The Other Side of the Nearly Neutral Theory, Evidence of Slightly Advantageous Back-Mutations von Charlesworth, Jane, Eyre-Walker, Adam

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Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus von Everitt, Richard G., Didelot, Xavier, Batty, Elizabeth M., Miller, Ruth R, Knox, Kyle, Young, Bernadette C., Bowden, Rory, Auton, Adam, Votintseva, Antonina, Larner-Svensson, Hanna, Charlesworth, Jane, Golubchik, Tanya, Ip, Camilla L. C., Godwin, Heather, Fung, Rowena, Peto, Tim E. A., Walker, A. Sarah, Crook, Derrick W., Wilson, Daniel J.

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Severe infections emerge from commensal bacteria by adaptive evolution von Young, Bernadette C, Wu, Chieh-Hsi, Gordon, N Claire, Cole, Kevin, Price, James R, Liu, Elian, Sheppard, Anna E, Perera, Sanuki, Charlesworth, Jane, Golubchik, Tanya, Iqbal, Zamin, Bowden, Rory, Massey, Ruth C, Paul, John, Crook, Derrick W, Peto, Timothy E, Walker, A Sarah, Llewelyn, Martin J, Wyllie, David H, Wilson, Daniel J

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Accurate reconstruction of bacterial pan- and core genomes with PEPPAN von Zhou, Zhemin, Charlesworth, Jane, Achtman, Mark

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HierCC: a multi-level clustering scheme for population assignments based on core genome MLST von Zhou, Zhemin, Charlesworth, Jane, Achtman, Mark

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EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations von Achtman, Mark, Zhou, Zhemin, Charlesworth, Jane, Baxter, Laura

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The McDonald-Kreitman Test and Slightly Deleterious Mutations von Charlesworth, Jane, Eyre-Walker, Adam

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The rate of adaptive evolution in enteric bacteria von Charlesworth, Jane, Eyre-Walker, Adam

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Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence von Murray, Gemma G R, Charlesworth, Jane, Miller, Eric L, Casey, Michael J, Lloyd, Catrin T, Gottschalk, Marcelo, Tucker, Alexander W (Dan), Welch, John J, Weinert, Lucy A

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Where next for the reproducibility agenda in computational biology? von Lewis, Joanna, Breeze, Charles E, Charlesworth, Jane, Maclaren, Oliver J, Cooper, Jonathan

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Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the healthcare environment: a bacterial genome- wide association study von Young, Bernadette C., Wu, Chieh-Hsi, Charlesworth, Jane, Earle, Sarah, Price, James R., Gordon, N. Claire, Cole, Kevin, Dunn, Laura, Liu, Elian, Oakley, Sarah, Godwin, Heather, Fung, Rowena, Miller, Ruth, Knox, Kyle, Votintseva, Antonina, Quan, T. Phuong, Tilley, Robert, Scarborough, Matthew, Crook, Derrick W., Peto, Timothy E., Walker, A. Sarah, Llewelyn, Martin J., Wilson, Daniel J.

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MicroRNA expression profiles in avian haemopoietic cells von Yao, Yongxiu, Charlesworth, Jane, Nair, Venugopal, Watson, Mick

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Table S8 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations von Achtman, Mark, Zhou, Zhemin, Charlesworth, Jane, Baxter, Laura

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Table S9 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations von Achtman, Mark, Zhou, Zhemin, Charlesworth, Jane, Baxter, Laura

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Table S5 - S7 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations von Achtman, Mark, Zhou, Zhemin, Charlesworth, Jane, Baxter, Laura

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Table S3 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations von Achtman, Mark, Zhou, Zhemin, Charlesworth, Jane, Baxter, Laura

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Table S10 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations von Achtman, Mark, Zhou, Zhemin, Charlesworth, Jane, Baxter, Laura

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Table S2 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations von Achtman, Mark, Zhou, Zhemin, Charlesworth, Jane, Baxter, Laura

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Table S1 from Enterobase: hierarchical clustering of 100,000 s of bacterial genomes into species/sub-species and populations von Achtman, Mark, Zhou, Zhemin, Charlesworth, Jane, Baxter, Laura

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Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence von Murray, Gemma GR, Charlesworth, Jane, Miller, Eric L, Casey, Michael J, Lloyd, Catrin T, Gottschalk, Marcelo, Tucker, Alexander W Dan, Welch, John J, Weinert, Lucy A

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