Amy Ibrahim
Research Fellow
Moon Group, LSHTM, London
Research
I work within the Moon Group at LSHTM investigating how the inrtacellular parasite, Plasmodium knowlesi invades human erythrocytes. My research is funded under a Wellcome Trust Discovery Award. I use CRISPR-Cas9 based genome editing to target known and unknown genes associated with erythrocyte invasion and investigate parasite phenotypes.
Previously, I have worked on whole genomoe sequencing for malaria parasites, using both Illumina and Oxford Nanopore systems, and I use the Nanopore MinION frequently to assess the genomics of modified parasite lines.
Associated publications
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Ibrahim, A. et al. Genome sequencing of Plasmodium malariae identifies continental segregation and mutations associated with reduced pyrimethamine susceptibility. Nature communications. 15, 10779 (2024).
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Ibrahim, A. et al. Population genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America. Lancet Reg. Heal. - Am. 18, 100420 (2023).
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Ibrahim, A. et al. Selective whole genome amplification of Plasmodium malariae DNA from clinical samples reveals insights into population structure. Sci Rep. 10, 10832 (2020).
Lab Training
Computational Training
graph TD;
A[Sequence your samples using Nanopore] --> B["`[Basecall sequence data with Dorado](https://amyibrahim.github.io/Nanopore_Dorado_basecalling_for_all.html)`"];
B--->C[Map your sequence data to an available reference genome];
B--->D[Generate a genome assembly for this parasite line];
C ---> E[Look for variants in specific genes];
D ---> F[Genome assembly using Pilon/RagTag]
Initial computer set up for coding - mac users
Initial computer set up for coding - windows users
Initial computational set up for coding - Linux servers
Nanopore analysis for custom barcodes
Nanopore analysis for genome assembly
Nanopore basecalling using Dorado (basic)