Thomas D. Otto
Thomas D. Otto
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A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
MA Quail, M Smith, P Coupland, TD Otto, SR Harris, TR Connor, A Bertoni, ...
BMC genomics 13 (1), 1-13, 2012
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
JOK Keith R Bradnam, Joseph N Fass, Anton Alexandrov
GigaScience 2 (10), 2013
Circlator: automated circularization of genome assemblies using long sequencing reads
M Hunt, ND Silva, TD Otto, J Parkhill, JA Keane, SR Harris
Genome biology 16 (1), 1-10, 2015
Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis
M Zhang, C Wang, TD Otto, J Oberstaller, X Liao, SR Adapa, K Udenze, ...
Science 360 (6388), eaap7847, 2018
ABACAS: algorithm-based automatic contiguation of assembled sequences
S Assefa, TM Keane, TD Otto, C Newbold, M Berriman
Bioinformatics 25 (15), 1968-1969, 2009
Two Nonrecombining Sympatric Forms of the Human Malaria Parasite Plasmodium ovale Occur Globally
CJ Sutherland, N Tanomsing, D Nolder, M Oguike, C Jennison, ...
The Journal of infectious diseases 201 (10), 1544-1550, 2010
Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
MB Rogers, JD Hilley, NJ Dickens, J Wilkes, PA Bates, DP Depledge, ...
Genome research 21 (12), 2129-2142, 2011
A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni
AV Protasio, IJ Tsai, A Babbage, S Nichol, M Hunt, MA Aslett, N De Silva, ...
PLoS neglected tropical diseases 6 (1), e1455, 2012
New insights into the blood‐stage transcriptome of Plasmodium falciparum using RNA‐Seq
TD Otto, D Wilinski, S Assefa, TM Keane, LR Sarry, U Böhme, J Lemieux, ...
Molecular microbiology 76 (1), 12-24, 2010
REAPR: a universal tool for genome assembly evaluation
M Hunt, T Kikuchi, M Sanders, C Newbold, M Berriman, TD Otto
Genome biology 14, 1-10, 2013
A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium
A Sinha, KR Hughes, KK Modrzynska, TD Otto, C Pfander, NJ Dickens, ...
Nature 507 (7491), 253-257, 2014
Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus
T Kikuchi, JA Cotton, JJ Dalzell, K Hasegawa, N Kanzaki, P McVeigh, ...
PLoS pathogens 7 (9), e1002219, 2011
A novel multiple-stage antimalarial agent that inhibits protein synthesis
B Baragaña, I Hallyburton, MCS Lee, NR Norcross, R Grimaldi, TD Otto, ...
Nature 522 (7556), 315-320, 2015
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps
IJ Tsai, TD Otto, M Berriman
Genome biology 11, 1-9, 2010
RATT: rapid annotation transfer tool
TD Otto, GP Dillon, WS Degrave, M Berriman
Nucleic acids research 39 (9), e57-e57, 2011
A comprehensive evaluation of rodent malaria parasite genomes and gene expression
TD Otto, U Böhme, AP Jackson, M Hunt, B Franke-Fayard, ...
BMC biology 12 (1), 1-18, 2014
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology
TD Otto, M Sanders, M Berriman, C Newbold
Bioinformatics 26 (14), 1704-1707, 2010
Distinct synovial tissue macrophage subsets regulate inflammation and remission in rheumatoid arthritis
S Alivernini, L MacDonald, A Elmesmari, S Finlay, B Tolusso, MR Gigante, ...
Nature medicine 26 (8), 1295-1306, 2020
Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes
SO Oyola, TD Otto, Y Gu, G Maslen, M Manske, S Campino, DJ Turner, ...
BMC genomics 13, 1-12, 2012
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
MT Swain, IJ Tsai, SA Assefa, C Newbold, M Berriman, TD Otto
Nature protocols 7 (7), 1260-1284, 2012
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