A5007181859- Malaria Research and Control
- Trypanosoma species research and implications
- Mosquito-borne diseases and control
- Invertebrate Immune Response Mechanisms
- vaccines and immunoinformatics approaches
- Genomics and Phylogenetic Studies
- Research on Leishmaniasis Studies
- Parasite Biology and Host Interactions
- Vector-borne infectious diseases
- Parasites and Host Interactions
- Insect symbiosis and bacterial influences
- Evolution and Genetic Dynamics
- Bioinformatics and Genomic Networks
- Aquaculture disease management and microbiota
- Biomedical Text Mining and Ontologies
- Biochemical and Molecular Research
- Bird parasitology and diseases
- HIV Research and Treatment
- Livestock and Poultry Management
- Genetics, Bioinformatics, and Biomedical Research
- Antibiotic Resistance in Bacteria
- RNA and protein synthesis mechanisms
- Plant Pathogens and Fungal Diseases
- Helminth infection and control
- Bacteriophages and microbial interactions
University of Liverpool
2021-2024
University of Georgia
2023
Wellcome Sanger Institute
2008-2021
University of Copenhagen
2019
University of Colorado Boulder
2019
The Francis Crick Institute
2019
Pennsylvania State University
2019
Genomics (United Kingdom)
2019
Carnegie Institution for Science
2010
George Washington University
2005
African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence analysis of 11 megabase-sized chromosomes Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive 806 variant surface glycoprotein (VSG) genes used by parasite to evade mammalian immune system. Most VSG are pseudogenes, which may be...
Abstract Motivation: Artemis and Comparison Tool (ACT) have become mainstream tools for viewing annotating sequence data, particularly microbial genomes. Since its first release, has been continuously developed supported with additional functionality editing analysing sequences based on feedback from an active user community of laboratory biologists professional annotators. Nevertheless, utility somewhat restricted by limitation to reading writing flat files. Therefore, a new version...
The oomycete Phytophthora infestans causes late blight, the potato disease that precipitated Irish famines in 1846 and 1847. It represents a reemerging threat to production is one of >70 species are arguably most devastating pathogens dicotyledonous plants. Nevertheless, little known about molecular bases pathogenicity these algae-like organisms or avirulence molecules perceived by host defenses. Disease resistance alleles, products which recognize corresponding pathogen, have been...
Recent advances in high-throughput sequencing present a new opportunity to deeply probe an organism's transcriptome. In this study, we used Illumina-based massively parallel gain insight into the transcriptome (RNA-Seq) of human malaria parasite, Plasmodium falciparum. Using data collected at seven time points during intraerythrocytic developmental cycle, (i) detect novel gene transcripts; (ii) correct hundreds models; (iii) propose alternative splicing events; and (iv) predict 5' 3'...
Abstract The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with EuPathDB projects. As a Bioinformatics Center funded by National Institutes Health, additional support from Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists fungi) relevant free-living or non-pathogenic species hosts. Designed to empower researchers access Omics data...
Four distinct Plasmodium species are known to regularly infect humans: falciparum, P. vivax, malariae and ovale. The genome sequence of the cause most severe type human malaria, was completed in 2002 at same time as mosquito vector, Anopheles gambiae. In this week's Nature, which focuses on malaria parasite, two further sequences described. First that contributes significant numbers incidence humans, though contrast resulting disease is usually not fatal. rather neglected presented together...
Although eukaryotic protein kinases (ePKs) contribute to many cellular processes, only three Plasmodium falciparum ePKs have thus far been identified as essential for parasite asexual blood stage development. To identify pathways transmission between their mammalian host and mosquito vector, we undertook a systematic functional analysis of in the genetically tractable rodent berghei. Modeling domain signatures conventional 66 putative ePKs. Kinomes are highly conserved species. Using reverse...
Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and chabaudi AS (PcAS). Although availability these made a significant impact on recent research, were highly fragmented annotated with little manual curation. The nature the has hampered genome wide analysis gene regulation function.
Elucidation of the evolutionary history and interrelatedness Plasmodium species that infect humans has been hampered by a lack genetic information for three human-infective species: P. malariae two ovale (P. o. curtisi wallikeri). These are prevalent across most regions in which malaria is endemic often undetectable light microscopy, rendering their study human populations difficult. The exact relationship these to other contested. Using new reference genome manually curated draft genome, we...
Abstract The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Center funded by the National Institutes of Health with additional funding from Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists fungi) relevant free-living or non-pathogenic species hosts. Since 2004, has analyzed omics data public domain using contemporary bioinformatic workflows, including...
Parasitic diseases caused by kinetoplastid parasites are a burden to public health throughout tropical and subtropical regions of the world. TriTrypDB ( https://tritrypdb.org ) is free online resource for data mining genomic functional from these part VEuPathDB Bioinformatics Resource Center https://veupathdb.org ). As release 59, hosts 83 genomes, nine which, including Trypanosoma brucei TREU927, cruzi CL Brener Leishmania major Friedlin, undergo manual curation integrating information...
<ns4:p><ns4:italic>Plasmodium vivax</ns4:italic>is now the predominant cause of malaria in Asia-Pacific, South America and Horn Africa. Laboratory studies this species are constrained by inability to maintain parasite continuous<ns4:italic>ex vivo</ns4:italic>culture, but genomic approaches provide an alternative complementary avenue investigate parasite’s biology epidemiology. To date, molecular of<ns4:italic>P. vivax</ns4:italic>have relied on Salvador-I reference genome sequence, derived...
Background: Although thousands of clinical isolates Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve highly variable subtelomeric regions genomes that contain polymorphic gene families involved in immune evasion pathogenesis. There is also no current standard definition boundaries these regions. Methods: Using long-read sequence (Pacific Biosciences SMRT technology), we assembled annotated 15 P. isolates, ten which newly cultured...
Plasmodium falciparum causes most human malaria deaths, having prehistorically evolved from parasites of African Great Apes. Here we explore the genomic basis P. adaptation to hosts by fully sequencing genome closely related chimpanzee parasite species reichenowi, and obtaining partial sequence data a more distantly (P. gaboni). The close relationship between reichenowi is emphasized almost complete conservation synteny, but against this strikingly conserved background observe major...
Avian malaria parasites are prevalent around the world and infect a wide diversity of bird species. Here, we report sequencing analysis high-quality draft genome sequences for two avian species, Plasmodium relictum gallinaceum . We identify 50 genes that specific to malaria, located in an otherwise conserved core shares gene synteny with all other sequenced genomes. Phylogenetic suggests species form outgroup mammalian using amino acid divergence between estimate avian- mammalian-infective...
<ns7:p>The <ns7:italic>var </ns7:italic>gene family of the human malaria parasite <ns7:italic>Plasmodium falciparum</ns7:italic> encode proteins that are crucial determinants both pathogenesis and immune evasion highly polymorphic. Here we have assembled nearly complete repertoires from 2398 field isolates analysed a normalised set 714 across 12 countries. This therefore represents first large scale attempt to catalogue worldwide distribution <ns7:italic>var</ns7:italic> gene...
Abstract FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for wide range of fungal oomycete species. As an integral part the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), continually both published unpublished addressing various aspects biology. Established in early 2011, database has evolved to support 674 datasets. The datasets include over 300 genomes spanning taxa (e.g. Ascomycota,...
Many variant proteins encoded by Plasmodium-specific multigene families are exported into red blood cells (RBC). P. falciparum-specific the var, stevor and rifin onto surface of infected (iRBC) mediate interactions between iRBC host resulting in tissue sequestration rosetting. However, precise function most other Plasmodium encoding is unknown. To understand role RBC-exported rodent malaria parasites (RMP) we analysed expression cellular location fluorescent-tagging members pir, fam-a fam-b...
<ns4:p>Here we describe the ways in which sequence and annotation of <ns4:italic>Plasmodium falciparum</ns4:italic> reference genome has changed since its publication 2002. As malaria species responsible for most deaths worldwide, richness accuracy are important resources <ns4:italic>P. falciparum </ns4:italic>research community as well basis interpreting genomes subsequently sequenced species. At time 2002 over 60% predicted genes had unknown functions. March 2019, this number been...
<ns4:p>Here we describe the ways in which sequence and annotation of <ns4:italic>Plasmodium falciparum</ns4:italic> reference genome has changed since its publication 2002. As malaria species responsible for most deaths worldwide, richness accuracy are important resources <ns4:italic>P. falciparum </ns4:italic>research community as well basis interpreting genomes subsequently sequenced species. At time 2002 over 60% predicted genes had unknown functions. March 2019, this number been...
Abstract Summary: BamView is an interactive Java application for visualizing the large amounts of data stored sequence reads which are aligned against a reference genome sequence. It supports BAM (Binary Alignment/Map) format. can be used in number contexts including SNP calling and structural annotation. has also been integrated into Artemis so that viewed context nucleotide genomic features. Availability: freely available (under GPL licence) download (for MacOSX, UNIX Windows) at:...
Abstract Summary: An XML-based Java application is described that provides a function-oriented overview of the results cluster analysis gene-expression microarray data based on Gene Ontology terms and associations. The generates one HTML page with listings frequencies explicit implicit annotations for each cluster, separate, linked pages gene in cluster. Availability: http://www.charite.de/ch/medgen/ontologizer
<ns4:p><ns4:bold>Background: </ns4:bold><ns4:italic>Plasmodium cynomolgi, </ns4:italic>a non-human primate malaria parasite species, has been an important model since its discovery in 1907. Similarities the biology of <ns4:italic>P. cynomolgi</ns4:italic> to closely related, but less tractable, human vivax</ns4:italic> make it choice for liver and vaccine studies pertinent vivax </ns4:italic>malaria. Molecular genome-scale have relied on current reference genome sequence, which remains...