Dominic P. Kwiatkowski

Pfcrt copy number amplification detected in a Plasmodium falciparum outbreak

The paper identifies pfcrt copy number amplification as a new antimalarial resistance mechanism in Plasmodium falciparum and develops a TaqMan assay for its detection.

A genomic toolkit for surveillance and elimination of the principal malaria vectors in Southeast Asia.

The paper provides genomic resources for malaria vector surveillance in Southeast Asia, revealing population structure and resistance regions in Anopheles dirus.

Characterising recent antimalarial resistance in West Africa: Insights from amplicon sequencing of 17,384 Plasmodium falciparum infection samples

The paper analyzes amplicon sequencing data from 17,384 Plasmodium falciparum samples in West Africa to characterize antimalarial resistance patterns and their geographic distribution.

Decoding Ethiopia's unique and structurally divergent Plasmodium falciparum populations using genomics

The paper analyzes whole-genome sequencing data from Plasmodium falciparum isolates in Ethiopia and sub-Saharan Africa to characterize genetic diversity and resistance markers.

Genomic diversity of the African malaria vector Anopheles funestus

The paper analyzes genomic diversity in Anopheles funestus across Africa, identifying genetic variation, adaptation signals, and conservation of a gene drive target.

New insights on malaria parasite adaptation yielded by samples archived for more than 50 years

The paper analyzes old Plasmodium falciparum genomes to study malaria parasite adaptation over 50 years, finding strong positive selection at surface protein loci and changes in allele frequencies.

Large-scale genotyping and meta-analysis of PIEZO1 short tandem repeat alleles suggest a modest association with malaria susceptibility

The paper genotypes PIEZO1 STR alleles in malaria cases and controls, finding a modest protective effect of E756del against malaria.

A complex Plasmodium falciparum cryptotype circulating at low frequency across the African continent

The paper identifies a cryptotype in Plasmodium falciparum genomes across Africa, characterized by a complex genetic background that is geographically widespread but genetically distinct.

Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae s.l.

This study identifies novel genetic loci associated with resistance to pyrethroid and organophosphate insecticides in Anopheles gambiae s.l. through genome-wide association analyses.

A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax

The paper develops a molecular barcode and online tool to identify and map imported Plasmodium vivax infections using SNP analysis and machine learning.

Nanopore sequencing for real-time genomic surveillance of Plasmodium falciparum

This study implements a Nanopore sequencing workflow for P. falciparum genomic surveillance in Ghana, identifying drug resistance patterns and vaccine antigen variations.

Non-O ABO blood group genotypes differ in their associations with Plasmodium falciparum rosetting and severe malaria

The paper investigates how non-O ABO blood group genotypes relate to Plasmodium falciparum rosetting and severe malaria risk in Kenyan children.

An amino acid transporter AAT1 plays a pivotal role in chloroquine resistance evolution in malaria parasites

This study identifies pfaat1 as a key gene in chloroquine resistance evolution in malaria parasites, showing it modulates resistance and fitness through amino acid transport.

The protective effect of sickle cell haemoglobin against severe malaria depends on parasite genotype

The paper investigates the association between host sickle cell haemoglobin and parasite genetic variation in malaria severity, finding that parasite alleles linked to HbS show strong linkage disequilibrium and frequency covariation with HbS.

Population genomics reveal distinct and diverging populations of An. minimus in Cambodia - a widespread malaria vector in Southeast Asia

The paper uses whole-genome sequencing to analyze genetic diversity and population structure of An. minimus in Cambodia, identifying four distinct populations with unique selection signals.

Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria

This paper develops a combined genetic-epidemiological model to explore relationships between Plasmodium falciparum prevalence and genetic diversity, finding that mixed infection statistics respond quickly to prevalence changes.

Patterns of within-host genetic diversity in SARS-CoV-2

This study analyzes within-host genetic diversity in 1,181 SARS-CoV-2 samples, finding high mutation rates, strand asymmetries, and purifying selection, with implications for transmission chain reconstruction.

The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii

This study identifies novel genetic variants and haplotypes associated with pyrethroid resistance in malaria vectors, revealing complex resistance mechanisms and geographical spread.

Resistance to pirimiphos-methyl in West African Anopheles is spreading via duplication and introgression of the Ace1 locus

The paper identifies a resistance mechanism to pirimiphos-methyl in Anopheles mosquitoes through duplication and introgression of the Ace1 locus, showing its spread in West Africa.

Genome variation and population structure among 1,142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

The paper analyzes genome variation in 1,142 Anopheles mosquitoes to study population structure and insecticide resistance.

Red blood cell tension controls Plasmodium falciparum invasion and protects against severe malaria in the Dantu blood group

The paper shows that Dantu blood group variant increases red blood cell tension, reducing Plasmodium falciparum invasion and protecting against severe malaria.

Detection of simple and complex de novo mutations without, with, or with multiple reference sequences

The paper introduces Corticall, a graph-based method to detect de novo mutations using short-read and long-read data, validated on Plasmodium falciparum crosses.

Development of copy number assays for detection and surveillance of piperaquine resistance associated plasmepsin 2/3 copy number variation in Plasmodium falciparum

The paper develops and validates PCR assays to detect plasmepsin 2/3 and pfmdr1 copy number variations in Plasmodium falciparum field isolates, finding increasing plasmepsin 2/3 duplications and loss of pfmdr1 mutations in Cambodia.

New insights into malaria susceptibility from the genomes of 17,000 individuals from Africa, Asia, and Oceania

This study identifies five genome-wide associations with severe malaria risk in 17,000 individuals from Africa, Asia, and Oceania, including a new variant linked to cerebral malaria.

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples

The paper presents an open dataset of Plasmodium falciparum genome variation from 7,000 worldwide samples, revealing widespread drug resistance and geographic genetic differentiation.

Natural diversity of the malaria vector Anopheles gambiae

The paper sequences genomes of 765 malaria vector mosquitoes to study genetic diversity and insecticide resistance.

Resistance to malaria through structural variation of red blood cell invasion receptors

The paper identifies a structural variant in GYPA and GYPB genes associated with reduced risk of severe malaria in sub-Saharan African populations.

Elusive Plasmodium Species Complete the Human Malaria Genome Set

This paper completes the human malaria genome set by presenting reference genomes for Plasmodium malariae and P. ovale, revealing unique genomic features and cryptic species within P. ovale.

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

This paper develops a method to sequence Plasmodium falciparum genomes from dried blood spots using selective whole genome amplification, achieving high concordance with venous blood samples.

Genome variation and meiotic recombination in Plasmodium falciparum: insights from deep sequencing of genetic crosses

The paper uses deep sequencing of genetic crosses in Plasmodium falciparum to analyze genome variation and meiotic recombination, revealing INDELs as dominant polymorphisms and providing insights into recombination patterns and drug resistance mechanisms.