List of works - Thomas D Otto

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

scientific article

A comprehensive evaluation of assembly scaffolding tools ⬇️

scientific article published on 3 March 2014

A comprehensive evaluation of rodent malaria parasite genomes and gene expression

scientific article

A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways ⬇️

scientific article published on 29 November 2018

A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei ⬇️

scientific article published on 15 December 2017

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

scientific article

A novel multiple-stage antimalarial agent that inhibits protein synthesis

scientific article (publication date: 18 June 2015)

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

scientific article published on 7 June 2012

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

scientific article

A single-nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity

scientific article published on 05 February 2020

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

scientific article

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

scientific article

ABACAS: algorithm-based automatic contiguation of assembled sequences

scientific article published on 3 June 2009

An Experimental Human Blood-Stage Model for Studying Plasmodium malariae Infection

scientific article published on 01 March 2020

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

scientific article

An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion

scientific article

AnEnPi: identification and annotation of analogous enzymes

scientific article

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

scientific article

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

scientific article

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

scientific article (publication date: September 2013)

Author Correction: Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria

scientific article published on 14 August 2020

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

scientific article

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

scientific article (publication date: March 2013)

Cereal killers

scientific article

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

scientific article

ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility.

scientific article published on 23 September 2008

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

scientific article

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

scientific article published on 28 October 2011

Circlator: automated circularization of genome assemblies using long sequencing reads

scientific article

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

scientific article published on 21 April 2016

Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites

scientific article published on 29 January 2016

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

scientific article published in May 2013

Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

scientific article published on 2 March 2018

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

scientific article

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

scientific article published on 17 January 2017

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

scientific article published on 14 December 2016

Corrigendum: A novel multiple-stage antimalarial agent that inhibits protein synthesis

scientific article published on 25 May 2016

Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis

scientific article published in Nature

Distinct synovial tissue macrophage subsets regulate inflammation and remission in rheumatoid arthritis

scientific article published on 29 June 2020

Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites.

scientific article

Efficient depletion of host DNA contamination in malaria clinical sequencing

scientific article

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

scientific article published on 25 January 2016

Evolutionary analysis of the most polymorphic gene family in falciparum malaria

scientific article published on 03 December 2019

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

scientific article

Extreme mutation bias and high AT content in Plasmodium falciparum

scientific article

From Sequence Mapping to Genome Assemblies

scientific article published on 01 January 2015

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

scientific article published on 18 December 2014

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

scientific article

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

scientific article

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

scientific article published on 30 September 2013

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

scientific article published on 17 February 2015

Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria.

scientific article

Genomic Characterization of Recrudescent Plasmodium malariae after Treatment with Artemether/Lumefantrine

scientific article published on 15 August 2017

Genomic analysis of the causative agents of coccidiosis in domestic chickens

scientific article

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

scientific article

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

scientific article

Genomics illuminates parasite biology

scientific article published in November 2014

Host cell maturation modulates parasite invasion and sexual differentiation in <i>Plasmodium berghei</i>

scientific article published on 27 April 2022

Human vaccination against Plasmodium vivax Duffy-binding protein induces strain-transcending antibodies.

scientific article

IVA: accurate de novo assembly of RNA virus genomes

scientific article

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

scientific article published on 13 April 2010

In silico guided reconstruction and analysis of ICAM-1-binding var genes from Plasmodium falciparum.

scientific article published on 19 February 2018

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

scientific article published on 23 September 2008

Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season

scientific article published on 26 October 2020

Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria

scientific article published in June 2018

Integrated transcriptomic and proteomic analysis of pathogenic mycobacteria and their esx-1 mutants reveal secretion-dependent regulation of ESX-1 substrates and WhiB6 as a transcriptional regulator

scientific article published in PLoS ONE

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

scientific article published on 18 June 2010

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

scientific article

Last parasite standing

scientific article published in December 2016

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

scientific article published on 8 June 2010

Long read assemblies of geographically dispersed isolates reveal highly structured subtelomeres

article

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

scientific article

Low sulfated heparins target multiple proteins for central nervous system repair

scientific article published on 26 December 2018

Machine learning approaches classify clinical malaria outcomes based on haematological parameters

scientific article published on 30 November 2020

Modelling pathogen load dynamics to elucidate mechanistic determinants of host-Plasmodium falciparum interactions

scientific article published on 17 June 2019

Molecular differentiation of sex chromosomes probed by comparative genomic hybridization.

scientific article published on July 1999

Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development

scientific article published in Scientific Reports

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

scientific article

Optimal enzymes for amplifying sequencing libraries

scientific article published on 28 December 2011

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

scientific article

Plasmodium falciparum schizont stage transcriptome variation among clinical isolates and laboratory-adapted clones

Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism

scientific article published on April 2015

Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution ⬇️

scientific article

Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

scientific article published on 24 August 2018

Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach ⬇️

scientific article

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

scientific article published on 28 May 2019

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

scientific article published on 19 January 2010

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

scientific article published on 28 November 2012

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

scientific article

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

scientific article

RATT: Rapid Annotation Transfer Tool

scientific article published on 8 February 2011

REAPR: a universal tool for genome assembly evaluation

scientific article

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

scientific article

Real-time sequencing

scientific article published on 12 August 2011

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

scientific article

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

scientific article published on 31 January 2017

Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum

scientific article published on 10 December 2018

Seeking perfection

scientific article published on 01 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

scientific article

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

scientific article

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

scientific article

Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions

scholarly article by Hyun Jae Lee et al published 1 June 2018 in Microbiology and Molecular Biology Reviews

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

scientific article

Uncovering the essential genes of the human malaria parasitePlasmodium falciparumby saturation mutagenesis

scientific article

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

scientific article (publication date: November 2016)

Whole genome sequencing and microsatellite analysis of the Plasmodium falciparum E5 NF54 strain show that the var, rifin and stevor gene families follow Mendelian inheritance

article

Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

scientific article (publication date: 11 August 2016)

peaks2utr: a robust Python tool for the annotation of 3′ UTRs

scientific article published in 2023

pfk13-Independent Treatment Failure in Four Imported Cases of Plasmodium falciparum Malaria Treated with Artemether-Lumefantrine in the United Kingdom

scientific article published on 30 January 2017

β2 Integrins differentially regulate γδ T cell subset thymic development and peripheral maintenance

scientific article published on 26 August 2020

List of works by Thomas D Otto

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

A comprehensive evaluation of assembly scaffolding tools ⬇️

A comprehensive evaluation of rodent malaria parasite genomes and gene expression

A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways ⬇️

A hybrid-hierarchical genome assembly strategy to sequence the invasive golden mussel Limnoperna fortunei ⬇️

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

A novel multiple-stage antimalarial agent that inhibits protein synthesis

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

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

A single-nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor alters the development of host immunity

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

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

ABACAS: algorithm-based automatic contiguation of assembled sequences

An Experimental Human Blood-Stage Model for Studying Plasmodium malariae Infection

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

An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion

AnEnPi: identification and annotation of analogous enzymes

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

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

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

Author Correction: Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria

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

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

Cereal killers

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

ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility.

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

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

Circlator: automated circularization of genome assemblies using long sequencing reads

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

Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites

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

Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

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

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

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

Corrigendum: A novel multiple-stage antimalarial agent that inhibits protein synthesis

Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis

Distinct synovial tissue macrophage subsets regulate inflammation and remission in rheumatoid arthritis

Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites.

Efficient depletion of host DNA contamination in malaria clinical sequencing

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

Evolutionary analysis of the most polymorphic gene family in falciparum malaria

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

Extreme mutation bias and high AT content in Plasmodium falciparum

From Sequence Mapping to Genome Assemblies

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

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

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

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

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

Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria.

Genomic Characterization of Recrudescent Plasmodium malariae after Treatment with Artemether/Lumefantrine

Genomic analysis of the causative agents of coccidiosis in domestic chickens

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

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

Genomics illuminates parasite biology

Host cell maturation modulates parasite invasion and sexual differentiation in <i>Plasmodium berghei</i>

Human vaccination against Plasmodium vivax Duffy-binding protein induces strain-transcending antibodies.

IVA: accurate de novo assembly of RNA virus genomes

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

In silico guided reconstruction and analysis of ICAM-1-binding var genes from Plasmodium falciparum.

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

Increased circulation time of Plasmodium falciparum underlies persistent asymptomatic infection in the dry season

Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria

Integrated transcriptomic and proteomic analysis of pathogenic mycobacteria and their esx-1 mutants reveal secretion-dependent regulation of ESX-1 substrates and WhiB6 as a transcriptional regulator

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

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

Last parasite standing

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

Long read assemblies of geographically dispersed isolates reveal highly structured subtelomeres

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

Low sulfated heparins target multiple proteins for central nervous system repair

Machine learning approaches classify clinical malaria outcomes based on haematological parameters

Modelling pathogen load dynamics to elucidate mechanistic determinants of host-Plasmodium falciparum interactions

Molecular differentiation of sex chromosomes probed by comparative genomic hybridization.

Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development

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

Optimal enzymes for amplifying sequencing libraries