Aaron Darling
Aaron Darling
Professor of computational (meta)genomics, University of Technology Sydney
Verified email at uts.edu.au - Homepage
TitleCited byYear
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
F Ronquist, M Teslenko, P Van Der Mark, DL Ayres, A Darling, S Höhna, ...
Systematic biology 61 (3), 539-542, 2012
110202012
Mauve: multiple alignment of conserved genomic sequence with rearrangements
ACE Darling, B Mau, FR Blattner, NT Perna
Genome research 14 (7), 1394-1403, 2004
25072004
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement
AE Darling, B Mau, NT Perna
PloS one 5 (6), e11147, 2010
23832010
Insights into the phylogeny and coding potential of microbial dark matter
C Rinke, P Schwientek, A Sczyrba, NN Ivanova, IJ Anderson, JF Cheng, ...
Nature 499 (7459), 431, 2013
13072013
The Amphimedon queenslandica genome and the evolution of animal complexity
M Srivastava, O Simakov, J Chapman, B Fahey, MEA Gauthier, T Mitros, ...
Nature 466 (7307), 720, 2010
8332010
The design, implementation, and evaluation of mpiBLAST
AE Darling, L Carey, WC Feng
Los Alamos National Laboratory, 2003
5032003
Assemblathon 1: a competitive assessment of de novo short read assembly methods
D Earl, K Bradnam, JS John, A Darling, D Lin, J Fass, HOK Yu, V Buffalo, ...
Genome research 21 (12), 2224-2241, 2011
4952011
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
D Coil, G Jospin, AE Darling
Bioinformatics 31 (4), 587-589, 2014
4682014
Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T
J Wei, MB Goldberg, V Burland, MM Venkatesan, W Deng, G Fournier, ...
Infection and immunity 71 (5), 2775-2786, 2003
4282003
PhyloSift: phylogenetic analysis of genomes and metagenomes
AE Darling, G Jospin, E Lowe, FA Matsen IV, HM Bik, JA Eisen
PeerJ 2, e243, 2014
379*2014
Reordering contigs of draft genomes using the Mauve aligner
AI Rissman, B Mau, BS Biehl, AE Darling, JD Glasner, NT Perna
Bioinformatics 25 (16), 2071-2073, 2009
3792009
An integrated pipeline for de novo assembly of microbial genomes
A Tritt, JA Eisen, MT Facciotti, AE Darling
PloS one 7 (9), e42304, 2012
3622012
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics
DL Ayres, A Darling, DJ Zwickl, P Beerli, MT Holder, PO Lewis, ...
Systematic biology 61 (1), 170-173, 2011
3452011
Metagenomic sequencing of an in vitro-simulated microbial community
JL Morgan, AE Darling, JA Eisen
PloS one 5 (4), e10209, 2010
2092010
Dynamics of genome rearrangement in bacterial populations
AE Darling, I Miklós, MA Ragan
PLoS genetics 4 (7), e1000128, 2008
2042008
Critical assessment of metagenome interpretation—a benchmark of metagenomics software
A Sczyrba, P Hofmann, P Belmann, D Koslicki, S Janssen, J Dröge, ...
Nature methods 14 (11), 1063, 2017
1992017
ASAP, a systematic annotation package for community analysis of genomes
JD Glasner, P Liss, G Plunkett III, A Darling, T Prasad, M Rusch, A Byrnes, ...
Nucleic Acids Research 31 (1), 147-151, 2003
1822003
Patterns of gene flow define species of thermophilic Archaea
H Cadillo-Quiroz, X Didelot, NL Held, A Herrera, A Darling, ML Reno, ...
PLoS biology 10 (2), e1001265, 2012
1622012
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
TJ Treangen, S Koren, DD Sommer, B Liu, I Astrovskaya, B Ondov, ...
Genome biology 14 (1), R2, 2013
1512013
Inference of homologous recombination in bacteria using whole-genome sequences
X Didelot, D Lawson, A Darling, D Falush
Genetics 186 (4), 1435-1449, 2010
1412010
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Articles 1–20