Dr Thomas Otto

  • Senior Lecturer (Immunology)

Biography

The long-standing theme of my research has been to generate new approaches to analyse and mind big biological data sets. In the past, I have generated new methods to improve the assembly of genomes (PAGIT) or to analyse expression data. Those I applied to study the evolution of parasites and host pathogen interactions.

The focus of my new group at the University of Glasgow is to generate new methods to combine and analyse high throughput biological data, starting with questions around host pathogen interactions. The challenge to overcome is to combine the huge amount of data, incorporate the different ‘omics technologies, fit the best algorithm and generate a pragmatic solution that works and does not take years to be implemented.

 

Find out about our Bioinformatics Summer School 2018


Publications

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Jump to: 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2004 | 2003 | 1999
Number of items: 96.

2018

Kumar, K. et al. (2018) Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach. Scientific Reports, 7, 17146. (doi:10.1038/s41598-017-17505-9) (PMID:29215067) (PMCID:PMC5719419)

Gilabert, A. et al. (2018) Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution. PLoS Biology, 16(8), e2006035. (doi:10.1371/journal.pbio.2006035) (PMID:30142149)

Lee, H. J., Georgiadou, A., Walther, M., Nwakanma, D., Stewart, L. B., Levin, M., Otto, T. D. , Conway, D. J., Coin, L. J. and Cunnington, A. J. (2018) Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria. Science Translational Medicine, 10(447), eaar3619. (doi:10.1126/scitranslmed.aar3619) (PMID:29950443)

Lee, H. J., Georgiadou, A., Otto, T. D. , Levin, M., Coin, L. J., Conway, D. J. and Cunnington, A. J. (2018) Transcriptomic studies of Malaria: a paradigm for investigation of systemic host-pathogen interactions. Microbiology and Molecular Biology Reviews, 82(2), e00071-17. (doi:10.1128/mmbr.00071-17) (PMID:29695497)

Zhang, M. et al. (2018) Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science, 360(6388), eaap7847. (doi:10.1126/science.aap7847) (PMID:29724925)

Otto, T. D. et al. (2018) Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Research, 3, 52. (doi:10.12688/wellcomeopenres.14571.1)

Böhme, U. et al. (2018) Complete avian malaria parasite genomes reveal features associated with lineage specific evolution in birds and mammals. Genome Research, 28(4), pp. 547-560. (doi:10.1101/gr.218123.116) (PMID:29500236) (PMCID:PMC5880244)

Carrington, E., Otto, T. D. , Szestak, T., Lennartz, F., Higgins, M. K., Newbold, C. I. and Craig, A. G. (2018) In silico guided reconstruction and analysis of ICAM-1-binding var genes from Plasmodium falciparum. Scientific Reports, 8, 3282. (doi:10.1038/s41598-018-21591-8) (PMID:29459671) (PMCID:PMC5818487)

Uliano-Silva, M., Dondero, F., Otto, T. D. , Costa, I., Lima, N. C. B., Americo, J. A., Mazzoni, C. J., Prosdocimi, F. and Rebelo, M. d. F. (2018) A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei. GigaScience, 7(2), pp. 1-10. (doi:10.1093/gigascience/gix128) (PMID:29267857)

Otto, T. D. et al. (2018) Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria. Nature Microbiology, 3, pp. 687-697. (doi:10.1038/s41564-018-0162-2) (PMID:29784978)

Wyllie, S. et al. (2018) Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis. Nature, 560, pp. 192-197. (doi:10.1038/s41586-018-0356-z) (PMID:30046105)

2017

Rutledge, G. G. et al. (2017) Genomic characterization of recrudescent Plasmodium malariae after treatment with artemether/lumefantrine. Emerging Infectious Diseases, 23(8), pp. 1300-1307. (doi:10.3201/eid2308.161582) (PMID:28430103) (PMCID:PMC5547787)

Pasini, E. M., Böhme, U., Rutledge, G. G., Voorberg-Van der Wel, A., Sanders, M., Berriman, M., Kocken, C. H.M. and Otto, T. D. (2017) An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome Open Research, 2, 42. (doi:10.12688/wellcomeopenres.11864.1) (PMID:28748222) (PMCID:PMC5500898)

Payne, R. O. et al. (2017) Human vaccination against Plasmodium vivax Duffy-binding protein induces strain-transcending antibodies. JCI Insight, 2(12), e93683. (doi:10.1172/jci.insight.93683) (PMID:28614791) (PMCID:PMC5470884)

Hamilton, W. L., Claessens, A., Otto, T. D. , Kekre, M., Fairhurst, R. M., Rayner, J. C. and Kwiatkowski, D. (2017) Extreme mutation bias and high AT content in Plasmodium falciparum. Nucleic Acids Research, 45(4), pp. 1889-1901. (doi:10.1093/nar/gkw1259) (PMID:27994033) (PMCID:PMC5389722)

Rutledge, G. G. et al. (2017) Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature, 542(7639), pp. 101-104. (doi:10.1038/nature21038) (PMID:28117441) (PMCID:PMC5326575)

Pegoraro, S. et al. (2017) SC83288 is a clinical development candidate for the treatment of severe malaria. Nature Communications, 8, 14193. (doi:10.1038/ncomms14193) (PMID:28139658) (PMCID:PMC5290327)

Rutledge, G. G. and Otto, T. D. (2017) Last parasite standing. Nature Reviews Microbiology, 15(1), p. 4. (doi:10.1038/nrmicro.2016.181) (PMID:27932794)

Sutherland, C. J. et al. (2017) pfk13 -Independent treatment failure in four imported cases of Plasmodium falciparum malaria treated with artemether-lumefantrine in the United Kingdom. Antimicrobial Agents and Chemotherapy, 61(3), -16. e02382. (doi:10.1128/aac.02382-16) (PMID:28137810) (PMCID:PMC5328508)

2016

Oyola, S. O. et al. (2016) Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malaria Journal, 15(1), 597. (doi:10.1186/s12936-016-1641-7) (PMID:27998271) (PMCID:PMC5175302)

Fougère, A. et al. (2016) Variant exported blood-stage proteins encoded by Plasmodium multigene families are expressed in liver stages where they are exported into the parasitophorous vacuole. PLoS Pathogens, 12(11), e1005917. (doi:10.1371/journal.ppat.1005917) (PMID:27851824) (PMCID:PMC5113031)

Auburn, S. et al. (2016) A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes. Wellcome Open Research, 1, 4. (doi:10.12688/wellcomeopenres.9876.1) (PMID:28008421) (PMCID:PMC5172418)

Page, A. J., De Silva, N., Hunt, M., Quail, M. A., Parkhill, J., Harris, S. R., Otto, T. and Keane, J. A. (2016) Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microbial Genomics, 2(8), e000083. (doi:10.1099/mgen.0.000083) (PMID:28348874) (PMCID:PMC5320598)

Steinbiss, S., Silva-Franco, F., Brunk, B., Foth, B., Hertz-Fowler, C., Berriman, M. and Otto, T. D. (2016) Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Research, 44(W1), W29-W34. (doi:10.1093/nar/gkw292) (PMID:27105845) (PMCID:PMC4987884)

Bronner, I. F., Otto, T. D. , Zhang, M., Udenze, K., Wang, C., Quail, M. A., Jiang, R. H. Y., Adams, J. H. and Rayner, J. C. (2016) Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants. Genome Research, 26(7), pp. 980-989. (doi:10.1101/gr.200279.115) (PMID:27197223) (PMCID:PMC4937560)

Ponsuwanna, P. et al. (2016) Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites. Malaria Journal, 15, 51. (doi:10.1186/s12936-016-1097-9) (PMID:26821618) (PMCID:PMC4731938)

Jackson, A. P. et al. (2016) Kinetoplastid phylogenomics reveals the evolutionary innovations associated with the origins of parasitism. Current Biology, 26(2), pp. 161-172. (doi:10.1016/j.cub.2015.11.055) (PMID:26725202) (PMCID:PMC4728078)

Klemm, E. J. et al. (2016) Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host. Nature Microbiology, 1, 15023. (doi:10.1038/nmicrobiol.2015.23) (PMID:27572160)

2015

Hunt, M., Silva, N. D., Otto, T. D. , Parkhill, J., Keane, J. A. and Harris, S. R. (2015) Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biology, 16, 294. (doi:10.1186/s13059-015-0849-0) (PMID:26714481) (PMCID:PMC4699355)

Abdallah, A. M. et al. (2015) Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific Reports, 5, 15443. (doi:10.1038/srep15443) (PMID:26487098) (PMCID:PMC4614345)

Hunt, M., Gall, A., Ong, S. H., Brener, J., Ferns, B., Goulder, P., Nastouli, E., Keane, J. A., Kellam, P. and Otto, T. D. (2015) IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics, 31(14), pp. 2374-2376. (doi:10.1093/bioinformatics/btv120) (PMID:25725497) (PMCID:PMC4495290)

Woo, Y. H. et al. (2015) Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife, 4, e06974. (doi:10.7554/eLife.06974) (PMID:26175406) (PMCID:PMC4501334)

Baragaña, B. et al. (2015) A novel multiple-stage antimalarial agent that inhibits protein synthesis. Nature, 522(7556), pp. 315-320. (doi:10.1038/nature14451) (PMID:26085270) (PMCID:PMC4700930)

Flegontov, P. et al. (2015) Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. Molecular Biology and Evolution, 32(5), pp. 1115-1131. (doi:10.1093/molbev/msv021) (PMID:25660376)

Weerdenburg, E. M. et al. (2015) Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts. Infection and Immunity, 83(5), pp. 1778-1788. (doi:10.1128/IAI.03050-14) (PMID:25690095) (PMCID:PMC4399070)

Ramaprasad, A., Mourier, T., Naeem, R., Malas, T. B., Moussa, E., Panigrahi, A., Vermont, S. J., Otto, T. D. , Wastling, J. and Pain, A. (2015) Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features. PLoS ONE, 10(4), e0124473. (doi:10.1371/journal.pone.0124473) (PMID:25875305) (PMCID:PMC4395442)

Pinheiro, M. M., Ahmed, M. A., Millar, S. B., Sanderson, T., Otto, T. D. , Lu, W. C., Krishna, S., Rayner, J. C. and Cox-Singh, J. (2015) Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. PLoS ONE, 10(4), e0121303. (doi:10.1371/journal.pone.0121303) (PMID:25830531) (PMCID:PMC4382175)

Otto, T. D. (2015) From sequence mapping to genome assemblies. In: Peacock, C. (ed.) Parasite Genomics Protocols [2nd ed.]. Series: Methods in molecular biology (1201). Humana Press: New York, pp. 19-50. ISBN 9781493914371 (doi:10.1007/978-1-4939-1438-8_2)

2014

Claessens, A., Hamilton, W. L., Kekre, M., Otto, T. D. , Faizullabhoy, A., Rayner, J. C. and Kwiatkowski, D. (2014) Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis. PLoS Genetics, 10(12), e1004812. (doi:10.1371/journal.pgen.1004812) (PMID:25521112) (PMCID:PMC4270465)

Vaidya, A. B. et al. (2014) Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum. Nature Communications, 5, 5521. (doi:10.1038/ncomms6521) (PMID:25422853) (PMCID:PMC4263321)

Foth, B. J. and Otto, T. D. (2014) Genomics illuminates parasite biology. Nature reviews. Microbiology, 12(11), p. 727. (doi:10.1038/nrmicro3368) (PMID:25402362)

Otto, T. D. et al. (2014) A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biology, 12(1), p. 86. (doi:10.1186/s12915-014-0086-0) (PMID:25359557) (PMCID:PMC4242472)

Reid, A. J. et al. (2014) Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Research, 24(10), pp. 1676-1685. (doi:10.1101/gr.168955.113) (PMID:25015382) (PMCID:PMC4199364)

Otto, T. D. et al. (2014) Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nature Communications, 5, 4754. (doi:10.1038/ncomms5754) (PMID:25203297) (PMCID:PMC4166903)

Sinha, A. et al. (2014) A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium. Nature, 507(7491), pp. 253-257. (doi:10.1038/nature12970) (PMID:24572359) (PMCID:PMC4105895)

Hunt, M., Newbold, C., Berriman, M. and Otto, T. D. (2014) A comprehensive evaluation of assembly scaffolding tools. Genome Biology, 15(3), R42. (PMID:24581555) (PMCID:PMC4053845)

Jackson, A. P. et al. (2014) The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. Nucleic Acids Research, 42(11), pp. 7113-7131. (doi:10.1093/nar/gku322) (PMID:24799432) (PMCID:PMC4066756)

2013

Bradnam, K. R. et al. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2(1), pp. 1-31. (doi:10.1186/2047-217X-2-10) (PMID:22678431) (PMCID:PMC3844414)

Lemieux, J. E., Kyes, S. A., Otto, T. D. , Feller, A. I., Eastman, R. T., Pinches, R. A., Berriman, M., Su, X.-Z. and Newbold, C. I. (2013) Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation. Molecular Microbiology, 90(3), pp. 519-537. (PMID:23980881) (PMCID:PMC3894959)

Otto, T. D. and Reid, A. J. (2013) Cereal killers. Nature reviews. Microbiology, 11, p. 744. (doi:10.1038/nrmicro3144) (PMID:24129509)

Balu, B. et al. (2013) Atypical mitogen-activated protein kinase phosphatase implicated in regulating transition from pre-S-Phase asexual intraerythrocytic development of Plasmodium falciparum. Eukaryotic cell, 12(9), pp. 1171-8. (doi:10.1128/EC.00028-13) (PMID:23813392) (PMCID:PMC3811562)

Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M. and Otto, T. D. (2013) REAPR: a universal tool for genome assembly evaluation. Genome Biology, 14(5), R47. (doi:10.1186/gb-2013-14-5-r47) (PMID:22678431) (PMCID:PMC3648784)

Ning, J. et al. (2013) Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. Genes and Development, 27(10), pp. 1198-1215. (PMID:3699412) (PMCID:PMC3672651)

Carver, T., Harris, S. R., Otto, T. D. , Berriman, M., Parkhill, J. and McQuillan, J. A. (2013) BamView: visualizing and interpretation of next-generation sequencing read alignments. Briefings in Bioinformatics, 14(2), pp. 203-12. (PMID:22253280) (PMCID:PMC3603209)

Oyola, S. O. et al. (2013) Efficient depletion of host DNA contamination in malaria clinical sequencing. Journal of Clinical Microbiology, 51(3), pp. 745-751. (doi:10.1128/JCM.02507-12) (PMID:23224084) (PMCID:PMC3592063)

Pasini, E. M. et al. (2013) Proteomic and genetic analyses demonstrate that Plasmodium berghei blood stages export a large and diverse repertoire of proteins. Molecular and Cellular Proteomics, 12(2), pp. 426-48. (doi:10.1074/mcp.M112.021238) (PMID:23197789) (PMCID:PMC3567864)

2012

Quail, M. A., Smith, M., Coupland, P., Otto, T. D. , Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P. and Gu, Y. (2012) A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics, 13(1), p. 341. (doi:10.1186/1471-2164-13-341) (PMID:22827831) (PMCID:PMC3431227)

Lawton, J. et al. (2012) Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS). BMC Genomics, 13(125), (doi:10.1186/1471-2164-13-125) (PMID:22458863) (PMCID:PMC3384456)

Jackson, A. P. et al. (2012) Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species. Proceedings of the National Academy of Sciences of the United States of America, 109(9), pp. 3416-3421. (doi:10.1073/pnas.1117313109) (PMID:22331916) (PMCID:PMC3295286)

Protasio, A. V. et al. (2012) A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. PLoS Neglected Tropical Diseases, 6(1), e1455. (doi:10.1371/journal.pntd.0001455) (PMID:22253936) (PMCID:PMC3254664)

Oyola, S. O. et al. (2012) Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes. BMC Genomics, 13(1), (doi:10.1186/1471-2164-13-1) (PMID:22214261) (PMCID:PMC3312816)

Oyola, S. O. et al. (2012) Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics, 13, p. 1. (PMID:22214261) (PMCID:PMC3312816)

Smith, M. et al. (2012) An in-solution hybridisation method for the isolation of pathogen DNA from human DNA-rich clinical samples for analysis by NGS. Open Genomics Journal, 5(1), pp. 18-29. (doi:10.2174/1875693X01205010018) (PMID:24273626) (PMCID:PMC3837216)

Swain, M. T., Tsai, I. J., Assefa, S. A., Newbold, C., Berriman, M. and Otto, T. D. (2012) A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nature Protocols, 7(7), pp. 1260-1284. (doi:10.1038/nprot.2012.068) (PMID:22678431) (PMCID:PMC3648784)

2011

Quail, M. A., Otto, T. D. , Gu, Y., Harris, S. R., Skelly, T. F., McQuillan, J. A., Swerdlow, H. P. and Oyola, S. O. (2011) Optimal enzymes for amplifying sequencing libraries. Nature Methods, 9(1), pp. 10-11. (doi:10.1038/nmeth.1814) (PMID:22205512)

Pfander, C. et al. (2011) A scalable pipeline for highly effective genetic modification of a malaria parasite. Nature Methods, 8(12), pp. 1078-1082. (doi:10.1038/nmeth.1742) (PMID:22020067) (PMCID:PMC3431185)

Gomes, L. H. F., Otto, T. D. , Vasconcellos, E. A., Ferrao, P., Maia, R. M., Moreira, A. S., Ferreira, M. A., Castello-Branco, L. R. R., Degrave, W. M. and Mendonca-Lima, L. (2011) Genome sequence of Mycobacterium bovis BCG Moreau, the Brazilian vaccine strain against tuberculosis. Journal of Bacteriology, 193(19), pp. 5600-5601. (doi:10.1128/JB.05827-11) (PMID:21914899) (PMCID:PMC3187452)

Kikuchi, T. et al. (2011) Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathogens, 7(9), e1002219. (doi:10.1371/journal.ppat.1002219) (PMID:21909270) (PMCID:PMC3164644)

Otto, T. D. (2011) Real-time sequencing. Nature Reviews Microbiology, 9(9), p. 633. (doi:10.1038/nrmicro2638) (PMID:28298449)

Kazura, J. W., Ogun, S. A., Tewari, R., Otto, T. D. , Howell, S. A., Knuepfer, E., Cunningham, D. A., Xu, Z., Pain, A. and Holder, A. A. (2011) Targeted disruption of py235ebp-1: Invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein. PLoS Pathogens, 7(2), e1001288. (doi:10.1371/journal.ppat.1001288) (PMID:21379566) (PMCID:PMC3040676)

Otto, T. D. , Dillon, G. P., Degrave, W. S. and Berriman, M. (2011) RATT: Rapid annotation transfer tool. Nucleic Acids Research, 39(9), -. e57. (doi:10.1093/nar/gkq1268) (PMID:21306991) (PMCID:PMC3089447)

Rogers, M.B. et al. (2011) Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Research, 21(12), pp. 2129-2142. (doi:10.1101/gr.122945.111)

2010

Rebello, K. M. et al. (2010) Leishmania (Viannia) braziliensis: Influence of successive in vitro cultivation on the expression of promastigote proteinases. Experimental Parasitology, 126(4), pp. 570-576. (doi:10.1016/j.exppara.2010.06.009) (PMID:20553928)

Capriles, P. V.S.Z., Guimarães, A. C.R., Otto, T. D. , Miranda, A. B., Dardenne, L. E. and Degrave, W. M. (2010) Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment. BMC Genomics, 11, 610. (doi:10.1186/1471-2164-11-610) (PMID:21034488) (PMCID:PMC3091751)

Otto, T. D. (2010) Seeking perfection. Nature Reviews Microbiology, 8, p. 681. (doi:10.1038/nrmicro2446) (PMID:20844555)

Hunt, P. et al. (2010) Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics, 11, 499. (doi:10.1186/1471-2164-11-499) (PMID:20846421) (PMCID:PMC2996995)

Nygaard, S. et al. (2010) Long- and short-term selective forces on malaria parasite genomes. PLoS Genetics, 6(9), e1001099. (doi:10.1371/journal.pgen.1001099) (PMID:20838588) (PMCID:PMC2936524)

Otto, T. D. , Sanders, M., Berriman, M. and Newbold, C. (2010) Iterative correction of reference nucleotides (iCORN) using second generation sequencing technology. Bioinformatics, 26(14), pp. 1704-1707. (doi:10.1093/bioinformatics/btq269) (PMID:20562415) (PMCID:PMC2894513)

Sutherland, C. J. et al. (2010) Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally. Journal of Infectious Diseases, 201(10), pp. 1544-1550. (doi:10.1086/652240) (PMID:20380562)

Tsai, I. J., Otto, T. D. and Berriman, M. (2010) Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology, 11, R41. (doi:10.1186/gb-2010-11-4-r41) (PMID:20388197) (PMCID:PMC2884544)

Otto, T. D. et al. (2010) New insights into the blood-stage transcriptome of Plasmodium falciparumusing RNA-Seq. Molecular Microbiology, 76(1), pp. 12-24. (doi:10.1111/j.1365-2958.2009.07026.x) (PMID:20141604) (PMCID:PMC2859250)

Otto, T. D. et al. (2010) ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes. Bioinformatics, 26(5), pp. 705-707. (doi:10.1093/bioinformatics/btq011) (PMID:20089515) (PMCID:PMC2828119)

Carver, T., Bohme, U., Otto, T. D. , Parkhill, J. and Berriman, M. (2010) BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics, 26(5), pp. 676-677. (doi:10.1093/bioinformatics/btq010) (PMID:20071372) (PMCID:PMC2828118)

2009

Assefa, S., Keane, T. M., Otto, T. D. , Newbold, C. and Berriman, M. (2009) ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics, 25(15), pp. 1968-1969. (doi:10.1093/bioinformatics/btp347) (PMID:19497936) (PMCID:PMC2712343)

2008

Otto, T. D. , Guimaraes, A. C. R., Degrave, W. M. and de Miranda, A. B. (2008) AnEnPi: Identification and annotation of analogous enzymes. BMC Bioinformatics, 9(1), 544. (doi:10.1186/1471-2105-9-544) (PMID:19091081) (PMCID:PMC2628392)

Guimares, A.C., Otto, T.D. , Alves-Ferreira, M., Miranda, A.B. and Degrave, W.M. (2008) In silico reconstruction of the amino acid metabolic pathways of Trypanosoma cruzi. Genetics and Molecular Research, 7(3), pp. 872-882. (PMID:18949706)

Otto, T.D. , Vasconcellos, E.A., Gomes, L.H.F., Moreira, A.S., Degrave, W.M., Mendonca-Lima, L. and Alves-Ferreira, M. (2008) ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility. Genetics and Molecular Research, 7(3), pp. 861-871. (PMID:18949705)

Otto, T. D. , Gomes, L. H.F., Alves-Ferreira, M., de Miranda, A. B. and Degrave, W. M. (2008) ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinformatics, 9, 366. (doi:10.1186/1471-2105-9-366) (PMID:18782453) (PMCID:PMC2559850)

2007

Otto, T. D. and Thurnherr, A. M. (2007) Efficient algorithms for finding sills in digital topographic maps. Computers and Geosciences, 33(5), pp. 678-684. (doi:10.1016/j.cageo.2006.10.003)

Otto, T. D. and Catanho, M. (2007) A plataforma PDTIS de bioinformática: da seqüência à função. Revista electronica de comunicacao, informacao & inovacao em saude : RECIIS, 1(2), (doi:10.3395/reciis.v1i2.Sup.98pt)

Otto, T. D. and Miranda, A. B. d. (2007) The PDTIS bioinformatics platform: from sequence to function. Revista electronica de comunicacao, informacao & inovacao em saude : RECIIS, 1(2), (doi:10.3395/reciis.v1i2.Sup.98en)

de Macedo, J.A.F., Lifschitz, S., Porto, F., Picouet, P., de Miranda, A.B. and Otto, T.D. (2007) Towards a Conceptual Modeling Language for Biological Domains. In: Second Brazilian Symposium on Bioinformatics, BSB 2007, Angra dos Reis, Brazil, 29-31 Aug 2007,

2004

Wismueller, A., Meyer-Base, A., Lange, O., Otto, T. D. and Auer, D. (2004) Data Partitioning and Independent Component Analysis Techniques Applied to fMRI. In: Defense and Security, Orlando, Florida, 12-16 Apr 2004, pp. 104-115. (doi:10.1117/12.542219)

2003

Otto, T. D. , Meyer-Baese, A., Hurdal, M., Sumners, D., Auer, D. and Wismuller, A. (2003) Model-free Functional MRI Analysis Using Cluster-Based Methods. In: AeroSense 2003, Orlando, Florida, 21-25 Apr 2003, pp. 17-24. (doi:10.1117/12.487254)

Otto, T. D. , Meyer-Baese, A., Hurdal, M., Sunmers, D., Wismuller, A. and Auer, D. (2003) Model-free Functional MRI Analysis Using Transformation-based Methods. In: AeroSense 2003, Orlando, Florida, 21 - 25 April 2003, pp. 156-167. (doi:10.1117/12.487368)

1999

Traut, W., Sahara, K., Otto, T. D. and Marec, F. (1999) Molecular differentiation of sex chromosomes probed by comparative genomic hybridization. Chromosoma, 108(3), pp. 173-180. (doi:10.1007/s004120050366) (PMID:10398846)

This list was generated on Mon Oct 15 16:24:50 2018 BST.
Number of items: 96.

Articles

Kumar, K. et al. (2018) Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach. Scientific Reports, 7, 17146. (doi:10.1038/s41598-017-17505-9) (PMID:29215067) (PMCID:PMC5719419)

Gilabert, A. et al. (2018) Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution. PLoS Biology, 16(8), e2006035. (doi:10.1371/journal.pbio.2006035) (PMID:30142149)

Lee, H. J., Georgiadou, A., Walther, M., Nwakanma, D., Stewart, L. B., Levin, M., Otto, T. D. , Conway, D. J., Coin, L. J. and Cunnington, A. J. (2018) Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria. Science Translational Medicine, 10(447), eaar3619. (doi:10.1126/scitranslmed.aar3619) (PMID:29950443)

Lee, H. J., Georgiadou, A., Otto, T. D. , Levin, M., Coin, L. J., Conway, D. J. and Cunnington, A. J. (2018) Transcriptomic studies of Malaria: a paradigm for investigation of systemic host-pathogen interactions. Microbiology and Molecular Biology Reviews, 82(2), e00071-17. (doi:10.1128/mmbr.00071-17) (PMID:29695497)

Zhang, M. et al. (2018) Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science, 360(6388), eaap7847. (doi:10.1126/science.aap7847) (PMID:29724925)

Otto, T. D. et al. (2018) Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Research, 3, 52. (doi:10.12688/wellcomeopenres.14571.1)

Böhme, U. et al. (2018) Complete avian malaria parasite genomes reveal features associated with lineage specific evolution in birds and mammals. Genome Research, 28(4), pp. 547-560. (doi:10.1101/gr.218123.116) (PMID:29500236) (PMCID:PMC5880244)

Carrington, E., Otto, T. D. , Szestak, T., Lennartz, F., Higgins, M. K., Newbold, C. I. and Craig, A. G. (2018) In silico guided reconstruction and analysis of ICAM-1-binding var genes from Plasmodium falciparum. Scientific Reports, 8, 3282. (doi:10.1038/s41598-018-21591-8) (PMID:29459671) (PMCID:PMC5818487)

Uliano-Silva, M., Dondero, F., Otto, T. D. , Costa, I., Lima, N. C. B., Americo, J. A., Mazzoni, C. J., Prosdocimi, F. and Rebelo, M. d. F. (2018) A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei. GigaScience, 7(2), pp. 1-10. (doi:10.1093/gigascience/gix128) (PMID:29267857)

Otto, T. D. et al. (2018) Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria. Nature Microbiology, 3, pp. 687-697. (doi:10.1038/s41564-018-0162-2) (PMID:29784978)

Wyllie, S. et al. (2018) Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis. Nature, 560, pp. 192-197. (doi:10.1038/s41586-018-0356-z) (PMID:30046105)

Rutledge, G. G. et al. (2017) Genomic characterization of recrudescent Plasmodium malariae after treatment with artemether/lumefantrine. Emerging Infectious Diseases, 23(8), pp. 1300-1307. (doi:10.3201/eid2308.161582) (PMID:28430103) (PMCID:PMC5547787)

Pasini, E. M., Böhme, U., Rutledge, G. G., Voorberg-Van der Wel, A., Sanders, M., Berriman, M., Kocken, C. H.M. and Otto, T. D. (2017) An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome Open Research, 2, 42. (doi:10.12688/wellcomeopenres.11864.1) (PMID:28748222) (PMCID:PMC5500898)

Payne, R. O. et al. (2017) Human vaccination against Plasmodium vivax Duffy-binding protein induces strain-transcending antibodies. JCI Insight, 2(12), e93683. (doi:10.1172/jci.insight.93683) (PMID:28614791) (PMCID:PMC5470884)

Hamilton, W. L., Claessens, A., Otto, T. D. , Kekre, M., Fairhurst, R. M., Rayner, J. C. and Kwiatkowski, D. (2017) Extreme mutation bias and high AT content in Plasmodium falciparum. Nucleic Acids Research, 45(4), pp. 1889-1901. (doi:10.1093/nar/gkw1259) (PMID:27994033) (PMCID:PMC5389722)

Rutledge, G. G. et al. (2017) Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature, 542(7639), pp. 101-104. (doi:10.1038/nature21038) (PMID:28117441) (PMCID:PMC5326575)

Pegoraro, S. et al. (2017) SC83288 is a clinical development candidate for the treatment of severe malaria. Nature Communications, 8, 14193. (doi:10.1038/ncomms14193) (PMID:28139658) (PMCID:PMC5290327)

Rutledge, G. G. and Otto, T. D. (2017) Last parasite standing. Nature Reviews Microbiology, 15(1), p. 4. (doi:10.1038/nrmicro.2016.181) (PMID:27932794)

Sutherland, C. J. et al. (2017) pfk13 -Independent treatment failure in four imported cases of Plasmodium falciparum malaria treated with artemether-lumefantrine in the United Kingdom. Antimicrobial Agents and Chemotherapy, 61(3), -16. e02382. (doi:10.1128/aac.02382-16) (PMID:28137810) (PMCID:PMC5328508)

Oyola, S. O. et al. (2016) Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malaria Journal, 15(1), 597. (doi:10.1186/s12936-016-1641-7) (PMID:27998271) (PMCID:PMC5175302)

Fougère, A. et al. (2016) Variant exported blood-stage proteins encoded by Plasmodium multigene families are expressed in liver stages where they are exported into the parasitophorous vacuole. PLoS Pathogens, 12(11), e1005917. (doi:10.1371/journal.ppat.1005917) (PMID:27851824) (PMCID:PMC5113031)

Auburn, S. et al. (2016) A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes. Wellcome Open Research, 1, 4. (doi:10.12688/wellcomeopenres.9876.1) (PMID:28008421) (PMCID:PMC5172418)

Page, A. J., De Silva, N., Hunt, M., Quail, M. A., Parkhill, J., Harris, S. R., Otto, T. and Keane, J. A. (2016) Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microbial Genomics, 2(8), e000083. (doi:10.1099/mgen.0.000083) (PMID:28348874) (PMCID:PMC5320598)

Steinbiss, S., Silva-Franco, F., Brunk, B., Foth, B., Hertz-Fowler, C., Berriman, M. and Otto, T. D. (2016) Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Research, 44(W1), W29-W34. (doi:10.1093/nar/gkw292) (PMID:27105845) (PMCID:PMC4987884)

Bronner, I. F., Otto, T. D. , Zhang, M., Udenze, K., Wang, C., Quail, M. A., Jiang, R. H. Y., Adams, J. H. and Rayner, J. C. (2016) Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants. Genome Research, 26(7), pp. 980-989. (doi:10.1101/gr.200279.115) (PMID:27197223) (PMCID:PMC4937560)

Ponsuwanna, P. et al. (2016) Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites. Malaria Journal, 15, 51. (doi:10.1186/s12936-016-1097-9) (PMID:26821618) (PMCID:PMC4731938)

Jackson, A. P. et al. (2016) Kinetoplastid phylogenomics reveals the evolutionary innovations associated with the origins of parasitism. Current Biology, 26(2), pp. 161-172. (doi:10.1016/j.cub.2015.11.055) (PMID:26725202) (PMCID:PMC4728078)

Klemm, E. J. et al. (2016) Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host. Nature Microbiology, 1, 15023. (doi:10.1038/nmicrobiol.2015.23) (PMID:27572160)

Hunt, M., Silva, N. D., Otto, T. D. , Parkhill, J., Keane, J. A. and Harris, S. R. (2015) Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biology, 16, 294. (doi:10.1186/s13059-015-0849-0) (PMID:26714481) (PMCID:PMC4699355)

Abdallah, A. M. et al. (2015) Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Scientific Reports, 5, 15443. (doi:10.1038/srep15443) (PMID:26487098) (PMCID:PMC4614345)

Hunt, M., Gall, A., Ong, S. H., Brener, J., Ferns, B., Goulder, P., Nastouli, E., Keane, J. A., Kellam, P. and Otto, T. D. (2015) IVA: accurate de novo assembly of RNA virus genomes. Bioinformatics, 31(14), pp. 2374-2376. (doi:10.1093/bioinformatics/btv120) (PMID:25725497) (PMCID:PMC4495290)

Woo, Y. H. et al. (2015) Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife, 4, e06974. (doi:10.7554/eLife.06974) (PMID:26175406) (PMCID:PMC4501334)

Baragaña, B. et al. (2015) A novel multiple-stage antimalarial agent that inhibits protein synthesis. Nature, 522(7556), pp. 315-320. (doi:10.1038/nature14451) (PMID:26085270) (PMCID:PMC4700930)

Flegontov, P. et al. (2015) Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. Molecular Biology and Evolution, 32(5), pp. 1115-1131. (doi:10.1093/molbev/msv021) (PMID:25660376)

Weerdenburg, E. M. et al. (2015) Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts. Infection and Immunity, 83(5), pp. 1778-1788. (doi:10.1128/IAI.03050-14) (PMID:25690095) (PMCID:PMC4399070)

Ramaprasad, A., Mourier, T., Naeem, R., Malas, T. B., Moussa, E., Panigrahi, A., Vermont, S. J., Otto, T. D. , Wastling, J. and Pain, A. (2015) Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features. PLoS ONE, 10(4), e0124473. (doi:10.1371/journal.pone.0124473) (PMID:25875305) (PMCID:PMC4395442)

Pinheiro, M. M., Ahmed, M. A., Millar, S. B., Sanderson, T., Otto, T. D. , Lu, W. C., Krishna, S., Rayner, J. C. and Cox-Singh, J. (2015) Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. PLoS ONE, 10(4), e0121303. (doi:10.1371/journal.pone.0121303) (PMID:25830531) (PMCID:PMC4382175)

Claessens, A., Hamilton, W. L., Kekre, M., Otto, T. D. , Faizullabhoy, A., Rayner, J. C. and Kwiatkowski, D. (2014) Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis. PLoS Genetics, 10(12), e1004812. (doi:10.1371/journal.pgen.1004812) (PMID:25521112) (PMCID:PMC4270465)

Vaidya, A. B. et al. (2014) Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum. Nature Communications, 5, 5521. (doi:10.1038/ncomms6521) (PMID:25422853) (PMCID:PMC4263321)

Foth, B. J. and Otto, T. D. (2014) Genomics illuminates parasite biology. Nature reviews. Microbiology, 12(11), p. 727. (doi:10.1038/nrmicro3368) (PMID:25402362)

Otto, T. D. et al. (2014) A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biology, 12(1), p. 86. (doi:10.1186/s12915-014-0086-0) (PMID:25359557) (PMCID:PMC4242472)

Reid, A. J. et al. (2014) Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Research, 24(10), pp. 1676-1685. (doi:10.1101/gr.168955.113) (PMID:25015382) (PMCID:PMC4199364)

Otto, T. D. et al. (2014) Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nature Communications, 5, 4754. (doi:10.1038/ncomms5754) (PMID:25203297) (PMCID:PMC4166903)

Sinha, A. et al. (2014) A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium. Nature, 507(7491), pp. 253-257. (doi:10.1038/nature12970) (PMID:24572359) (PMCID:PMC4105895)

Hunt, M., Newbold, C., Berriman, M. and Otto, T. D. (2014) A comprehensive evaluation of assembly scaffolding tools. Genome Biology, 15(3), R42. (PMID:24581555) (PMCID:PMC4053845)

Jackson, A. P. et al. (2014) The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. Nucleic Acids Research, 42(11), pp. 7113-7131. (doi:10.1093/nar/gku322) (PMID:24799432) (PMCID:PMC4066756)

Bradnam, K. R. et al. (2013) Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. GigaScience, 2(1), pp. 1-31. (doi:10.1186/2047-217X-2-10) (PMID:22678431) (PMCID:PMC3844414)

Lemieux, J. E., Kyes, S. A., Otto, T. D. , Feller, A. I., Eastman, R. T., Pinches, R. A., Berriman, M., Su, X.-Z. and Newbold, C. I. (2013) Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation. Molecular Microbiology, 90(3), pp. 519-537. (PMID:23980881) (PMCID:PMC3894959)

Otto, T. D. and Reid, A. J. (2013) Cereal killers. Nature reviews. Microbiology, 11, p. 744. (doi:10.1038/nrmicro3144) (PMID:24129509)

Balu, B. et al. (2013) Atypical mitogen-activated protein kinase phosphatase implicated in regulating transition from pre-S-Phase asexual intraerythrocytic development of Plasmodium falciparum. Eukaryotic cell, 12(9), pp. 1171-8. (doi:10.1128/EC.00028-13) (PMID:23813392) (PMCID:PMC3811562)

Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M. and Otto, T. D. (2013) REAPR: a universal tool for genome assembly evaluation. Genome Biology, 14(5), R47. (doi:10.1186/gb-2013-14-5-r47) (PMID:22678431) (PMCID:PMC3648784)

Ning, J. et al. (2013) Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. Genes and Development, 27(10), pp. 1198-1215. (PMID:3699412) (PMCID:PMC3672651)

Carver, T., Harris, S. R., Otto, T. D. , Berriman, M., Parkhill, J. and McQuillan, J. A. (2013) BamView: visualizing and interpretation of next-generation sequencing read alignments. Briefings in Bioinformatics, 14(2), pp. 203-12. (PMID:22253280) (PMCID:PMC3603209)

Oyola, S. O. et al. (2013) Efficient depletion of host DNA contamination in malaria clinical sequencing. Journal of Clinical Microbiology, 51(3), pp. 745-751. (doi:10.1128/JCM.02507-12) (PMID:23224084) (PMCID:PMC3592063)

Pasini, E. M. et al. (2013) Proteomic and genetic analyses demonstrate that Plasmodium berghei blood stages export a large and diverse repertoire of proteins. Molecular and Cellular Proteomics, 12(2), pp. 426-48. (doi:10.1074/mcp.M112.021238) (PMID:23197789) (PMCID:PMC3567864)

Quail, M. A., Smith, M., Coupland, P., Otto, T. D. , Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P. and Gu, Y. (2012) A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics, 13(1), p. 341. (doi:10.1186/1471-2164-13-341) (PMID:22827831) (PMCID:PMC3431227)

Lawton, J. et al. (2012) Characterization and gene expression analysis of the cir multi-gene family of plasmodium chabaudi chabaudi (AS). BMC Genomics, 13(125), (doi:10.1186/1471-2164-13-125) (PMID:22458863) (PMCID:PMC3384456)

Jackson, A. P. et al. (2012) Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species. Proceedings of the National Academy of Sciences of the United States of America, 109(9), pp. 3416-3421. (doi:10.1073/pnas.1117313109) (PMID:22331916) (PMCID:PMC3295286)

Protasio, A. V. et al. (2012) A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. PLoS Neglected Tropical Diseases, 6(1), e1455. (doi:10.1371/journal.pntd.0001455) (PMID:22253936) (PMCID:PMC3254664)

Oyola, S. O. et al. (2012) Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes. BMC Genomics, 13(1), (doi:10.1186/1471-2164-13-1) (PMID:22214261) (PMCID:PMC3312816)

Oyola, S. O. et al. (2012) Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics, 13, p. 1. (PMID:22214261) (PMCID:PMC3312816)

Smith, M. et al. (2012) An in-solution hybridisation method for the isolation of pathogen DNA from human DNA-rich clinical samples for analysis by NGS. Open Genomics Journal, 5(1), pp. 18-29. (doi:10.2174/1875693X01205010018) (PMID:24273626) (PMCID:PMC3837216)

Swain, M. T., Tsai, I. J., Assefa, S. A., Newbold, C., Berriman, M. and Otto, T. D. (2012) A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nature Protocols, 7(7), pp. 1260-1284. (doi:10.1038/nprot.2012.068) (PMID:22678431) (PMCID:PMC3648784)

Quail, M. A., Otto, T. D. , Gu, Y., Harris, S. R., Skelly, T. F., McQuillan, J. A., Swerdlow, H. P. and Oyola, S. O. (2011) Optimal enzymes for amplifying sequencing libraries. Nature Methods, 9(1), pp. 10-11. (doi:10.1038/nmeth.1814) (PMID:22205512)

Pfander, C. et al. (2011) A scalable pipeline for highly effective genetic modification of a malaria parasite. Nature Methods, 8(12), pp. 1078-1082. (doi:10.1038/nmeth.1742) (PMID:22020067) (PMCID:PMC3431185)

Gomes, L. H. F., Otto, T. D. , Vasconcellos, E. A., Ferrao, P., Maia, R. M., Moreira, A. S., Ferreira, M. A., Castello-Branco, L. R. R., Degrave, W. M. and Mendonca-Lima, L. (2011) Genome sequence of Mycobacterium bovis BCG Moreau, the Brazilian vaccine strain against tuberculosis. Journal of Bacteriology, 193(19), pp. 5600-5601. (doi:10.1128/JB.05827-11) (PMID:21914899) (PMCID:PMC3187452)

Kikuchi, T. et al. (2011) Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathogens, 7(9), e1002219. (doi:10.1371/journal.ppat.1002219) (PMID:21909270) (PMCID:PMC3164644)

Otto, T. D. (2011) Real-time sequencing. Nature Reviews Microbiology, 9(9), p. 633. (doi:10.1038/nrmicro2638) (PMID:28298449)

Kazura, J. W., Ogun, S. A., Tewari, R., Otto, T. D. , Howell, S. A., Knuepfer, E., Cunningham, D. A., Xu, Z., Pain, A. and Holder, A. A. (2011) Targeted disruption of py235ebp-1: Invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein. PLoS Pathogens, 7(2), e1001288. (doi:10.1371/journal.ppat.1001288) (PMID:21379566) (PMCID:PMC3040676)

Otto, T. D. , Dillon, G. P., Degrave, W. S. and Berriman, M. (2011) RATT: Rapid annotation transfer tool. Nucleic Acids Research, 39(9), -. e57. (doi:10.1093/nar/gkq1268) (PMID:21306991) (PMCID:PMC3089447)

Rogers, M.B. et al. (2011) Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Research, 21(12), pp. 2129-2142. (doi:10.1101/gr.122945.111)

Rebello, K. M. et al. (2010) Leishmania (Viannia) braziliensis: Influence of successive in vitro cultivation on the expression of promastigote proteinases. Experimental Parasitology, 126(4), pp. 570-576. (doi:10.1016/j.exppara.2010.06.009) (PMID:20553928)

Capriles, P. V.S.Z., Guimarães, A. C.R., Otto, T. D. , Miranda, A. B., Dardenne, L. E. and Degrave, W. M. (2010) Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment. BMC Genomics, 11, 610. (doi:10.1186/1471-2164-11-610) (PMID:21034488) (PMCID:PMC3091751)

Otto, T. D. (2010) Seeking perfection. Nature Reviews Microbiology, 8, p. 681. (doi:10.1038/nrmicro2446) (PMID:20844555)

Hunt, P. et al. (2010) Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. BMC Genomics, 11, 499. (doi:10.1186/1471-2164-11-499) (PMID:20846421) (PMCID:PMC2996995)

Nygaard, S. et al. (2010) Long- and short-term selective forces on malaria parasite genomes. PLoS Genetics, 6(9), e1001099. (doi:10.1371/journal.pgen.1001099) (PMID:20838588) (PMCID:PMC2936524)

Otto, T. D. , Sanders, M., Berriman, M. and Newbold, C. (2010) Iterative correction of reference nucleotides (iCORN) using second generation sequencing technology. Bioinformatics, 26(14), pp. 1704-1707. (doi:10.1093/bioinformatics/btq269) (PMID:20562415) (PMCID:PMC2894513)

Sutherland, C. J. et al. (2010) Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally. Journal of Infectious Diseases, 201(10), pp. 1544-1550. (doi:10.1086/652240) (PMID:20380562)

Tsai, I. J., Otto, T. D. and Berriman, M. (2010) Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology, 11, R41. (doi:10.1186/gb-2010-11-4-r41) (PMID:20388197) (PMCID:PMC2884544)

Otto, T. D. et al. (2010) New insights into the blood-stage transcriptome of Plasmodium falciparumusing RNA-Seq. Molecular Microbiology, 76(1), pp. 12-24. (doi:10.1111/j.1365-2958.2009.07026.x) (PMID:20141604) (PMCID:PMC2859250)

Otto, T. D. et al. (2010) ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes. Bioinformatics, 26(5), pp. 705-707. (doi:10.1093/bioinformatics/btq011) (PMID:20089515) (PMCID:PMC2828119)

Carver, T., Bohme, U., Otto, T. D. , Parkhill, J. and Berriman, M. (2010) BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics, 26(5), pp. 676-677. (doi:10.1093/bioinformatics/btq010) (PMID:20071372) (PMCID:PMC2828118)

Assefa, S., Keane, T. M., Otto, T. D. , Newbold, C. and Berriman, M. (2009) ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics, 25(15), pp. 1968-1969. (doi:10.1093/bioinformatics/btp347) (PMID:19497936) (PMCID:PMC2712343)

Otto, T. D. , Guimaraes, A. C. R., Degrave, W. M. and de Miranda, A. B. (2008) AnEnPi: Identification and annotation of analogous enzymes. BMC Bioinformatics, 9(1), 544. (doi:10.1186/1471-2105-9-544) (PMID:19091081) (PMCID:PMC2628392)

Guimares, A.C., Otto, T.D. , Alves-Ferreira, M., Miranda, A.B. and Degrave, W.M. (2008) In silico reconstruction of the amino acid metabolic pathways of Trypanosoma cruzi. Genetics and Molecular Research, 7(3), pp. 872-882. (PMID:18949706)

Otto, T.D. , Vasconcellos, E.A., Gomes, L.H.F., Moreira, A.S., Degrave, W.M., Mendonca-Lima, L. and Alves-Ferreira, M. (2008) ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility. Genetics and Molecular Research, 7(3), pp. 861-871. (PMID:18949705)

Otto, T. D. , Gomes, L. H.F., Alves-Ferreira, M., de Miranda, A. B. and Degrave, W. M. (2008) ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS). BMC Bioinformatics, 9, 366. (doi:10.1186/1471-2105-9-366) (PMID:18782453) (PMCID:PMC2559850)

Otto, T. D. and Thurnherr, A. M. (2007) Efficient algorithms for finding sills in digital topographic maps. Computers and Geosciences, 33(5), pp. 678-684. (doi:10.1016/j.cageo.2006.10.003)

Otto, T. D. and Catanho, M. (2007) A plataforma PDTIS de bioinformática: da seqüência à função. Revista electronica de comunicacao, informacao & inovacao em saude : RECIIS, 1(2), (doi:10.3395/reciis.v1i2.Sup.98pt)

Otto, T. D. and Miranda, A. B. d. (2007) The PDTIS bioinformatics platform: from sequence to function. Revista electronica de comunicacao, informacao & inovacao em saude : RECIIS, 1(2), (doi:10.3395/reciis.v1i2.Sup.98en)

Traut, W., Sahara, K., Otto, T. D. and Marec, F. (1999) Molecular differentiation of sex chromosomes probed by comparative genomic hybridization. Chromosoma, 108(3), pp. 173-180. (doi:10.1007/s004120050366) (PMID:10398846)

Book Sections

Otto, T. D. (2015) From sequence mapping to genome assemblies. In: Peacock, C. (ed.) Parasite Genomics Protocols [2nd ed.]. Series: Methods in molecular biology (1201). Humana Press: New York, pp. 19-50. ISBN 9781493914371 (doi:10.1007/978-1-4939-1438-8_2)

Conference Proceedings

de Macedo, J.A.F., Lifschitz, S., Porto, F., Picouet, P., de Miranda, A.B. and Otto, T.D. (2007) Towards a Conceptual Modeling Language for Biological Domains. In: Second Brazilian Symposium on Bioinformatics, BSB 2007, Angra dos Reis, Brazil, 29-31 Aug 2007,

Wismueller, A., Meyer-Base, A., Lange, O., Otto, T. D. and Auer, D. (2004) Data Partitioning and Independent Component Analysis Techniques Applied to fMRI. In: Defense and Security, Orlando, Florida, 12-16 Apr 2004, pp. 104-115. (doi:10.1117/12.542219)

Otto, T. D. , Meyer-Baese, A., Hurdal, M., Sumners, D., Auer, D. and Wismuller, A. (2003) Model-free Functional MRI Analysis Using Cluster-Based Methods. In: AeroSense 2003, Orlando, Florida, 21-25 Apr 2003, pp. 17-24. (doi:10.1117/12.487254)

Otto, T. D. , Meyer-Baese, A., Hurdal, M., Sunmers, D., Wismuller, A. and Auer, D. (2003) Model-free Functional MRI Analysis Using Transformation-based Methods. In: AeroSense 2003, Orlando, Florida, 21 - 25 April 2003, pp. 156-167. (doi:10.1117/12.487368)

This list was generated on Mon Oct 15 16:24:50 2018 BST.