Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control

[1]  G. Dorsey,et al.  Evolution of Partial Resistance to Artemisinins in Malaria Parasites in Uganda. , 2023, The New England journal of medicine.

[2]  T. Clark,et al.  High throughput human genotyping for variants associated with malarial disease outcomes using custom targeted amplicon sequencing , 2023, Scientific reports.

[3]  Thomas Walker,et al.  Identification of two insecticide resistance markers in Ethiopian Anopheles stephensi mosquitoes using a multiplex amplicon sequencing assay , 2023, Scientific Reports.

[4]  T. Clark,et al.  Population genetic analysis of Plasmodium knowlesi reveals differential selection and exchange events between Borneo and Peninsular sub-populations , 2023, Scientific Reports.

[5]  T. Clark,et al.  Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America , 2023, Lancet regional health. Americas.

[6]  T. Clark,et al.  A next generation targeted amplicon sequencing method to screen for insecticide resistance mutations in Aedes aegypti populations reveals a rdl mutation in mosquitoes from Cabo Verde , 2022, PLoS neglected tropical diseases.

[7]  T. Clark,et al.  Geographical classification of malaria parasites through applying machine learning to whole genome sequence data , 2022, Scientific Reports.

[8]  S. Campino,et al.  The primate malaria parasites Plasmodium malariae, Plasmodium brasilianum and Plasmodium ovale spp.: genomic insights into distribution, dispersal and host transitions , 2022, Malaria journal.

[9]  Diego F. Echeverry,et al.  An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples , 2022, Wellcome open research.

[10]  Chim W. Chan,et al.  Characterizing the genomic variation and population dynamics of Plasmodium falciparum malaria parasites in and around Lake Victoria, Kenya , 2021, Scientific Reports.

[11]  T. Horii,et al.  Evidence of Artemisinin-Resistant Malaria in Africa. , 2021, The New England journal of medicine.

[12]  T. Clark,et al.  Using deep learning to identify recent positive selection in malaria parasite sequence data , 2021, Malaria Journal.

[13]  T. Bousema,et al.  A portfolio of geographically distinct laboratory-adapted Plasmodium falciparum clones with consistent infection rates in Anopheles mosquitoes , 2021, Malaria journal.

[14]  T. Clark,et al.  Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa , 2021, Nature Communications.

[15]  T. Clark,et al.  Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies , 2020, Genome medicine.

[16]  T. Clark,et al.  Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance , 2020, PLoS genetics.

[17]  T. Clark,et al.  Selective whole genome amplification of Plasmodium malariae DNA from clinical samples reveals insights into population structure , 2020, Scientific Reports.

[18]  R. Moon,et al.  CRISPR-Cas9 Genome Editing of Plasmodium knowlesi. , 2020, Bio-protocol.

[19]  D. V. van Schalkwyk,et al.  A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections , 2020, bioRxiv.

[20]  T. Clark,et al.  A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria , 2020, PLoS genetics.

[21]  D. Kwiatkowski,et al.  An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples , 2019, bioRxiv.

[22]  T. Clark,et al.  Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations , 2019, Scientific Reports.

[23]  Jim F Huggett,et al.  Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs , 2019, Genome Medicine.

[24]  T. Clark,et al.  An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene , 2019, Scientific Reports.

[25]  T. Clark,et al.  Artemisinin resistance-associated markers in Plasmodium falciparum parasites from the China-Myanmar border: predicted structural stability of K13 propeller variants detected in a low-prevalence area , 2019, PloS one.

[26]  Brent S. Pedersen,et al.  Bioconda: sustainable and comprehensive software distribution for the life sciences , 2018, Nature Methods.

[27]  Sudhir Kumar,et al.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.

[28]  T. Clark,et al.  Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis. , 2018, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[29]  Mauricio O. Carneiro,et al.  Scaling accurate genetic variant discovery to tens of thousands of samples , 2017, bioRxiv.

[30]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[31]  T. Clark,et al.  Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure , 2017, PloS one.

[32]  Sesh A. Sundararaman,et al.  Selective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples , 2017, mBio.

[33]  Sebastian Deorowicz,et al.  KMC 3: counting and manipulating k‐mer statistics , 2017, Bioinform..

[34]  D. Kwiatkowski,et al.  Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi , 2016, Malaria Journal.

[35]  A. Pain,et al.  Normocyte-binding protein required for human erythrocyte invasion by the zoonotic malaria parasite Plasmodium knowlesi , 2016, Proceedings of the National Academy of Sciences.

[36]  S. Salzberg,et al.  Centrifuge: rapid and sensitive classification of metagenomic sequences , 2016, bioRxiv.

[37]  Hanif M. Samad,et al.  Imputation-Based Population Genetics Analysis of Plasmodium falciparum Malaria Parasites , 2015, PLoS genetics.

[38]  Samuel A. Assefa,et al.  Whole-Genome Scans Provide Evidence of Adaptive Evolution in Malawian Plasmodium falciparum Isolates , 2014, The Journal of infectious diseases.

[39]  Samuel A. Assefa,et al.  A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains , 2014, Nature Communications.

[40]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[41]  B. Genton,et al.  A molecular marker of artemisinin-resistant Plasmodium falciparum malaria , 2013, Nature.

[42]  Gabor T. Marth,et al.  Haplotype-based variant detection from short-read sequencing , 2012, 1207.3907.

[43]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[44]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[45]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[46]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[47]  D. Warhurst.  A molecular marker for chloroquine-resistant falciparum malaria. , 2001, The New England journal of medicine.

[48]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.