A5080784333- Malaria Research and Control
- Genomics and Phylogenetic Studies
- Mosquito-borne diseases and control
- Digital Imaging for Blood Diseases
- Chromosomal and Genetic Variations
- Bird parasitology and diseases
- HIV Research and Treatment
- Genetics, Bioinformatics, and Biomedical Research
- vaccines and immunoinformatics approaches
- Vector-borne infectious diseases
- Genetic diversity and population structure
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Complement system in diseases
- Plant Diversity and Evolution
- Trypanosoma species research and implications
- Plant Taxonomy and Phylogenetics
- Biomedical Text Mining and Ontologies
- Research Data Management Practices
- Scientific Computing and Data Management
- Digital literacy in education
- Evolution and Genetic Dynamics
- Insect symbiosis and bacterial influences
- Peptidase Inhibition and Analysis
- Invertebrate Immune Response Mechanisms
University of Georgia
2014-2023
Emory University
2017-2023
Institute of Bioinformatics
2019
J. Craig Venter Institute
2012
North China University of Science and Technology
2012
Texas A&M University
2008
MCScan is an algorithm able to scan multiple genomes or subgenomes in order identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements adjusted for detection of synteny collinearity that extends the original software by incorporating 14 utility programs visualization results additional downstream analyses. Applications several sequenced plant gene families are shown examples. can be used effectively analyze chromosome...
Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) lycophytes. We report here genome sequence lycophyte Selaginella moellendorffii (Selaginella), first nonseed vascular plant reported. By comparing gene content in evolutionarily diverse taxa, we found that transition from a gametophyte- to sporophyte-dominated life cycle required far fewer new genes than flowering plant, whereas secondary...
Date palm is one of the most economically important woody crops cultivated in Middle East and North Africa a good candidate for improving agricultural yields arid environments. Nonetheless, long generation times (5-8 years) dioecy (separate male female trees) have complicated its cultivation genetic analysis. To address these issues, we assembled draft genome Khalas variety date palm, first publicly available resource type member order Arecales. The ∼380 Mb sequence, spanning mainly...
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...
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...
ABSTRACT Accurate and rapid diagnosis of malaria infections is crucial for implementing species-appropriate treatment saving lives. Molecular diagnostic tools are the most accurate sensitive method detecting Plasmodium , differentiating between species, subclinical infections. Despite available whole-genome sequence data falciparum P. vivax majority PCR-based methods still rely on 18S rRNA gene targets. Historically, this has served as best target assays. However, it limited in its ability...
Plasmodium vivax infections remain a major source of malaria-related morbidity and mortality. Early accurate diagnosis is an integral component effective malaria control programs. Conventional molecular diagnostic methods provide results but are often resource-intensive, expensive, have long turnaround time beyond the capacity most malaria-endemic countries. Our laboratory has recently developed new platform called RealAmp, which combines loop-mediated isothermal amplification (LAMP) with...
The phylogenetic relationships among hemosporidian parasites, including the origin of Plasmodium falciparum, most virulent malaria parasite humans, have been heavily debated for decades. Studies based on multiple-gene sequences helped settle many these controversial issues. However, denser taxon sampling and genome-wide analyses are needed to confidently resolve evolutionay parasites. Genome several parasites available but only species infecting primates rodents. To root tree Plasmodium,...
Apomixis, asexual reproduction through seed, is widespread among angiosperm families. Gametophytic apomixis in Pennisetum squamulatum and Cenchrus ciliaris controlled by the apospory-specific genomic region (ASGR), which highly conserved macrosyntenic between these species. Thirty-two ASGR bacterial artificial chromosomes (BACs) isolated from both species one ASGR-recombining BAC P. squamulatum, together cover approximately 2.7 Mb of DNA, were used to investigate structure this region. Phrap...
Whole-genome comparisons provide insight into genome evolution by informing on gene repertoires, gains/losses, and organization. Most of our knowledge about eukaryotic is derived from studies multicellular model organisms. The phylum Apicomplexa contains obligate intracellular protist parasites responsible for a wide range human veterinary diseases (e.g., malaria, toxoplasmosis, theileriosis). We have developed an in silico protein-encoding based pipeline to investigate synteny across 12...
Chronic malaria is a major public health problem and significant challenge for disease eradication efforts. Despite its importance, the biological factors underpinning chronic are not fully understood. Recent studies have shown that host metabolic state can influence pathogenesis transmission, but role in chronicity known. Here, with goal of identifying distinct modifications metabolite profiles acute versus malaria, metabolomics was performed on plasma from Plasmodium-infected humans...
Background Recent studies in Southeast Asia have demonstrated substantial zoonotic transmission of Plasmodium knowlesi to humans. Microscopically, P. exhibits several stage-dependent morphological similarities malariae and falciparum. These often lead misdiagnosis as either or falciparum PCR-based molecular diagnostic tests are required accurately detect The most commonly used PCR test has been found give false positive results, especially with a proportion vivax isolates. To address the...
SUMMARY Plasmodium knowlesi has risen in importance as a zoonotic parasite that been causing regular episodes of malaria throughout South East Asia. The P. genome sequence generated 2008 highlighted and confirmed many similarities differences species, including global view several multigene families, such the large SICAvar family encoding variant antigens known schizont-infected cell agglutination proteins. However, repetitive DNA sequences are bane any project, this other projects have not...
Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number raw reads, their short length, relative Sanger, PacBio or Nanopore complicates assembly genomic repeats. Many genome tools available, but highly repetitive sequences using only NGS reads remains challenging. Genome organisms responsible for important neglected diseases such as Trypanosoma cruzi, aetiological agent Chagas disease, is...
Plasmodium relapses are attributed to the activation of dormant liver-stage parasites and responsible for a significant number recurring malaria blood-stage infections. While characteristic human infections caused by P. vivax ovale, their relative contribution disease burden transmission remains poorly understood. This is largely because it difficult identify 'bona fide' relapse due ongoing in most endemic areas. Here, we use cynomolgi–rhesus macaque model relapsing demonstrate that clinical...
Mild to severe anaemia is a common complication of malaria that caused in part by insufficient erythropoiesis the bone marrow. This study used systems biology evaluate transcriptional and alterations cell populations marrow during Plasmodium cynomolgi infection rhesus macaques (a model vivax malaria) may affect erythropoiesis. An appropriate erythropoietic response did not occur compensate for acute despite an increase erythropoietin levels. During this period, there were significant...
We describe a multi-omic approach to understanding the effects that anti-malarial drug pyrimethamine has on immune physiology in rhesus macaques (Macaca mulatta). Whole blood and bone marrow RNA-Seq plasma metabolome profiles (each with over 15,000 features) have been generated for five naïve individuals at up seven time-points before, during after three rounds of administration. Linear modelling Bayesian network analyses are both considered, alongside investigations impact statistical...
Previous studies have suggested that a relationship exists between severity and transmissibility of malaria variations in the gut microbiome, yet only limited information on temporal dynamics microbial community during malarial infection. Here, using rhesus macaque model relapsing malaria, we investigate how affects microbiome. In this study, performed 16S sequencing DNA isolated from rectal swabs macaques over course an experimental infection with Plasmodium cynomolgi analyzed bacterial...
Higher eukaryotic genomes are typically large, complex and filled with both genes multiple classes of repetitive DNA. The DNAs, primarily transposable elements, a rapidly evolving genome component that can provide the raw material for novel selected functions also indicate mechanisms history evolution in any ancestral lineage. Despite their abundance, universality significance, studies genomic repeat content have been largely limited to analyses repeats fully sequenced genomes.In order...
Kra monkeys (Macaca fascicularis), a natural host of Plasmodium knowlesi, control parasitaemia caused by this parasite species and escape death without treatment. Knowledge the disease progression resilience in kra will aid effective use to study mechanisms malaria. This longitudinal aimed define clinical, physiological pathological changes infected with P. which could explain their resilient phenotype.
We characterize the prevalence, distribution, divergence, and putative functions of detectable two-copy paralogs segmental duplications in Apicomplexa, a phylum parasitic protists. Apicomplexans are mostly obligate intracellular parasites responsible for human animal diseases (e.g. malaria toxoplasmosis). Gene loss is major force phylum. Genomes small protein-encoding gene repertoires reduced. Despite this genomic streamlining, family amplifications present. The potential innovation...