A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data von Coil, David, Jospin, Guillaume, Darling, Aaron E

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progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement von Darling, Aaron E, Mau, Bob, Perna, Nicole T

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bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes von DeMaere, Matthew Z, Darling, Aaron E

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qc3C: Reference-free quality control for Hi-C sequencing data von DeMaere, Matthew Z, Darling, Aaron E

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An integrated pipeline for de novo assembly of microbial genomes von Tritt, Andrew, Eisen, Jonathan A, Facciotti, Marc T, Darling, Aaron E

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Strainberry: automated strain separation in low-complexity metagenomes using long reads von Vicedomini, Riccardo, Quince, Christopher, Darling, Aaron E., Chikhi, Rayan

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Rhometa: Population recombination rate estimation from metagenomic read datasets von Krishnan, Sidaswar, DeMaere, Matthew Z, Beck, Dominik, Ostrowski, Martin, Seymour, Justin R, Darling, Aaron E

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Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices von Lang, Jenna Morgan, Darling, Aaron E, Eisen, Jonathan A

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Use of double-blind peer review to increase author diversity von Darling, E. S.

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STRONG: metagenomics strain resolution on assembly graphs von Quince, Christopher, Nurk, Sergey, Raguideau, Sebastien, James, Robert, Soyer, Orkun S, Summers, J Kimberly, Limasset, Antoine, Eren, A Murat, Chikhi, Rayan, Darling, Aaron E

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Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software von Sczyrba, Alexander, Hofmann, Peter, Belmann, Peter, Koslicki, David, Janssen, Stefan, Dröge, Johannes, Gregor, Ivan, Majda, Stephan, Fiedler, Jessika, Dahms, Eik, Bremges, Andreas, Fritz, Adrian, Garrido-Oter, Ruben, Jørgensen, Tue Sparholt, Shapiro, Nicole, Blood, Philip D, Gurevich, Alexey, Bai, Yang, Turaev, Dmitrij, DeMaere, Matthew Z, Chikhi, Rayan, Nagarajan, Niranjan, Quince, Christopher, Meyer, Fernando, Balvočiūtė, Monika, Hansen, Lars Hestbjerg, Sørensen, Søren J, Chia, Burton K H, Denis, Bertrand, Froula, Jeff L, Wang, Zhong, Egan, Robert, Don Kang, Dongwan, Cook, Jeffrey J, Deltel, Charles, Beckstette, Michael, Lemaitre, Claire, Peterlongo, Pierre, Rizk, Guillaume, Lavenier, Dominique, Wu, Yu-Wei, Singer, Steven W, Jain, Chirag, Strous, Marc, Klingenberg, Heiner, Meinicke, Peter, Barton, Michael D, Lingner, Thomas, Lin, Hsin-Hung, Liao, Yu-Chieh, Silva, Genivaldo Gueiros Z, Cuevas, Daniel A, Edwards, Robert A, Saha, Surya, Piro, Vitor C, Renard, Bernhard Y, Pop, Mihai, Klenk, Hans-Peter, Göker, Markus, Kyrpides, Nikos C, Woyke, Tanja, Vorholt, Julia A, Schulze-Lefert, Paul, Rubin, Edward M, Darling, Aaron E, Rattei, Thomas, McHardy, Alice C

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DESMAN: a new tool for de novo extraction of strains from metagenomes von Quince, Christopher, Delmont, Tom O, Raguideau, Sébastien, Alneberg, Johannes, Darling, Aaron E, Collins, Gavin, Eren, A Murat

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Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response von Becker, Erin A, Seitzer, Phillip M, Tritt, Andrew, Larsen, David, Krusor, Megan, Yao, Andrew I, Wu, Dongying, Madern, Dominique, Eisen, Jonathan A, Darling, Aaron E, Facciotti, Marc T

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Metagenomic sequencing of an in vitro-simulated microbial community von Morgan, Jenna L, Darling, Aaron E, Eisen, Jonathan A

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Dynamics of genome rearrangement in bacterial populations von Darling, Aaron E, Miklós, István, Ragan, Mark A

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PhyloSift: phylogenetic analysis of genomes and metagenomes von Darling, Aaron E, Jospin, Guillaume, Lowe, Eric, Matsen, 4th, Frederick A, Bik, Holly M, Eisen, Jonathan A

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The impact of migratory flyways on the spread of avian influenza virus in North America von Fourment, Mathieu, Darling, Aaron E, Holmes, Edward C

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Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli von Didelot, Xavier, Méric, Guillaume, Falush, Daniel, Darling, Aaron E

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Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics von Fourment, Mathieu, Darling, Aaron E

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Targeted versus non-targeted HIV testing offered via electronic questionnaire in a Swiss emergency department: A randomized controlled study von Gillet, Cleo, Darling, Katharine E A, Senn, Nicolas, Cavassini, Matthias, Hugli, Olivier

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