Aaron E. Darling

51.6k total citations · 6 hit papers
101 papers, 34.1k citations indexed

About

Aaron E. Darling is a scholar working on Molecular Biology, Ecology and Genetics. According to data from OpenAlex, Aaron E. Darling has authored 101 papers receiving a total of 34.1k indexed citations (citations by other indexed papers that have themselves been cited), including 76 papers in Molecular Biology, 31 papers in Ecology and 25 papers in Genetics. Recurrent topics in Aaron E. Darling's work include Genomics and Phylogenetic Studies (66 papers), Microbial Community Ecology and Physiology (22 papers) and Gut microbiota and health (17 papers). Aaron E. Darling is often cited by papers focused on Genomics and Phylogenetic Studies (66 papers), Microbial Community Ecology and Physiology (22 papers) and Gut microbiota and health (17 papers). Aaron E. Darling collaborates with scholars based in Australia, United States and United Kingdom. Aaron E. Darling's co-authors include John P. Huelsenbeck, Daniel L. Ayres, Marc A. Suchard, Fredrik Ronquist, Paul van der Mark, Liang Liu, Sebastian Höhna, Maxim Teslenko, Bret Larget and Nicole T. Perna and has published in prestigious journals such as Nature Communications, Bioinformatics and PLoS ONE.

In The Last Decade

Aaron E. Darling

99 papers receiving 33.6k citations

Hit Papers

5 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

2012 20.9k citations Aaron E. Darling et al. Systematic Biology profile →
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements

2004 3.6k citations Aaron E. Darling, Bob Mau et al. profile →
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

2010 3.0k citations Aaron E. Darling, Bob Mau et al. PLoS ONE profile →
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

2014 887 citations Aaron E. Darling et al. profile →
BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

2011 461 citations Aaron E. Darling et al. Systematic Biology profile →
PhyloSift: phylogenetic analysis of genomes and metagenomes

2014 442 citations Aaron E. Darling, F. A. Matsen et al. PeerJ profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name	h						Papers	Cites
Aaron E. Darling Australia	39	15.2k	9.6k	8.0k	7.5k	6.4k	101	34.1k
Stéphane Guindon France	21	16.3k 1.1×	10.0k 1.0×	8.8k 1.1×	7.3k 1.0×	8.3k 1.3×	39	39.8k
Olivier Gascuel France	35	21.0k 1.4×	11.1k 1.2×	10.8k 1.3×	6.5k 0.9×	8.7k 1.4×	136	46.4k
Liang Liu United States	32	10.7k 0.7×	6.4k 0.7×	6.4k 0.8×	8.0k 1.1×	7.3k 1.1×	69	25.9k
Bret Larget United States	24	9.6k 0.6×	6.8k 0.7×	6.8k 0.8×	7.9k 1.1×	6.1k 1.0×	41	25.4k
Daron M. Standley Japan	36	17.9k 1.2×	7.0k 0.7×	9.0k 1.1×	6.6k 0.9×	5.4k 0.8×	113	35.8k
Heiko A. Schmidt Austria	20	13.3k 0.9×	6.5k 0.7×	6.3k 0.8×	5.2k 0.7×	5.5k 0.9×	33	28.3k
Daniel L. Ayres United States	7	8.3k 0.5×	6.3k 0.7×	6.0k 0.7×	7.3k 1.0×	5.2k 0.8×	9	23.9k
Sebastian Höhna Germany	22	8.4k 0.6×	6.1k 0.6×	5.7k 0.7×	7.4k 1.0×	5.3k 0.8×	47	23.0k
Alan Filipski United States	11	16.4k 1.1×	8.0k 0.8×	12.6k 1.6×	4.9k 0.6×	6.4k 1.0×	14	41.5k
Daniel S. Peterson United States	28	16.1k 1.1×	7.9k 0.8×	12.5k 1.6×	4.7k 0.6×	6.1k 1.0×	96	42.9k

Countries citing papers authored by Aaron E. Darling

Since Specialization

Citations

This map shows the geographic impact of Aaron E. Darling's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Aaron E. Darling with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Aaron E. Darling more than expected).

Fields of papers citing papers by Aaron E. Darling

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Aaron E. Darling. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Aaron E. Darling. The network helps show where Aaron E. Darling may publish in the future.

Co-authorship network of co-authors of Aaron E. Darling

This figure shows the co-authorship network connecting the top 25 collaborators of Aaron E. Darling. A scholar is included among the top collaborators of Aaron E. Darling based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Aaron E. Darling. Aaron E. Darling is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

Maghini, Dylan G., Yuya Kiguchi, Aaron E. Darling, et al.. (2025). Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes. mSystems. 10(8). e0153124–e0153124.

Brito, Bárbara, et al.. (2023). Evaluation of recombination detection methods for viral sequencing. Virus Evolution. 9(2). vead066–vead066. 2 indexed citations

To, Joyce, et al.. (2022). Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction. Microbial Genomics. 8(1). 40 indexed citations

Meyer, Fernando, David Koslicki, Adrian Fritz, et al.. (2021). Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit. Nature Protocols. 16(4). 1785–1801. 29 indexed citations

Bogema, Daniel R., Jessica McKinnon, Carola Venturini, et al.. (2019). Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups. Microbial Genomics. 6(1). 21 indexed citations

Chowdhury, Piklu Roy, Mathieu Fourment, Matthew Z. DeMaere, et al.. (2019). Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids. Plasmid. 102. 56–61. 6 indexed citations

Bogema, Daniel R., Melinda L. Micallef, Michael Liu, et al.. (2018). Analysis of Theileria orientalis draft genome sequences reveals potential species-level divergence of the Ikeda, Chitose and Buffeli genotypes. BMC Genomics. 19(1). 298–298. 25 indexed citations

Fourment, Mathieu & Aaron E. Darling. (2018). Local and relaxed clocks: the best of both worlds. PeerJ. 6. e5140–e5140. 14 indexed citations

Fourment, Mathieu, et al.. (2017). Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided Proposals. Systematic Biology. 67(3). 490–502. 22 indexed citations

10.

Reid, Cameron J., Ethan R. Wyrsch, Piklu Roy Chowdhury, et al.. (2017). Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26. Microbial Genomics. 3(12). 79 indexed citations

11.

DeMaere, Matthew Z. & Aaron E. Darling. (2017). Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies. GigaScience. 7(2). 27 indexed citations

12.

Gardiner, Melissa, Mauro Vicaretti, Stephen Bush, et al.. (2017). A longitudinal study of the diabetic skin and wound microbiome. PeerJ. 5. e3543–e3543. 99 indexed citations

13.

Monahan, Leigh G., Matthew Z. DeMaere, Catherine Burke, et al.. (2017). Evaluation of ddRADseq for reduced representation metagenome sequencing. PeerJ. 5. e3837–e3837. 11 indexed citations

14.

DeMaere, Matthew Z. & Aaron E. Darling. (2016). Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C). PeerJ. 4. e2676–e2676. 6 indexed citations

15.

Rands, Chris M., Aaron E. Darling, Matthew K. Fujita, et al.. (2013). Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics. 14(1). 95–95. 35 indexed citations

16.

Darling, Aaron E., et al.. (2013). Algorithms in bioinformatics 13th international workshop, WABI 2013, Sophia Antipolis, France, September 2 - 4, 2013 ; proceedings. 1 indexed citations

17.

Darling, Aaron E., Bob Mau, & Nicole T. Perna. (2010). progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. PLoS ONE. 5(6). e11147–e11147. 2979 indexed citations breakdown →

18.

Didelot, Xavier, Daniel J. Lawson, Aaron E. Darling, & Daniel Falush. (2010). Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences. Genetics. 186(4). 1435–1449. 120 indexed citations

19.

Morgan, Jenna, Aaron E. Darling, & Jonathan A. Eisen. (2010). Metagenomic Sequencing of an In Vitro-Simulated Microbial Community. University of North Texas Digital Library (University of North Texas). 52 indexed citations

20.

Darling, Aaron E., Mark Craven, Bob Mau, & Nicole T. Perna. (2004). Multiple alignment of rearranged genomes. 738–739. 2 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

Explore authors with similar magnitude of impact