Thomas D Otto

Thomas D Otto

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Thomas D Otto

Thomas D Otto

Publications by authors named "Thomas D Otto"

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Evolutionary analysis of the most polymorphic gene family in malaria.

Wellcome Open Res 2019 3;4:193. Epub 2019 Dec 3.

Parasite Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.15590.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001760PMC
December 2019

Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania.

PLoS Genet 2019 11 11;15(11):e1008452. Epub 2019 Nov 11.

Department of Biochemistry, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1008452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872171PMC
November 2019

Progression of the canonical reference malaria parasite genome from 2002-2019.

Wellcome Open Res 2019 28;4:58. Epub 2019 May 28.

Parasite Genomics, Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.15194.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6484455.2PMC
May 2019

Low sulfated heparins target multiple proteins for central nervous system repair.

Glia 2019 04 26;67(4):668-687. Epub 2018 Dec 26.

Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.

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http://doi.wiley.com/10.1002/glia.23562
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http://dx.doi.org/10.1002/glia.23562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6492281PMC
April 2019

Uncovering the essential genes of the human malaria parasite by saturation mutagenesis.

Science 2018 05;360(6388)

Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.

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http://dx.doi.org/10.1126/science.aap7847DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360947PMC
May 2018

Extreme mutation bias and high AT content in Plasmodium falciparum.

Nucleic Acids Res 2017 02;45(4):1889-1901

Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkw1259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389722PMC
February 2017

Last parasite standing.

Nat Rev Microbiol 2016 Dec;15(1)

Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nrmicro.2016.181DOI Listing
December 2016

Robust high-throughput prokaryote assembly and improvement pipeline for Illumina data.

Microb Genom 2016 08 25;2(8):e000083. Epub 2016 Aug 25.

1​Pathogen Informatics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire, UK.

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http://www.microbiologyresearch.org/content/journal/mgen/10.
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http://dx.doi.org/10.1099/mgen.0.000083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320598PMC
August 2016

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

Nucleic Acids Res 2016 07 21;44(W1):W29-34. Epub 2016 Apr 21.

Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkw292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987884PMC
July 2016

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

Genome Res 2016 07 10;26(7):980-9. Epub 2016 May 10.

Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom;

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http://dx.doi.org/10.1101/gr.200279.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937560PMC
July 2016

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

PLoS One 2015 1;10(4):e0121303. Epub 2015 Apr 1.

School of Medicine, University of St Andrews, Medical and Biological Sciences Building, North Haugh, St Andrews, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121303PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4382175PMC
April 2016

Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features.

PLoS One 2015 13;10(4):e0124473. Epub 2015 Apr 13.

Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, Kingdom of Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124473PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395442PMC
April 2016

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

Genome Biol 2015 Dec 29;16:294. Epub 2015 Dec 29.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1186/s13059-015-0849-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4699355PMC
December 2015

From sequence mapping to genome assemblies.

Authors:
Thomas D Otto

Methods Mol Biol 2015 ;1201:19-50

Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK,

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http://dx.doi.org/10.1007/978-1-4939-1438-8_2DOI Listing
July 2015

IVA: accurate de novo assembly of RNA virus genomes.

Bioinformatics 2015 Jul 28;31(14):2374-6. Epub 2015 Feb 28.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btv120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4495290PMC
July 2015

Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites.

Mol Biol Evol 2015 May 6;32(5):1115-31. Epub 2015 Feb 6.

Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic Canadian Institute for Advanced Research, Toronto, ON, Canada

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http://dx.doi.org/10.1093/molbev/msv021DOI Listing
May 2015

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

PLoS Genet 2014 Dec 18;10(12):e1004812. Epub 2014 Dec 18.

Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom; MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom.

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http://dx.plos.org/10.1371/journal.pgen.1004812
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http://dx.doi.org/10.1371/journal.pgen.1004812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270465PMC
December 2014

Genomics illuminates parasite biology.

Nat Rev Microbiol 2014 Nov;12(11):727

Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nrmicro3368DOI Listing
November 2014

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

Mol Microbiol 2013 Nov 30;90(3):519-37. Epub 2013 Sep 30.

Weatherall Institute of Molecular Medicine, Headington, Oxford, OX3 9DS, UK; National Institute of Allergy and Infectious Disease, NIH, Rockville, MD, 20892, USA.

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http://dx.doi.org/10.1111/mmi.12381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894959PMC
November 2013

Cereal killers.

Nat Rev Microbiol 2013 Nov;11(11):744

Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nrmicro3144DOI Listing
November 2013

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

Gigascience 2013 Jul 22;2(1):10. Epub 2013 Jul 22.

Genome Center, UC, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/2047-217X-2-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844414PMC
July 2013

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

Brief Bioinform 2013 Mar 16;14(2):203-12. Epub 2012 Jan 16.

Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1093/bib/bbr073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603209PMC
March 2013

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

Nat Protoc 2012 Jun 7;7(7):1260-84. Epub 2012 Jun 7.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/nprot.2012.068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648784PMC
June 2012

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

J Bacteriol 2011 Oct;193(19):5600-1

Laboratório de Genômica Funcional e Bioinformática, Pavilhão Leonidas Deane sala 104, Instituto Oswaldo Cruz, Fiocruz Av., Brasil 4365, Manguinhos, 21040-900 Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1128/JB.05827-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187452PMC
October 2011

Real-time sequencing.

Authors:
Thomas D Otto

Nat Rev Microbiol 2011 Aug 12;9(9):633. Epub 2011 Aug 12.

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http://dx.doi.org/10.1038/nrmicro2638DOI Listing
August 2011

RATT: Rapid Annotation Transfer Tool.

Nucleic Acids Res 2011 May 8;39(9):e57. Epub 2011 Feb 8.

Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1093/nar/gkq1268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3089447PMC
May 2011

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.

Genome Biol 2010 13;11(4):R41. Epub 2010 Apr 13.

Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2010-11-4-r41DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884544PMC
October 2010

Seeking perfection.

Authors:
Thomas D Otto

Nat Rev Microbiol 2010 Oct;8(10):681

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http://dx.doi.org/10.1038/nrmicro2446DOI Listing
October 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 2010 Oct 29;11:610. Epub 2010 Oct 29.

Grupo de Modelagem Molecular de Sistemas Biológicos, Laboratório Nacional de Computação Científica, LNCC/MCT, Petrópolis, CEP 25651-075, Brazil.

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http://dx.doi.org/10.1186/1471-2164-11-610DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091751PMC
October 2010

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

Bioinformatics 2010 Jul 18;26(14):1704-7. Epub 2010 Jun 18.

Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894513PMC
July 2010

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

Mol Microbiol 2010 Apr 4;76(1):12-24. Epub 2010 Feb 4.

Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1111/j.1365-2958.2009.07026.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859250PMC
April 2010

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

Bioinformatics 2010 Mar 12;26(5):676-7. Epub 2010 Jan 12.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828118PMC
March 2010

ABACAS: algorithm-based automatic contiguation of assembled sequences.

Bioinformatics 2009 Aug 3;25(15):1968-9. Epub 2009 Jun 3.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btp347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2712343PMC
August 2009

AnEnPi: identification and annotation of analogous enzymes.

BMC Bioinformatics 2008 Dec 17;9:544. Epub 2008 Dec 17.

Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1186/1471-2105-9-544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2628392PMC
December 2008

ReRep: computational detection of repetitive sequences in genome survey sequences (GSS).

BMC Bioinformatics 2008 Sep 9;9:366. Epub 2008 Sep 9.

Laboratory for Functional Genomics and Bioinformatics, IOC, Fiocruz, Rio de Janeiro, Brazil.

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http://dx.doi.org/10.1186/1471-2105-9-366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559850PMC
September 2008