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 | 25035 | 2012 |
Mauve: multiple alignment of conserved genomic sequence with rearrangements ACE Darling, B Mau, FR Blattner, NT Perna Genome research 14 (7), 1394-1403, 2004 | 4783 | 2004 |
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement AE Darling, B Mau, NT Perna PloS one 5 (6), e11147, 2010 | 3997 | 2010 |
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), 431-437, 2013 | 2370 | 2013 |
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), 720-726, 2010 | 1155 | 2010 |
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 | 1084 | 2014 |
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), 1063-1071, 2017 | 742 | 2017 |
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, 2012 | 674 | 2012 |
PhyloSift: phylogenetic analysis of genomes and metagenomes AE Darling, G Jospin, E Lowe, FA Matsen IV, HM Bik, JA Eisen PeerJ 2, e243, 2014 | 653* | 2014 |
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 | 635 | 2011 |
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 | 603 | 2009 |
The design, implementation, and evaluation of mpiBLAST A Darling, L Carey, W Feng proceedings of ClusterWorld 2003, 13-15, 2003 | 580 | 2003 |
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 | 508 | 2003 |
An integrated pipeline for de novo assembly of microbial genomes A Tritt, JA Eisen, MT Facciotti, AE Darling Public Library of Science 7 (9), e42304, 2012 | 494 | 2012 |
Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota A Van Deynze, P Zamora, PM Delaux, C Heitmann, D Jayaraman, ... PLoS biology 16 (8), e2006352, 2018 | 329 | 2018 |
Metagenomic sequencing of an in vitro-simulated microbial community JL Morgan, AE Darling, JA Eisen PloS one 5 (4), e10209, 2010 | 282 | 2010 |
Dynamics of genome rearrangement in bacterial populations AE Darling, I Miklós, MA Ragan PLoS genetics 4 (7), e1000128, 2008 | 268 | 2008 |
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 | 235 | 2012 |
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, 1-20, 2013 | 223 | 2013 |
A global metagenomic map of urban microbiomes and antimicrobial resistance D Danko, D Bezdan, EE Afshin, S Ahsanuddin, C Bhattacharya, DJ Butler, ... Cell 184 (13), 3376-3393. e17, 2021 | 218 | 2021 |