ArticleBioinformatics (Oxford, England)2018
Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it, 94 citations in OpenAlex.
- Pooled it
- Genetic diversity of Plasmodium falciparum and genetic profile in children affected by uncomplicated malaria in Cameroon.Malaria journal · 2020Trial
- Genome-targeted enrichment and sequencing of human-infecting Cryptosporidium spp.Nature communications · 2026Article
- Molecular surveillance of multiplicity of infection, haplotype frequencies, and prevalence in infectious diseases.PLoS computational biology · 2026Article
- hmmibd-rs: an enhanced hmmIBD implementation for parallelizable identity-by-descent detection from large-scale Plasmodium genomic data.Malaria journal · 2026Article
- Malaria-MOI: A flexible and scalable tool for predicting multiplicity of infection in malaria parasites.Genome medicine · 2026Article
- Article
- Genomic investigation of a non-travel Plasmodium falciparum case linked to imported malaria in China's post-elimination era.Malaria journal · 2025Article
- Article
- Potential and pitfalls of using identity-by-descent for malaria genomic surveillance.Trends in parasitology · 2025Review
- Regular Plasmodium falciparum importation onto Bioko Island, Equatorial Guinea, hampers malaria elimination from the island.PLOS global public health · 2025Article
- Review of MrsFreqPhase methods: methods designed to estimate statistically malaria parasite multiplicity of infection, relatedness, frequency and phase.Malaria journal · 2024Review
- SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts.Bioinformatics (Oxford, England) · 2024Article
- Phylogenomic reconstruction ofbioRxiv : the preprint server for biology · 2024Article
- Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum.Nature communications · 2024Article
- Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia.Scientific reports · 2023Article
- Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas.Scientific reports · 2023Article
- Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal.Nature communications · 2023Article
- Strong Positive Selection Biases Identity-By-Descent-Based Inferences of Recent Demography and Population Structure inbioRxiv : the preprint server for biology · 2023Article
- coiaf: Directly estimating complexity of infection with allele frequencies.PLoS computational biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
Motivation: The presence of multiple infecting strains of the malarial parasite Plasmodium falciparum affects key phenotypic traits, including drug resistance and risk of severe disease. Advances in protocols and sequencing technology have made it possible to obtain high-coverage genome-wide sequencing data from blood samples and blood spots taken in the field. However, analyzing and interpreting such data is challenging because of the high rate of multiple infections present. Results: We have developed a statistical method and implementation for deconvolving multiple genome sequences present in an individual with mixed infections. The software package DEploid uses haplotype structure within a reference panel of clonal isolates as a prior for haplotypes present in a given sample. It estimates the number of strains, their relative proportions and the haplotypes presented in a sample, allowing researchers to study multiple infection in malaria with an unprecedented level of detail. Availability and implementation: The open source implementation DEploid is freely available at https://github.com/mcveanlab/DEploid under the conditions of the GPLv3 license. An R version is available at https://github.com/mcveanlab/DEploid-r. Contact: joe.zhu@bdi.ox.ac.uk or gil.mcvean@bdi.ox.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.