Efficient Sampling of Parsimonious Inversion Histories with Application to Genome Rearrangement in Yersinia

od Miklós, István, Darling, Aaron E.
Wydane 2009

Local and relaxed clocks: the best of both worlds

od Fourment, Mathieu, Darling, Aaron E.
Wydane w PeerJ (2018)

Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics

od Fourment, Mathieu, Darling, Aaron E.
Wydane w PeerJ (2019)

A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq

od Burke, Catherine M., Darling, Aaron E.
Wydane w PeerJ (2016)

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

od Darling, Aaron E., Mau, Bob, Perna, Nicole T.
Wydane 2010

The rise and fall of breakpoint reuse depending on genome resolution

od Attie, Oliver, Darling, Aaron E, Yancopoulos, Sophia
Wydane 2011

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)

od DeMaere, Matthew Z., Darling, Aaron E.
Wydane w PeerJ (2016)

Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies

od DeMaere, Matthew Z, Darling, Aaron E
Wydane w Gigascience (2017)

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

od DeMaere, Matthew Z., Darling, Aaron E.
Wydane w Genome Biol (2019)

Dynamics of Genome Rearrangement in Bacterial Populations

od Darling, Aaron E., Miklós, István, Ragan, Mark A.
Wydane 2008

The impact of migratory flyways on the spread of avian influenza virus in North America

od Fourment, Mathieu, Darling, Aaron E., Holmes, Edward C.
Wydane w BMC Evol Biol (2017)

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

od Didelot Xavier, Méric Guillaume, Falush Daniel, Darling Aaron E
Wydane 2012-06-01

Seevolution: visualizing chromosome evolution

od Esteban-Marcos, Andrés, Darling, Aaron E., Ragan, Mark A.
Wydane 2009

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

od Morgan, Jenna L., Darling, Aaron E., Eisen, Jonathan A.
Wydane 2010

Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli

od Didelot, Xavier, Méric, Guillaume, Falush, Daniel, Darling, Aaron E
Wydane 2012

Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices

od Lang, Jenna Morgan, Darling, Aaron E., Eisen, Jonathan A.
Wydane 2013

Online Bayesian Phylogenetic Inference: Theoretical Foundations via Sequential Monte Carlo

od Dinh, Vu, Darling, Aaron E, Matsen IV, Frederick A
Wydane w Syst Biol (2018)

Strainberry: automated strain separation in low-complexity metagenomes using long reads

od Vicedomini, Riccardo, Quince, Christopher, Darling, Aaron E., Chikhi, Rayan
Wydane w Nat Commun (2021)

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli

od Mau, Bob, Glasner, Jeremy D, Darling, Aaron E, Perna, Nicole T
Wydane 2006

Mauve Assembly Metrics

od Darling, Aaron E., Tritt, Andrew, Eisen, Jonathan A., Facciotti, Marc T.
Wydane 2011