A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers von Quail, Michael A, Smith, Miriam, Coupland, Paul, Otto, Thomas D, Harris, Simon R, Connor, Thomas R, Bertoni, Anna, Swerdlow, Harold P, Gu, Yong

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Circlator: automated circularization of genome assemblies using long sequencing reads von Hunt, Martin, Silva, Nishadi De, Otto, Thomas D, Parkhill, Julian, Keane, Jacqueline A, Harris, Simon R

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Distinct synovial tissue macrophage subsets regulate inflammation and remission in rheumatoid arthritis von Alivernini, Stefano, MacDonald, Lucy, Elmesmari, Aziza, Finlay, Samuel, Tolusso, Barbara, Gigante, Maria Rita, Petricca, Luca, Di Mario, Clara, Bui, Laura, Perniola, Simone, Attar, Moustafa, Gessi, Marco, Fedele, Anna Laura, Chilaka, Sabarinadh, Somma, Domenico, Sansom, Stephen N., Filer, Andrew, McSharry, Charles, Millar, Neal L., Kirschner, Kristina, Nerviani, Alessandra, Lewis, Myles J., Pitzalis, Costantino, Clark, Andrew R., Ferraccioli, Gianfranco, Udalova, Irina, Buckley, Christopher D., Gremese, Elisa, McInnes, Iain B., Otto, Thomas D., Kurowska-Stolarska, Mariola

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ABACAS: algorithm-based automatic contiguation of assembled sequences von Assefa, Samuel, Keane, Thomas M., Otto, Thomas D., Newbold, Chris, Berriman, Matthew

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Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing von Briggs, Emma M., Rojas, Federico, McCulloch, Richard, Matthews, Keith R., Otto, Thomas D.

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IVA: accurate de novo assembly of RNA virus genomes von Hunt, Martin, Gall, Astrid, Ong, Swee Hoe, Brener, Jacqui, Ferns, Bridget, Goulder, Philip, Nastouli, Eleni, Keane, Jacqueline A, Kellam, Paul, Otto, Thomas D

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Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis von Claessens, Antoine, Hamilton, William L, Kekre, Mihir, Otto, Thomas D, Faizullabhoy, Adnan, Rayner, Julian C, Kwiatkowski, Dominic

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Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology von Otto, Thomas D., Sanders, Mandy, Berriman, Matthew, Newbold, Chris

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Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq von Chappell, Lia, Ross, Philipp, Orchard, Lindsey, Russell, Timothy J, Otto, Thomas D, Berriman, Matthew, Rayner, Julian C, Llinás, Manuel

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Varia: a tool for prediction, analysis and visualisation of variable genes von Mackenzie, Gavin, Jensen, Rasmus W, Lavstsen, Thomas, Otto, Thomas D

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Companion: a web server for annotation and analysis of parasite genomes von Steinbiss, Sascha, Silva-Franco, Fatima, Brunk, Brian, Foth, Bernardo, Hertz-Fowler, Christiane, Berriman, Matthew, Otto, Thomas D

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Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes von Oyola, Samuel O, Otto, Thomas D, Gu, Yong, Maslen, Gareth, Manske, Magnus, Campino, Susana, Turner, Daniel J, Macinnis, Bronwyn, Kwiatkowski, Dominic P, Swerdlow, Harold P, Quail, Michael A

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Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism von Jackson, Andrew P., Otto, Thomas D., Aslett, Martin, Armstrong, Stuart D., Bringaud, Frederic, Schlacht, Alexander, Hartley, Catherine, Sanders, Mandy, Wastling, Jonathan M., Dacks, Joel B., Acosta-Serrano, Alvaro, Field, Mark C., Ginger, Michael L., Berriman, Matthew

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Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania von Rogers, Matthew B, Hilley, James D, Dickens, Nicholas J, Wilkes, Jon, Bates, Paul A, Depledge, Daniel P, Harris, David, Her, Yerim, Herzyk, Pawel, Imamura, Hideo, Otto, Thomas D, Sanders, Mandy, Seeger, Kathy, Dujardin, Jean-Claude, Berriman, Matthew, Smith, Deborah F, Hertz-Fowler, Christiane, Mottram, Jeremy C

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The apicoplast link to fever-survival and artemisinin-resistance in the malaria parasite von Zhang, Min, Wang, Chengqi, Oberstaller, Jenna, Thomas, Phaedra, Otto, Thomas D., Casandra, Debora, Boyapalle, Sandhya, Adapa, Swamy R., Xu, Shulin, Button-Simons, Katrina, Mayho, Matthew, Rayner, Julian C., Ferdig, Michael T., Jiang, Rays H. Y., Adams, John H.

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Using topic modeling to detect cellular crosstalk in scRNA-seq von Pancheva, Alexandrina, Wheadon, Helen, Rogers, Simon, Otto, Thomas D

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Single cell and spatial transcriptomic analyses reveal microglia-plasma cell crosstalk in the brain during Trypanosoma brucei infection von Quintana, Juan F., Chandrasegaran, Praveena, Sinton, Matthew C., Briggs, Emma M., Otto, Thomas D., Heslop, Rhiannon, Bentley-Abbot, Calum, Loney, Colin, de Lecea, Luis, Mabbott, Neil A., MacLeod, Annette

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Genomic analysis of the causative agents of coccidiosis in domestic chickens von Reid, Adam J, Blake, Damer P, Ansari, Hifzur R, Billington, Karen, Browne, Hilary P, Bryant, Josephine, Dunn, Matt, Hung, Stacy S, Kawahara, Fumiya, Miranda-Saavedra, Diego, Malas, Tareq B, Mourier, Tobias, Naghra, Hardeep, Nair, Mridul, Otto, Thomas D, Rawlings, Neil D, Rivailler, Pierre, Sanchez-Flores, Alejandro, Sanders, Mandy, Subramaniam, Chandra, Tay, Yea-Ling, Woo, Yong, Wu, Xikun, Barrell, Bart, Dear, Paul H, Doerig, Christian, Gruber, Arthur, Ivens, Alasdair C, Parkinson, John, Rajandream, Marie-Adèle, Shirley, Martin W, Wan, Kiew-Lian, Berriman, Matthew, Tomley, Fiona M, Pain, Arnab

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Double-negative-2 B cells are the major synovial plasma cell precursor in rheumatoid arthritis von Wing, Elinor, Sutherland, Catherine, Miles, Katherine, Gray, David, Goodyear, Carl S, Otto, Thomas D, Breusch, Stefan, Cowan, Graeme, Gray, Mohini

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Protein KIC5 is a novel regulator of artemisinin stress response in the malaria parasite Plasmodium falciparum von Simmons, Caroline F., Gibbons, Justin, Zhang, Min, Oberstaller, Jenna, Pires, Camilla Valente, Casandra, Debora, Wang, Chengqi, Seyfang, Andreas, Otto, Thomas D., Rayner, Julian C., Adams, John H.

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