publications.md

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title	Science
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I'm a biological scientist with a strong interest in population and evolutionary biology, particularly in the context of pathogens and vectors of infectious diseases.

Below is a selection of scientific and technical articles that I had a significant role in creating.

• Chris S. Clarkson, Alistair Miles et al. (2021) The genetic architecture of target‐site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii. https://doi.org/10.1111/mec.15845

• The Anopheles gambiae 1000 Genomes Consortium (2020) Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii. https://doi.org/10.1101/gr.262790.120

• Eric R. Lucas, Alistair Miles et al. (2019) Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes. https://doi.org/10.1101/gr.245795.118

• The Anopheles gambiae 1000 Genomes Consortium (2017) Genetic diversity of the African malaria vector Anopheles gambiae. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026373/

• Alistair Miles et al. (2016) Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum. https://doi.org/10.1101/gr.203711.115

• Alistair Miles et al. (2010) OpenFlyData: An exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster. https://doi.org/10.1016/j.jbi.2010.04.004

• Alistair Miles and Sean Bechhofer (2009) SKOS Simple Knowledge Organization System Reference. http://www.w3.org/TR/skos-reference

• Diego Berrueta, Jon Phipps, Alistair Miles, Thomas Baker, Ralph Swick (2008) Best Practice Recipes for Publishing RDF Vocabularies. http://www.w3.org/TR/swbp-vocab-pub/

Since 2021 my team and I have focussed on building data resources, software tools and training resources to build capacity for other scientists to interrogate and make discoveries from large-scale genomic data resources. Here's a selection of papers and preprints that have built on these efforts.

• McCann et al. (2024) Variation in spatial population structure in the Anopheles gambiae species complex. https://doi.org/10.1101/2024.05.26.595955.

• Odero et al. (2024) Discovery of knock-down resistance in the major African malaria vector Anopheles funestus. https://doi.org/10.1101/2024.03.13.584754

• Kamau et al. (2024) The Anopheles coluzzii range extends into Kenya: detection, insecticide resistance profiles and population genetic structure in relation to conspecific populations in West and Central Africa. https://doi.org/10.1186/s12936-024-04950-x.

• della Torre et al. (2024) Speciation within the Anopheles gambiae complex: high-throughput whole genome sequencing reveals evidence of a putative new cryptic taxon in 'far-west' Africa. https://doi.org/10.21203/rs.3.rs-3914444/v1.

• Dennis et al. (2024) Cryptic population structure and insecticide resistance in Anopheles gambiae from the southern Democratic Republic of Congo. https://doi.org/10.1101/2024.03.12.584605.

• Lucas et al. (2024) Copy number variants underlie the major selective sweeps in insecticide resistance genes in Anopheles arabiensis from Tanzania. https://doi.org/10.1101/2024.03.11.583874.

• Nagi et al. (2024) Parallel evolution in mosquito vectors – a duplicated esterase locus is associated with resistance to pirimiphos-methyl in An. gambiae. https://doi.org/10.1101/2024.02.01.578361.

• Kientega et al. (2023) Whole-genome sequencing of major malaria vectors revealed an evolution of new insecticide resistance variants in a longitudinal study in Burkina Faso. https://doi.org/10.1101/2023.11.20.567800.

• Dyer et al. (2023) Mechanisms of transcriptional regulation in Anopheles gambiae revealed by allele specific expression. https://doi.org/10.1101/2023.11.22.568226.

• Lucas et al. (2023) Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae and Anopheles coluzzii. https://doi.org/10.1038/s41467-023-40693-0.

• Romero et al. (2023) Mitochondrial variation in Anopheles gambiae and An. coluzzii: phylogeographic legacy of species isolation and mito-nuclear associations with metabolic resistance to pathogens and insecticides. https://doi.org/10.1101/2023.07.18.549472

• St. Laurent et al. (2022) Population genomics reveal distinct and diverging populations of An. minimus in Cambodia. https://doi.org/10.1038/s42003-022-04259-y.

• Kientega et al. (2022) Analysis of the Genetic Variation of the Fruitless Gene within the Anopheles gambiae (Diptera: Culicidae) Complex Populations in Africa. https://doi.org/10.3390/insects13111048.

• Wagah et al. (2021) Genetic variation at the Cyp6m2 putative insecticide resistance locus in Anopheles gambiae and Anopheles coluzzii. https://doi.org/10.1186/s12936-021-03757-4.

• Xue et al. (2021) Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning. https://doi.org/10.1093/molbev/msaa259.