Publications
2012
Hidden breakpoints in genome alignments. Birte Kehr, Knut Reinert, Aaron E. Darling. Proceedings of the 10th Workshop on Algorithms in Bioinformatics (WABI 2012).
[Paper] [Software]
Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux. E. Lynch, M. G. I. Langille, A. Darling, E. G. Wilbanks, C. Haltiner, K. S. Y. Shao, M. O. Starr, C. Teiling, T. T. Harkins, R. A. Edwards, J. A. Eisen, M. T. Facciotti. PLoS One 2012.
[Publisher Link]
Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. Xavier Didelot, Guillaume Meric, Daniel Falush and Aaron E Darling. BMC Genomics 2012.
[Publisher Link]
A user-friendly pipeline for de novo assembly of microbial genomes. A. Tritt, J.A. Eisen, M.T. Facciotti and A.E. Darling. PLoS One. In press.
[]
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice across a Large Model Space. F. Ronquist, M. Teslenko, P. van der Mark, D. L. Ayres, A. Darling, S. Höhna, B. Larget, L. Liu, M. Suchard and J. Huelsenbeck. Systematic Biology
[Publisher Link] [Software]
Patterns of Gene Flow Define Species of Thermophilic Archaea. H. Cadillo-Quiroz, X. Didelot, N. Held, A. Herrera, A. Darling, M. Reno, D. Krause, R. J. Whitaker. PLoS Biology 10(2):e1001265.
[Publisher Link] [Popular press coverage]
Beagle: an application programming interface and high-performance computing library for statistical phylogenetics. D. L. Ayres, A. Darling, D. J. Zwickl, P. Beerli, M. T. Holder, P. O. Lewis, J. P. Huelsenbeck, F. Ronquist, D. L. Swofford, M. P. Cummings, A. Rambaut, and M. A. Suchard. Systematic Biology 61(1): 170-173. 2012
[Publisher Link] []
2011
Mauve Assembly Metrics. A. Darling, A. Tritt, J. A. Eisen, M. T. Facciotti. Bioinformatics. 2011.
[Publisher Link] []
The rise and fall of breakpoint reuse depending on genome resolution. Oliver Attie, Aaron E Darling, Sophia Yancopoulos. Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics. BMC Bioinformatics 2011, 12(Suppl 9):S1.
[Publisher Link]
Assemblathon 1: A competitive assessment of de novo short read assembly methods. D. Earl, K. Bradnam, J. St. John, A. Darling, et al. Genome Research 2011.
[Publisher Link] [Project webiste]
2010
Inference of homologous recombination in bacteria using whole genome sequences. X. Didelot, D. Lawson, A. Darling, D. Falush Genetics 2010.
[Publisher Link] [PDF]
The Amphimedon queenslandica genome and the evolution of animal complexity. Srivastava et al. Nature 466, 720-726.
[Publisher Link] [PDF]
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. Aaron E. Darling, Bob Mau, Nicole T. Perna. PLoS ONE 5(6) e11147. 2010.
[Publisher Link][Publisher PDF][Software]
[40-way E. coli/Shigella Genome Alignment]
[Human/Mouse Genome Alignment]
Metagenomic sequencing of an in-vitro simulated microbial community. Jenna L. Morgan, Aaron E. Darling, Jonathan A. Eisen. PLoS ONE 5(4) e10209. 2010.
[Publisher Link][Dataset]
2009
Lateral transfer of genes and gene fragments in prokaryotes. Cheong Xin Chan, Robert G. Beiko, Aaron E. Darling, and Mark A. Ragan. Genome Biology and Evolution. 2009:429. 2009.
[Publisher Link]
Efficient sampling of parsimonious inversion histories with application to genome rearrangement in Yersinia. Istvan Miklos and Aaron Darling. Genome Biology and Evolution. 2009:153-164.
[Publisher Link] [Software]
Inference of genomic flux in bacteria. Xavier Didelot, Aaron Darling, Daniel Falush. Genome Research 19(2):306-317. 2009.
[Preprint PDF] [Publisher Link] [Supplementary Material] [Software]
Reordering contigs of draft genomes using the Mauve Aligner. Anna I Rissman, Bob Mau, Bryan S. Biehl, Aaron E. Darling, Jeremy D. Glasner, and Nicole T. Perna. Bioinformatics. 25:2071-2073. 2009
[Publisher Link][Software]
Seevolution: visualizing chromosome evolution. A. Esteban-Marcos, A. E. Darling, M. A. Ragan. Bioinformatics. 25(7):960-961. 2009.
[Publisher Link] [Software]
A novel heuristic for local multiple alignment of interspersed DNA repeats. T. J. Treangen, A. E. Darling, G. Achaz, M. A. Ragan, X. Messeguer, E. P. C. Rocha. IEEE Transactions on Computatational Biology and Bioinformatics. 6(2):180-189. 2009.
[Publisher Link] [Software]
Phylogenetic and molecular analysis of hydrogen-producing green algae. M. Timmins, S. Thomas-Hall, E. Zhang, A. Darling, U. Marx, B. Hankamer, P. Scheenk. Journal of Experimental Botany. 60(6):1691-1702. [Publisher Link]
Are protein domains modules of lateral genetic transfer? Cheong-Xin Chan, Aaron Darling, Robert Bieko, Mark Ragan. PLoS ONE 4(2):e4524.
[Publisher Link]
2008
Dynamics of genome rearrangement in bacterial populations. Aaron E. Darling, Istvan Miklos, Mark A. Ragan. PLoS Genetics 2008. 4(7):e1000128
[Reprint PDF] [Publisher Link] [Talk video] [Software]
In-silico Detection of Genes in Bacteriophage Genomic Sequences. Andrew M. Kropinski, Mark Borodovsky, Tim J. Carver, Ana M. Cerdeno-Tarraga, Aaron Darling, Padmanabhan Mahadevan, Paul Stothard, Donald Seto, Gary Van Domselaar, David S. Wishart. Bacteriophages: Methods and Protocols. Volume 2. Chapter 6. pp 57-89. Springer Press. 2008.
[Publisher Link]
Gapped extension for local-multiple-alignment of interspersed DNA repeats. Todd J. Treangen, Aaron E. Darling, Mark A. Ragan, Xavier Messeguer. Lecture Notes in Computer Science. 2008. Springer-Verlag press. (4983):74-86
[Preprint PDF] [Publisher Link]
Genome Rearrangement by the Double Cut and Join Operation. Richard Friedburg, Aaron E. Darling, and Sophia Yancopoulos. Bioinformatics: Data, Sequence Analysis and Evolution. Vol 452. Chapter 18. pp 385-416. Springer Press 2008.
[Preprint PDF] [Publisher Link]
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, Anna I. Rissman, Sara Worzella, Sam Zaremba, Joel Fedorko, Tom Hampton, Paul Liss, Michael Rusch, Matthew Shaker, Lorie Shaull, Panna Shetty, Silpa Thotakura, Jon Whitmore, Frederick R. Blattner, John M. Greene, and Nicole T. Perna. Nucleic Acids Research. 2008 (36):D519.
[Reprint PDF] [Publisher Link]
2007
Analyzing patterns of microbial evolution using the Mauve genome alignment system. Aaron E. Darling, Todd J. Treangen, Xavier Messegeur, Nicole T. Perna. Comparative Genomics (Bergman Eds.), Springer Press, 2007.
[Preprint PDF] [Publisher Link]
2006
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. Glasner JD, Rusch M, Liss P, Plunkett G 3rd, Cabot EL, Darling A, Anderson BD, Infield-Harm P, Gilson MC, Perna NT. Nucleic Acids Research 2006 34:D41-5.
[Reprint PDF] [Publisher Link]
Genome-wide detection and analysis of homologous recombination among sequenced strains of E. coli. Bob Mau, Jeremy D. Glasner, Aaron E. Darling, Nicole T. Perna. Genome Biology 2006. 7(5):R44
[Reprint PDF] [Publisher Link]
Procrastination leads to efficient filtration for local multiple alignment. Aaron E Darling, Todd J Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna. Lecture Notes in Bioinformatics 4175:126-137, Springer-Verlag 2006.
[Preprint PDF] [Publisher Link]
2005
Identifying evolutionarily conserved segments among multiple divergent and rearranged genomes. Bob Mau, Aaron E. Darling, Nicole T. Perna. Presented at the RECOMB Comparative Genomics Meeting 2004, Bertinoro, Italy October 16-19 2004. Lecture Notes in Bioinformatics 3388:72-84, Springer-Verlag 2005.
[Preprint PDF] [Publisher Link] [PowerPoint Slides]
2004
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements. Aaron C. E. Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna. Genome Research 2004. 14(7):1394-1403.
[Reprint PDF] [Publisher Link]
GRIL: Genome Rearrangement and Inversion Locator. Aaron E. Darling, Bob Mau, Frederick R. Blattner, Nicole T. Perna. Bioinformatics 2004 20(1):122-124
[Reprint PDF] [Publisher Link]
2003
The design, implementation, and evaluation of mpiBLAST. Aaron Darling, Lucas Carey, Wu-chun Feng. Proceedings of the 4th International Conference on Linux Clusters & ClusterWorld 2003. June 23-26 2003, San Jose, CA.
[Reprint PDF] [Publisher Link]
Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G 3rd, Rose DJ, Darling A, Mau B, Perna NT, Payne SM, Runyen-Janecky LJ, Zhou S, Schwartz DC, Blattner FR. Infection & Immunity 2003 May;71(5):2775-86
[PubMedCentral] [Publisher Link]
ASAP, a systematic annotation package for community analysis of genomes. Jeremy D. Glasner, Paul Liss, Guy Plunkett III, Aaron Darling, Tejasvini Prasad, Michael Rusch, Alexis Byrnes, Michael Gilson, Bryan Biehl, Frederick R. Blattner, and Nicole T. Perna. Nucl. Acids. Res. 2003 31(1):147-151
[Reprint PDF] [Publisher Link]
