ABACAS: algorithm-based automatic contiguation of assembled sequences. by Assefa, S, Keane, T, Otto, T, Newbold, C, Berriman, M

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. by Otto, T, Sanders, M, Berriman, M, Newbold, C

REAPR: a universal tool for genome assembly evaluation. by Hunt, M, Kikuchi, T, Sanders, M, Newbold, C, Berriman, M, Otto, T

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. by Swain, M, Tsai, I, Assefa, SA, Newbold, C, Berriman, M, Otto, T

Plasmodium fialciparum antigenic variation: Differential expression of var gene subsets during clinical malaria [MIM-PB-40686] by Bull, P, Berriman, M, Kyes, S, Mosobo, M, Shafi, M, Marsh, K, Newbold, C

Plasmodium falciparum var gene expression patterns in children with different levels of immunity to malaria. by Warimwe, G, Berriman, M, Pain, A, Keane, T, Newbold, C, Marsh, K, Bull, P

Plasmodium falciparum variant surface antigen expression patterns during malaria by Bull, P, Berriman, M, Kyes, S, Quail, M, Hall, N, Kortok, M, Marsh, K, Newbold, C

Distinct var gene subsets associated with low host age and disease severity in Kenya. by Bull, P, Berriman, M, Pain, A, Keane, T, Buckee, C, Mosobo, M, Newbold, C, Marsh, K

Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation. by Lemieux, J, Kyes, SA, Otto, T, Feller, A, Eastman, RT, Pinches, R, Berriman, M, Su, X, Newbold, C

Analysis of Plasmodium vivax schizont transcriptomes from field isolates reveals heterogeneity of expression of genes involved in host-parasite interactions by Siegel, SV, Chappell, L, Hostetler, JB, Amaratunga, C, Suon, S, Böhme, U, Berriman, M, Fairhurst, RM, Rayner, JC

Plasmodium falciparum var gene expression is modified by host immunity. by Warimwe, G, Keane, T, Fegan, G, Musyoki, J, Newton, C, Pain, A, Berriman, M, Marsh, K, Bull, P

New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. by Otto, T, Wilinski, D, Assefa, S, Keane, T, Sarry, L, Böhme, U, Lemieux, J, Barrell, B, Pain, A, Berriman, M, Newbold, C, Llinás, M

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes by Auburn, S, Böhme, U, Steinbiss, S, Trimarsanto, H, Hostetler, J, Sanders, M, Gao, Q, Nosten, F, Newbold, C, Berriman, M, Price, R, Otto, T

Genomic characterization of recrudescent plasmodium malariae after treatment with artemether/lumefantrine by Rutledge, G, Marr, I, Huang, G, Auburn, S, Marfurt, J, Sanders, M, White, N, Berriman, M, Newbold, C, Anstey, N, Otto, T, Price, R

Efficient depletion of host DNA contamination in malaria clinical sequencing. by Oyola, S, Gu, Y, Manske, M, Otto, T, O'Brien, J, Alcock, D, Macinnis, B, Berriman, M, Newbold, C, Kwiatkowski, D, Swerdlow, H, Quail, M

Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum. by Mourier, T, Carret, C, Kyes, S, Christodoulou, Z, Gardner, P, Jeffares, D, Pinches, R, Barrell, B, Berriman, M, Griffiths-Jones, S, Ivens, A, Newbold, C, Pain, A

Optimized Whole-Genome Amplification Strategy for Extremely AT-Biased Template. by Oyola, S, Manske, M, Campino, S, Claessens, A, Hamilton, W, Kekre, M, Drury, E, Mead, D, Gu, Y, Miles, A, MacInnis, B, Newbold, C, Berriman, M, Kwiatkowski, D

Genome variation and evolution of the malaria parasite Plasmodium falciparum. by Jeffares, D, Pain, A, Berry, A, Cox, A, Stalker, J, Ingle, C, Thomas, A, Quail, M, Siebenthall, K, Uhlemann, A, Kyes, S, Krishna, S, Newbold, C, Dermitzakis, E, Berriman, M

Complete avian malaria parasite genomes reveal features associated with lineage specific evolution in birds and mammals by Böhme, U, Otto, T, Cotton, J, Steinbiss, S, Sanders, M, Oyola, S, Nicot, A, Gandon, S, Patra, K, Herd, C, Bushell, E, Modrzynska, K, Billker, O, Vinetz, J, Rivero, A, Newbold, C, Berriman, M

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification by Oyola, S, Ariani, C, Hamilton, W, Kekre, M, Amenga-Etego, L, Ghansah, A, Rutledge, G, Redmond, S, Manske, M, Jyothi, D, Jacob, C, Otto, T, Rockett, K, Newbold, C, Berriman, M, Kwiatkowski, D