise and fall of breakpoint reuse depending on genome resolution. - Oliver Attie; Aaron E. Darling; Sophia Yancopoulos (BMC Bioinform., 2011)

Hidden Breakpoints in Genome Alignments. - Birte Kehr; Knut Reinert; Aaron E. Darling (WABI, 2012)

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. - David Coil; Guillaume Jospin; Aaron E. Darling (Bioinform., 2015)

Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges. - Michael Liu; Aaron E. Darling (F1000Research, 2015)

qc3C: Reference-free quality control for Hi-C sequencing data. - Matthew Z. DeMaere; Aaron E. Darling (PLoS Comput. Biol., 2021)

Fidelity of hyperbolic space for Bayesian phylogenetic inference. - Matthew Macaulay; Aaron E. Darling; Mathieu Fourment (PLoS Comput. Biol., 2023)