Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster von Richardson, Mark F, Weinert, Lucy A, Welch, John J, Linheiro, Raquel S, Magwire, Michael M, Jiggins, Francis M, Bergman, Casey M

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Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster von Linheiro, Raquel S, Bergman, Casey M

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McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data von Nelson, Michael G, Linheiro, Raquel S, Bergman, Casey M

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On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves von Lobo, Diana, Linheiro, Raquel, Godinho, Raquel, Archer, John Patrick

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CView: A network based tool for enhanced alignment visualization von Linheiro, Raquel, Sabatino, Stephen, Lobo, Diana, Archer, John

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CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure von Linheiro, Raquel, Archer, John

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Genetic variation in the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain von Ferreira, Catarina, Bogas, Diana, Bikarolla, Santosh K., Varela, Ana Rita, Frykholm, Karolin, Linheiro, Raquel, Nunes, Olga C., Westerlund, Fredrik, Manaia, Célia M.

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Testing the palindromic target site model for DNA transposon insertion using the Drosophila melanogaster P-element von Linheiro, Raquel S, Bergman, Casey M

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Evaluation of a bacteriocinogenic Lactobacillus plantarum strain on the microbiological characteristics of “Alheira de Vitela” von Ariana Macieira, Helena Albano, Miguel Pinto, Raquel Linheiro, Joana Barbosa, Paula Teixeira

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Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly. [version 1; peer review: 2 approved with r... von Linheiro, Raquel, Archer, John

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The Drosophila melanogaster Genetic Reference Panel von Mackay, Trudy F. C., Richards, Stephen, Stone, Eric A., Barbadilla, Antonio, Ayroles, Julien F., Zhu, Dianhui, Casillas, Sònia, Han, Yi, Magwire, Michael M., Cridland, Julie M., Richardson, Mark F., Anholt, Robert R. H., Barrón, Maite, Bess, Crystal, Blankenburg, Kerstin Petra, Carbone, Mary Anna, Castellano, David, Chaboub, Lesley, Duncan, Laura, Harris, Zeke, Javaid, Mehwish, Jayaseelan, Joy Christina, Jhangiani, Shalini N., Jordan, Katherine W., Lara, Fremiet, Lawrence, Faye, Lee, Sandra L., Librado, Pablo, Linheiro, Raquel S., Lyman, Richard F., Mackey, Aaron J., Munidasa, Mala, Muzny, Donna Marie, Nazareth, Lynne, Newsham, Irene, Perales, Lora, Pu, Ling-Ling, Qu, Carson, Ràmia, Miquel, Reid, Jeffrey G., Rollmann, Stephanie M., Rozas, Julio, Saada, Nehad, Turlapati, Lavanya, Worley, Kim C., Wu, Yuan-Qing, Yamamoto, Akihiko, Zhu, Yiming, Bergman, Casey M., Thornton, Kevin R., Mittelman, David, Gibbs, Richard A.

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CView: tutorial 1 - overview (movie and script) von Linheiro, Raquel, Lobo, Diana, Sabatino, Stephen, Archer, John

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Genetic variation in the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain von Ferreira, Catarina, Bogas, Diana, Bikarolla, Santosh K., Varela, Ana Rita, Frykholm, Karolin, Linheiro, Raquel, Nunes, Olga, Westerlund, Fredrik, Manaia, Célia

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Quantification of the effects of chimerism: datasets von Archer, John, Linheiro, Raquel

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CStone paper: data for method S1 von Archer, John, Linheiro, Raquel

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CStone paper: Case study 1 - simulated data von Archer, John, Linheiro, Raquel

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On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves: Bowtie2 counts and kallisto abu... von Lobo, Diana, Linheiro, Raquel, Godinho, Raquel, Archer, John

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CView: test case dataset von Linheiro, Raquel, Lobo, Diana, Sabatino, Stephen, Archer, John

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Computational analysis of transposable element target site preferences in Drosophila melanogaster von Linheiro, Raquel

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Revised version of File S1 from Linheiro & Bergman 2012 von Bergman, Casey, Linheiro, Raquel

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