Dr Thomas D Otto | Senior Staff Scientist

This person is a member of Sanger Institute Alumni.

Otto, Thomas D

Thomas is a Senior Staff Scientist in the group of Matt Berriman. His interest is one hand to develop new approach to process big data and perform integrative biology. These algorithms he than applies to assemble genomes, perform comparative genomic and study the evolution of gene family in parasites, especially in Malaria.

One of my interests is the generation of programs to improve the assembly process of parasite genomes and to annotate them efficiently. All the tools are available, see figure below. They were cited more than 750 times so far.

I apply those algorithms in many projects. One research field is to understand the evolution of malaria genomes. We sequenced many new genomes, like Plasmodium ovale, P. malariae or the six novel laverania genomes, closely related to the deadliest Malaria parasite P. falciparum. Through comparative analysis I try to understand the differences between the genomes. One particular interest is the study of gene families involved in Host-parasite interaction, like the pir or var genes.

With this knowhow assembly, transcriptome analysis and programming, I collaborated with many groups in the parasite field to generate bespoke programs to solve their problem.

Publications

  • Companion: a web server for annotation and analysis of parasite genomes.

    Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C et al.

    Nucleic acids research 2016;44;W1;W29-34

  • Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.

    Otto TD, Rayner JC, Böhme U, Pain A, Spottiswoode N et al.

    Nature communications 2014;5;4754

  • A comprehensive evaluation of rodent malaria parasite genomes and gene expression.

    Otto TD, Böhme U, Jackson AP, Hunt M, Franke-Fayard B et al.

    BMC biology 2014;12;86

  • REAPR: a universal tool for genome assembly evaluation.

    Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M and Otto TD

    Genome biology 2013;14;5;R47

  • A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

    Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M and Otto TD

    Nature protocols 2012;7;7;1260-84

  • A comprehensive evaluation of assembly scaffolding tools.

    Hunt M, Newbold C, Berriman M and Otto TD

    Genome biology 2014;15;3;R42

  • Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites.

    Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M et al.

    eLife 2015;4;e06974

  • A novel multiple-stage antimalarial agent that inhibits protein synthesis.

    Baragaña B, Hallyburton I, Lee MC, Norcross NR, Grimaldi R et al.

    Nature 2015;522;7556;315-20

  • SC83288 is a clinical development candidate for the treatment of severe malaria.

    Pegoraro S, Duffey M, Otto TD, Wang Y, Rösemann R et al.

    Nature communications 2017;8;14193

  • Variant Exported Blood-Stage Proteins Encoded by Plasmodium Multigene Families Are Expressed in Liver Stages Where They Are Exported into the Parasitophorous Vacuole.

    Fougère A, Jackson AP, Paraskevi Bechtsi D, Braks JA, Annoura T et al.

    PLoS pathogens 2016;12;11;e1005917

  • Companion: a web server for annotation and analysis of parasite genomes.

    Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C et al.

    Nucleic acids research 2016;44;W1;W29-34

  • Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants.

    Bronner IF, Otto TD, Zhang M, Udenze K, Wang C et al.

    Genome research 2016;26;7;980-9

  • Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

    Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR et al.

    Nature microbiology 2016;1;3

  • Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host.

    Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR et al.

    Nature microbiology 2016;1;15023

  • Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism.

    Jackson AP, Otto TD, Aslett M, Armstrong SD, Bringaud F et al.

    Current biology : CB 2016;26;2;161-72

  • Circlator: automated circularization of genome assemblies using long sequencing reads.

    Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA and Harris SR

    Genome biology 2015;16;294

  • Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites.

    Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M et al.

    eLife 2015;4;e06974

  • IVA: accurate de novo assembly of RNA virus genomes.

    Hunt M, Gall A, Ong SH, Brener J, Ferns B et al.

    Bioinformatics (Oxford, England) 2015;31;14;2374-6

  • A novel multiple-stage antimalarial agent that inhibits protein synthesis.

    Baragaña B, Hallyburton I, Lee MC, Norcross NR, Grimaldi R et al.

    Nature 2015;522;7556;315-20

  • Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites.

    Flegontov P, Michálek J, Janouškovec J, Lai DH, Jirků M et al.

    Molecular biology and evolution 2015;32;5;1115-31

  • Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts.

    Weerdenburg EM, Abdallah AM, Rangkuti F, Abd El Ghany M, Otto TD et al.

    Infection and immunity 2015;83;5;1778-88

  • Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations.

    Abdallah AM, Hill-Cawthorne GA, Otto TD, Coll F, Guerra-Assunção JA et al.

    Scientific reports 2015;5;15443

  • Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism.

    Pinheiro MM, Ahmed MA, Millar SB, Sanderson T, Otto TD et al.

    PloS one 2015;10;4;e0121303

  • Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis.

    Claessens A, Hamilton WL, Kekre M, Otto TD, Faizullabhoy A et al.

    PLoS genetics 2014;10;12;e1004812

  • Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum.

    Vaidya AB, Morrisey JM, Zhang Z, Das S, Daly TM et al.

    Nature communications 2014;5;5521

  • Genomics illuminates parasite biology.

    Foth BJ and Otto TD

    Nature reviews. Microbiology 2014;12;11;727

  • A comprehensive evaluation of rodent malaria parasite genomes and gene expression.

    Otto TD, Böhme U, Jackson AP, Hunt M, Franke-Fayard B et al.

    BMC biology 2014;12;86

  • Genomic analysis of the causative agents of coccidiosis in domestic chickens.

    Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP et al.

    Genome research 2014;24;10;1676-85

  • Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.

    Otto TD, Rayner JC, Böhme U, Pain A, Spottiswoode N et al.

    Nature communications 2014;5;4754

  • The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

    Jackson AP, Otto TD, Darby A, Ramaprasad A, Xia D et al.

    Nucleic acids research 2014;42;11;7113-31

  • A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium.

    Sinha A, Hughes KR, Modrzynska KK, Otto TD, Pfander C et al.

    Nature 2014;507;7491;253-257

  • A comprehensive evaluation of assembly scaffolding tools.

    Hunt M, Newbold C, Berriman M and Otto TD

    Genome biology 2014;15;3;R42

  • Cereal killers.

    Otto TD and Reid AJ

    Nature reviews. Microbiology 2013;11;11;744

  • Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation.

    Lemieux JE, Kyes SA, Otto TD, Feller AI, Eastman RT et al.

    Molecular microbiology 2013;90;3;519-37

  • Atypical mitogen-activated protein kinase phosphatase implicated in regulating transition from pre-S-Phase asexual intraerythrocytic development of Plasmodium falciparum.

    Balu B, Campbell C, Sedillo J, Maher S, Singh N et al.

    Eukaryotic cell 2013;12;9;1171-8

  • REAPR: a universal tool for genome assembly evaluation.

    Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M and Otto TD

    Genome biology 2013;14;5;R47

  • Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates.

    Ning J, Otto TD, Pfander C, Schwach F, Brochet M et al.

    Genes & development 2013;27;10;1198-215

  • BamView: visualizing and interpretation of next-generation sequencing read alignments.

    Carver T, Harris SR, Otto TD, Berriman M, Parkhill J and McQuillan JA

    Briefings in bioinformatics 2013;14;2;203-12

  • Efficient depletion of host DNA contamination in malaria clinical sequencing.

    Oyola SO, Gu Y, Manske M, Otto TD, O'Brien J et al.

    Journal of clinical microbiology 2013;51;3;745-51

  • Proteomic and genetic analyses demonstrate that Plasmodium berghei blood stages export a large and diverse repertoire of proteins.

    Pasini EM, Braks JA, Fonager J, Klop O, Aime E et al.

    Molecular & cellular proteomics : MCP 2013;12;2;426-48

  • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

    Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M et al.

    GigaScience 2013;2;1;10

  • A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

    Quail MA, Smith M, Coupland P, Otto TD, Harris SR et al.

    BMC genomics 2012;13;341

  • A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

    Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M and Otto TD

    Nature protocols 2012;7;7;1260-84

  • Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS).

    Lawton J, Brugat T, Yan YX, Reid AJ, Böhme U et al.

    BMC genomics 2012;13;125

  • Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species.

    Jackson AP, Berry A, Aslett M, Allison HC, Burton P et al.

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;9;3416-21

  • Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

    Oyola SO, Otto TD, Gu Y, Maslen G, Manske M et al.

    BMC genomics 2012;13;1

  • An In-Solution Hybridisation Method for the Isolation of Pathogen DNA from Human DNA-rich Clinical Samples for Analysis by NGS.

    Smith M, Campino S, Gu Y, Clark TG, Otto TD et al.

    The open genomics journal 2012;5

  • A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.

    Protasio AV, Tsai IJ, Babbage A, Nichol S, Hunt M et al.

    PLoS neglected tropical diseases 2012;6;1;e1455

  • Optimal enzymes for amplifying sequencing libraries.

    Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF et al.

    Nature methods 2011;9;1;10-1

  • Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania.

    Rogers MB, Hilley JD, Dickens NJ, Wilkes J, Bates PA et al.

    Genome research 2011;21;12;2129-42

  • A scalable pipeline for highly effective genetic modification of a malaria parasite.

    Pfander C, Anar B, Schwach F, Otto TD, Brochet M et al.

    Nature methods 2011;8;12;1078-82

  • Genome sequence of Mycobacterium bovis BCG Moreau, the Brazilian vaccine strain against tuberculosis.

    Gomes LH, Otto TD, Vasconcellos EA, Ferrão PM, Maia RM et al.

    Journal of bacteriology 2011;193;19;5600-1

  • Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.

    Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N et al.

    PLoS pathogens 2011;7;9;e1002219

  • Real-time sequencing.

    Otto TD

    Nature reviews. Microbiology 2011;9;9;633

  • RATT: Rapid Annotation Transfer Tool.

    Otto TD, Dillon GP, Degrave WS and Berriman M

    Nucleic acids research 2011;39;9;e57

  • Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein.

    Ogun SA, Tewari R, Otto TD, Howell SA, Knuepfer E et al.

    PLoS pathogens 2011;7;2;e1001288

  • Leishmania (Viannia) braziliensis: influence of successive in vitro cultivation on the expression of promastigote proteinases.

    Rebello KM, Britto C, Pereira BA, Pita-Pereira Dd, Moraes MO et al.

    Experimental parasitology 2010;126;4;570-6

  • Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment.

    Capriles PV, Guimarães AC, Otto TD, Miranda AB, Dardenne LE and Degrave WM

    BMC genomics 2010;11;610

  • Seeking perfection.

    Otto TD

    Nature reviews. Microbiology 2010;8;10;681

  • Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites.

    Hunt P, Martinelli A, Modrzynska K, Borges S, Creasey A et al.

    BMC genomics 2010;11;499

  • Long- and short-term selective forces on malaria parasite genomes.

    Nygaard S, Braunstein A, Malsen G, Van Dongen S, Gardner PP et al.

    PLoS genetics 2010;6;9;e1001099

  • Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.

    Otto TD, Sanders M, Berriman M and Newbold C

    Bioinformatics (Oxford, England) 2010;26;14;1704-7

  • Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally.

    Sutherland CJ, Tanomsing N, Nolder D, Oguike M, Jennison C et al.

    The Journal of infectious diseases 2010;201;10;1544-50

  • New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

    Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR et al.

    Molecular microbiology 2010;76;1;12-24

  • BamView: viewing mapped read alignment data in the context of the reference sequence.

    Carver T, Böhme U, Otto TD, Parkhill J and Berriman M

    Bioinformatics (Oxford, England) 2010;26;5;676-7

  • ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.

    Otto TD, Catanho M, Tristão C, Bezerra M, Fernandes RM et al.

    Bioinformatics (Oxford, England) 2010;26;5;705-7

  • ABACAS: algorithm-based automatic contiguation of assembled sequences.

    Assefa S, Keane TM, Otto TD, Newbold C and Berriman M

    Bioinformatics (Oxford, England) 2009;25;15;1968-9

  • AnEnPi: identification and annotation of analogous enzymes.

    Otto TD, Guimarães AC, Degrave WM and de Miranda AB

    BMC bioinformatics 2008;9;544

  • In silico reconstruction of the amino acid metabolic pathways of Trypanosoma cruzi.

    Guimarães AC, Otto TD, Alves-Ferreira M, Miranda AB and Degrave WM

    Genetics and molecular research : GMR 2008;7;3;872-82

  • Molecular differentiation of sex chromosomes probed by comparative genomic hybridization.

    Traut W, Sahara K, Otto TD and Marec F

    Chromosoma 1999;108;3;173-80

Career/Research Highlights

Otto, Thomas D
Thomas's Timeline
2015

Honorary Senior Lecturer at London School of Hygiene & Tropical Medicine

2011

Senior Staff Scientist at the Wellcome Trust Sanger Institute

2008

Senior Computer Biologist at the Wellcome Trust Sanger Institute

PhD in Molecular Biology and Cell Biology, Fondação Oswaldo Cruz, Rio de Janeiro, Brazil

2002

Master in Computer Science, Lübeck University, Germany