{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T23:29:25Z","timestamp":1791934165840,"version":"4.3.4"},"reference-count":100,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["INV-043618"],"award-info":[{"award-number":["INV-043618"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT2001083"],"award-info":[{"award-number":["GNT2001083"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1161066"],"award-info":[{"award-number":["GNT1161066"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1005653"],"award-info":[{"award-number":["GNT1005653"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1163420"],"award-info":[{"award-number":["GNT1163420"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["GNT1027108"],"award-info":[{"award-number":["GNT1027108"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/X020258\/1"],"award-info":[{"award-number":["MR\/X020258\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004752","name":"State Government of Victoria","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004752","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Trends in Parasitology"],"published-print":{"date-parts":[[2024,2]]},"DOI":"10.1016\/j.pt.2023.11.006","type":"journal-article","created":{"date-parts":[[2023,12,20]],"date-time":"2023-12-20T00:11:16Z","timestamp":1703031076000},"page":"147-163","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":30,"title":["Molecular markers for malaria genetic epidemiology: progress and pitfalls"],"prefix":"10.1016","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0495-179X","authenticated-orcid":false,"given":"Shazia","family":"Ruybal-Pes\u00e1ntez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2427-241X","authenticated-orcid":false,"given":"Kirsty","family":"McCann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6903-8400","authenticated-orcid":false,"given":"Jessy","family":"Vibin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1458-4348","authenticated-orcid":false,"given":"Sasha","family":"Siegel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4638-536X","authenticated-orcid":false,"given":"Sarah","family":"Auburn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1189-2310","authenticated-orcid":false,"given":"Alyssa E.","family":"Barry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.pt.2023.11.006_bb0005","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.62997","article-title":"Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination","volume":"10","author":"Jacob","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.pt.2023.11.006_bb0010","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/j.ijpddr.2021.06.004","article-title":"Surveillance of molecular markers of Plasmodium falciparum artemisinin resistance (kelch13 mutations) in Papua New Guinea between 2016 and 2018","volume":"16","author":"Lautu-Gumal","year":"2021","journal-title":"Int. J. Parasitol. Drugs Drug Resist."},{"key":"10.1016\/j.pt.2023.11.006_bb0015","doi-asserted-by":"crossref","first-page":"84","DOI":"10.4269\/ajtmh.21-1330","article-title":"The West Africa ICEMR Partnerships for guiding policy to improve the malaria prevention and control","volume":"107","author":"Doumbia","year":"2022","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"10.1016\/j.pt.2023.11.006_bb0020","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1186\/s12936-019-2784-0","article-title":"Use cases for genetic epidemiology in malaria elimination","volume":"18","author":"Dalmat","year":"2019","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0025","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1186\/s12936-020-03330-5","article-title":"Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia\u2013Pacific region","volume":"19","author":"Noviyanti","year":"2020","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0030","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1016\/j.pt.2023.08.007","article-title":"Sampling for malaria molecular surveillance","volume":"39","author":"Mayor","year":"2023","journal-title":"Trends Parasitol."},{"key":"10.1016\/j.pt.2023.11.006_bb0035","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1038\/s41576-021-00349-5","article-title":"Advances and opportunities in malaria population genomics","volume":"22","author":"Neafsey","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.pt.2023.11.006_bb0040","series-title":"Methods and Techniques for Clinical Trials on Antimalarial Drug Efficacy: Genotyping to Identify Parasite Populations: Informal Consultation Organized by the Medicines for Malaria Venture and Cosponsored by the World Health Organization, 29\u201331 May 2007","author":"World Health Organization","year":"2008"},{"key":"10.1016\/j.pt.2023.11.006_bb0045","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/1475-2875-10-79","article-title":"Plasmodium falciparum msp1, msp2 and glurp allele frequency and diversity in sub-Saharan Africa","volume":"10","author":"Mwingira","year":"2011","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0050","doi-asserted-by":"crossref","DOI":"10.1016\/j.meegid.2021.105143","article-title":"Genetic diversity of Plasmodium falciparum isolates in Minna, North Central Nigeria inferred by PCR genotyping of Merozoite surface protein 1 and 2","volume":"96","author":"Usman-Yamman","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.pt.2023.11.006_bb0055","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-54203-0","article-title":"Amplicon deep sequencing improves Plasmodium falciparum genotyping in clinical trials of antimalarial drugs","volume":"9","author":"Gruenberg","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.pt.2023.11.006_bb0060","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1016\/j.pt.2017.08.013","article-title":"Malaria epidemiology at the clone level","volume":"33","author":"Koepfli","year":"2017","journal-title":"Trends Parasitol."},{"key":"10.1016\/j.pt.2023.11.006_bb0065","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1006\/expr.1993.1094","article-title":"Plasmodium falciparum: a rapid technique for genotyping the merozoite surface protein 2","volume":"77","author":"Felger","year":"1993","journal-title":"Exp. Parasitol."},{"key":"10.1016\/j.pt.2023.11.006_bb0070","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1186\/s12864-017-4260-y","article-title":"Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections","volume":"18","author":"Lerch","year":"2017","journal-title":"BMC Genomics"},{"key":"10.1016\/j.pt.2023.11.006_bb0075","doi-asserted-by":"crossref","first-page":"718","DOI":"10.4269\/ajtmh.12-0056","article-title":"High levels of genetic diversity of Plasmodium falciparum populations in Papua New Guinea despite variable infection prevalence","volume":"88","author":"Barry","year":"2013","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"10.1016\/j.pt.2023.11.006_bb0080","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1186\/s12936-019-3023-4","article-title":"High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo","volume":"18","author":"Pringle","year":"2019","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0085","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1186\/s12936-021-03654-w","article-title":"Genetic characterization of Plasmodium vivax isolates from Pakistan using circumsporozoite protein (pvcsp) and merozoite surface protein-1 (pvmsp-1) genes as genetic markers","volume":"20","author":"Bibi","year":"2021","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0090","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1111\/1755-0998.13622","article-title":"Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study","volume":"22","author":"LaVerriere","year":"2022","journal-title":"Mol. Ecol. Resour."},{"key":"10.1016\/j.pt.2023.11.006_bb0095","doi-asserted-by":"crossref","first-page":"5615","DOI":"10.1038\/s41467-019-13578-4","article-title":"High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya","volume":"10","author":"Nelson","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.pt.2023.11.006_bb0100","doi-asserted-by":"crossref","first-page":"e01500","DOI":"10.1128\/AAC.01500-16","article-title":"Critical evaluation of molecular monitoring in malaria drug efficacy trials and pitfalls of length-polymorphic markers","volume":"61","author":"Messerli","year":"2017","journal-title":"Antimicrob. Agents Chemother."},{"key":"10.1016\/j.pt.2023.11.006_bb0105","doi-asserted-by":"crossref","first-page":"S3","DOI":"10.1017\/S0031182002002214","article-title":"Measuring immune selection","volume":"125","author":"Conway","year":"2002","journal-title":"Parasitology"},{"key":"10.1016\/j.pt.2023.11.006_bb0110","doi-asserted-by":"crossref","first-page":"10030","DOI":"10.1073\/pnas.1200841109","article-title":"Force of infection is key to understanding the epidemiology of Plasmodium falciparum malaria in Papua New Guinean children","volume":"109","author":"Mueller","year":"2012","journal-title":"Proc. Natl. Acad. Sci."},{"key":"10.1016\/j.pt.2023.11.006_bb0115","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1093\/oxfordjournals.molbev.a026247","article-title":"Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum","volume":"17","author":"Anderson","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.pt.2023.11.006_bb0120","doi-asserted-by":"crossref","first-page":"42","DOI":"10.12688\/wellcomeopenres.16168.1","article-title":"An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples","volume":"6","author":"Ahouidi","year":"2021","journal-title":"Wellcome Open Res."},{"key":"10.1016\/j.pt.2023.11.006_bb0125","doi-asserted-by":"crossref","first-page":"136","DOI":"10.12688\/wellcomeopenres.17795.1","article-title":"An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples","volume":"7","author":"Adam","year":"2022","journal-title":"Wellcome Open Res."},{"key":"10.1016\/j.pt.2023.11.006_bb0130","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/S1473-3099(17)30048-8","article-title":"The spread of artemisinin-resistant Plasmodium falciparum in the Greater Mekong subregion: a molecular epidemiology observational study","volume":"17","author":"Imwong","year":"2017","journal-title":"Lancet Infect. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0135","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1017\/S0031182099004552","article-title":"Twelve microsatellite markers for characterization of Plasmodium falciparum from finger-prick blood samples","volume":"119","author":"Anderson","year":"1999","journal-title":"Parasitology"},{"key":"10.1016\/j.pt.2023.11.006_bb0140","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0005465","article-title":"VivaxGEN: an open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations","volume":"11","author":"Trimarsanto","year":"2017","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0145","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1186\/s12936-020-03440-0","article-title":"SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics","volume":"19","author":"Fola","year":"2020","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0150","doi-asserted-by":"crossref","first-page":"4525","DOI":"10.1111\/mec.15654","article-title":"Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea","volume":"29","author":"Kattenberg","year":"2020","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.pt.2023.11.006_bb0155","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0177445","article-title":"Genetic micro-epidemiology of malaria in Papua Indonesia: extensive P. vivax diversity and a distinct subpopulation of asymptomatic P. falciparum infections","volume":"12","author":"Pava","year":"2017","journal-title":"PLoS One"},{"key":"10.1016\/j.pt.2023.11.006_bb0160","doi-asserted-by":"crossref","first-page":"3974","DOI":"10.1111\/mec.16029","article-title":"The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa","volume":"30","author":"Argyropoulos","year":"2021","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.pt.2023.11.006_bb0165","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1179\/2047773215Y.0000000012","article-title":"Uncovering the transmission dynamics of Plasmodium vivax using population genetics","volume":"109","author":"Barry","year":"2015","journal-title":"Pathog. Glob. Health"},{"key":"10.1016\/j.pt.2023.11.006_bb0170","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0007876","article-title":"Microsatellite analysis reveals connectivity among geographically distant transmission zones of Plasmodium vivax in the Peruvian Amazon: a critical barrier to regional malaria elimination","volume":"13","author":"Manrique","year":"2019","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0175","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0006146","article-title":"Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific","volume":"12","author":"Waltmann","year":"2018","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0180","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1186\/1475-2875-12-447","article-title":"A call to arms: on refining Plasmodium vivax microsatellite marker panels for comparing global diversity","volume":"12","author":"Sutton","year":"2013","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0185","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1007065","article-title":"Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent","volume":"13","author":"Taylor","year":"2017","journal-title":"PLoS Genet."},{"key":"10.1016\/j.pt.2023.11.006_bb0190","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1086\/597303","article-title":"Evaluation of Plasmodium vivax genotyping markers for molecular monitoring in clinical trials","volume":"199","author":"Koepfli","year":"2009","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0195","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1126\/science.1098876","article-title":"Intercontinental spread of pyrimethamine-resistant malaria","volume":"305","author":"Roper","year":"2004","journal-title":"Science"},{"key":"10.1016\/j.pt.2023.11.006_bb0200","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pmed.1000055","article-title":"Multiple origins and regional dispersal of resistant dhps in African Plasmodium falciparum malaria","volume":"6","author":"Pearce","year":"2009","journal-title":"PLoS Med."},{"key":"10.1016\/j.pt.2023.11.006_bb0205","doi-asserted-by":"crossref","first-page":"9376","DOI":"10.1002\/ece3.3425","article-title":"Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance","volume":"7","author":"Rougeron","year":"2017","journal-title":"Ecol. Evol."},{"key":"10.1016\/j.pt.2023.11.006_bb0210","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0003872","article-title":"Plasmodium vivax diversity and population structure across four continents","volume":"9","author":"Koepfli","year":"2015","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0215","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1186\/1475-2875-7-223","article-title":"A general SNP-based molecular barcode for Plasmodium falciparum identification and tracking","volume":"7","author":"Daniels","year":"2008","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0220","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0003539","article-title":"Development of a single nucleotide polymorphism barcode to genotype Plasmodium vivax infections","volume":"9","author":"Baniecki","year":"2015","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0225","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2022.953187","article-title":"Novel highly-multiplexed AmpliSeq targeted assay for Plasmodium vivax genetic surveillance use cases at multiple geographical scales","volume":"12","author":"Kattenberg","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.pt.2023.11.006_bb0230","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0020251","article-title":"Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay","volume":"6","author":"Campino","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.pt.2023.11.006_bb0235","article-title":"Defining malaria parasite population subdivisions, transmission dynamics and infection origins using SNP barcodes","author":"Harrison","year":"2023","journal-title":"medRxiv"},{"key":"10.1016\/j.pt.2023.11.006_bb0245","doi-asserted-by":"crossref","first-page":"2107","DOI":"10.1038\/s41467-020-15779-8","article-title":"The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC","volume":"11","author":"Verity","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.pt.2023.11.006_bb0250","doi-asserted-by":"crossref","first-page":"327","DOI":"10.12688\/f1000research.129581.1","article-title":"AmpSeqR: an R package for amplicon deep sequencing data analysis","volume":"12","author":"Han","year":"2023","journal-title":"F1000Res"},{"key":"10.1016\/j.pt.2023.11.006_bb0255","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkx1201","article-title":"SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing","volume":"46","author":"Hathaway","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.pt.2023.11.006_bb0260","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2023.1071896","article-title":"Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa","volume":"14","author":"Argyropoulos","year":"2023","journal-title":"Front. Genet."},{"key":"10.1016\/j.pt.2023.11.006_bb0265","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1186\/s12936-018-2623-8","article-title":"Characterization of Plasmodium falciparum structure in Nigeria with malaria SNPs barcode","volume":"17","author":"Bankole","year":"2018","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0270","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1186\/s12936-020-03386-3","article-title":"Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka","volume":"19","author":"Dewasurendra","year":"2020","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0275","doi-asserted-by":"crossref","first-page":"1337","DOI":"10.1534\/genetics.119.302120","article-title":"Estimating relatedness between malaria parasites","volume":"212","author":"Taylor","year":"2019","journal-title":"Genetics"},{"key":"10.1016\/j.pt.2023.11.006_bb0280","doi-asserted-by":"crossref","first-page":"4052","DOI":"10.1038\/ncomms5052","article-title":"A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains","volume":"5","author":"Preston","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.pt.2023.11.006_bb0285","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0197369","article-title":"Resistance screening and trend analysis of imported falciparum malaria in NSW, Australia (2010 to 2016)","volume":"13","author":"Prosser","year":"2018","journal-title":"PLoS One"},{"key":"10.1016\/j.pt.2023.11.006_bb0290","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1008576","article-title":"A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria","volume":"16","author":"Diez Benavente","year":"2020","journal-title":"PLoS Genet."},{"key":"10.1016\/j.pt.2023.11.006_bb0295","doi-asserted-by":"crossref","first-page":"1411","DOI":"10.1038\/s42003-022-04352-2","article-title":"A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria","volume":"5","author":"Trimarsanto","year":"2022","journal-title":"Commun. Biol."},{"key":"10.1016\/j.pt.2023.11.006_bb0300","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009801","article-title":"Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens","volume":"18","author":"Naung","year":"2022","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.pt.2023.11.006_bb0305","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1093\/infdis\/jiy223","article-title":"Drug-resistance and population structure of Plasmodium falciparum across the Democratic Republic of Congo using high-throughput molecular inversion probes","volume":"218","author":"Aydemir","year":"2018","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0310","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/j.ijpara.2021.12.001","article-title":"Age-specific patterns of DBL\u03b1 var diversity can explain why residents of high malaria transmission areas remain susceptible to Plasmodium falciparum blood stage infection throughout life","volume":"52","author":"Ruybal-Pes\u00e1ntez","year":"2022","journal-title":"Int. J. Parasitol."},{"key":"10.1016\/j.pt.2023.11.006_bb0315","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1111\/mec.13033","article-title":"Phylogeography of var gene repertoires reveals fine-scale geospatial clustering of Plasmodium falciparum populations in a highly endemic area","volume":"24","author":"Tessema","year":"2015","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.pt.2023.11.006_bb0320","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/0092-8674(95)90054-3","article-title":"Cloning the P. falciparum gene encoding PfEMP1, a malarial variant antigen and adherence receptor on the surface of parasitized human erythrocytes","volume":"82","author":"Baruch","year":"1995","journal-title":"Cell"},{"key":"10.1016\/j.pt.2023.11.006_bb0325","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004812","article-title":"Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of var genes during mitosis","volume":"10","author":"Claessens","year":"2014","journal-title":"PLoS Genet."},{"key":"10.1016\/j.pt.2023.11.006_bb0330","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-11814-9","article-title":"Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda","volume":"7","author":"Ruybal-Pesantez","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.pt.2023.11.006_bb0335","article-title":"Population genomics of the immune evasion (var) genes of Plasmodium falciparum","volume":"3","author":"Barry","year":"2007","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.pt.2023.11.006_bb0340","doi-asserted-by":"crossref","first-page":"E4103","DOI":"10.1073\/pnas.1613018114","article-title":"Evidence of strain structure in Plasmodium falciparum var gene repertoires in children from Gabon, West Africa","volume":"114","author":"Day","year":"2017","journal-title":"Proc. Natl. Acad. Sci."},{"key":"10.1016\/j.pt.2023.11.006_bb0345","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1009269","article-title":"Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents","volume":"17","author":"Tonkin-Hill","year":"2021","journal-title":"PLoS Genet."},{"key":"10.1016\/j.pt.2023.11.006_bb0350","doi-asserted-by":"crossref","DOI":"10.3389\/fpara.2022.1006341","article-title":"Unravelling var complexity: relationship between DBL\u03b1 types and var genes in Plasmodium falciparum","volume":"1","author":"Tan","year":"2023","journal-title":"Front. Parasitol."},{"key":"10.1016\/j.pt.2023.11.006_bb0355","doi-asserted-by":"crossref","first-page":"52","DOI":"10.12688\/wellcomeopenres.14571.1","article-title":"Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres","volume":"3","author":"Otto","year":"2018","journal-title":"Wellcome Open Res."},{"key":"10.1016\/j.pt.2023.11.006_bb0360","doi-asserted-by":"crossref","first-page":"193","DOI":"10.12688\/wellcomeopenres.15590.1","article-title":"Evolutionary analysis of the most polymorphic gene family in falciparum malaria","volume":"4","author":"Otto","year":"2019","journal-title":"Wellcome Open Res."},{"key":"10.1016\/j.pt.2023.11.006_bb0365","article-title":"Measuring changes in Plasmodium falciparum var census population size and structure in response to sequential malaria control interventions","author":"Tiedje","year":"2023","journal-title":"medRxiv"},{"key":"10.1016\/j.pt.2023.11.006_bb0370","doi-asserted-by":"crossref","first-page":"1817","DOI":"10.1038\/s41467-018-04219-3","article-title":"Networks of genetic similarity reveal non-neutral processes shape strain structure in Plasmodium falciparum","volume":"9","author":"He","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.pt.2023.11.006_bb0375","doi-asserted-by":"crossref","DOI":"10.3389\/fitd.2023.1085862","article-title":"Molecular epidemiology of continued Plasmodium falciparum disease transmission after an outbreak in Ecuador","volume":"4","author":"Ruybal-Pes\u00e1ntez","year":"2023","journal-title":"Front. Trop. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0380","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1010816","article-title":"Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections","volume":"19","author":"Labb\u00e9","year":"2023","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.pt.2023.11.006_bb0385","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1111\/1755-0998.12737","article-title":"Microhaplotypes provide increased power from short-read DNA sequences for relationship inference","volume":"18","author":"Baetscher","year":"2018","journal-title":"Mol. Ecol. Resour."},{"key":"10.1016\/j.pt.2023.11.006_bb0390","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1093\/infdis\/jiaa527","article-title":"Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome","volume":"225","author":"Tessema","year":"2022","journal-title":"J. Infect. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0395","doi-asserted-by":"crossref","first-page":"3699","DOI":"10.1038\/s41467-023-39417-1","article-title":"Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania","volume":"14","author":"Holzschuh","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.pt.2023.11.006_bb0400","article-title":"Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites","author":"Siegel","year":"2023","journal-title":"medRxiv"},{"key":"10.1016\/j.pt.2023.11.006_bb0405","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.pt.2023.11.006_bb0410","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1186\/s12936-019-2856-1","article-title":"Detection of low-density Plasmodium falciparum infections using amplicon deep sequencing","volume":"18","author":"Early","year":"2019","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0415","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1038\/nature07632","article-title":"A global network for investigating the genomic epidemiology of malaria","volume":"456","author":"The Malaria Genomic Epidemiology Network","year":"2008","journal-title":"Nature"},{"key":"10.1016\/j.pt.2023.11.006_bb0420","doi-asserted-by":"crossref","first-page":"22","DOI":"10.12688\/wellcomeopenres.18681.1","article-title":"Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples","volume":"8","author":"Abdel Hamid","year":"2023","journal-title":"Wellcome Open Res."},{"key":"10.1016\/j.pt.2023.11.006_bb0425","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pmed.1003560","article-title":"The changing epidemiology of Plasmodium vivax: insights from conventional and novel surveillance tools","volume":"18","author":"Auburn","year":"2021","journal-title":"PLoS Med."},{"key":"10.1016\/j.pt.2023.11.006_bb0430","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0002882","article-title":"A high resolution case study of a patient with recurrent Plasmodium vivax infections shows that relapses were caused by meiotic siblings","volume":"8","author":"Bright","year":"2014","journal-title":"PLoS Negl. Trop. Dis."},{"key":"10.1016\/j.pt.2023.11.006_bb0435","doi-asserted-by":"crossref","DOI":"10.1093\/genetics\/iyac126","article-title":"Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections","volume":"222","author":"Gerlovina","year":"2022","journal-title":"Genetics"},{"key":"10.1016\/j.pt.2023.11.006_bb0440","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1009604","article-title":"Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species","volume":"18","author":"Han","year":"2022","journal-title":"PLoS Genet."},{"key":"10.1016\/j.pt.2023.11.006_bb0445","article-title":"MOIRE: a software package for the estimation of allele frequencies and effective multiplicity of infection from polyallelic data","author":"Murphy","year":"2023","journal-title":"bioRxiv"},{"key":"10.1016\/j.pt.2023.11.006_bb0450","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s12961-022-00840-3","article-title":"STRIVE PNG: using a partnership-based approach in implementation research to strengthen surveillance and health systems in Papua New Guinea","volume":"20","author":"Farquhar","year":"2022","journal-title":"Health Res. Policy Syst."},{"key":"10.1016\/j.pt.2023.11.006_bb0455","series-title":"Preparing for Certification of Malaria Elimination","first-page":"46","author":"World Health Organization","year":"2022"},{"key":"10.1016\/j.pt.2023.11.006_bb0460","doi-asserted-by":"crossref","first-page":"434","DOI":"10.3390\/genes10060434","article-title":"The diversity, multiplicity of infection and population structure of P. falciparum parasites circulating in asymptomatic carriers living in high and low malaria transmission settings of Ghana","volume":"10","author":"Abukari","year":"2019","journal-title":"Genes"},{"key":"10.1016\/j.pt.2023.11.006_bb0465","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.pt.2016.10.001","article-title":"Genome-wide association studies of drug-resistance determinants","volume":"33","author":"Volkman","year":"2017","journal-title":"Trends Parasitol."},{"issue":"Database issue","key":"10.1016\/j.pt.2023.11.006_bb2005","doi-asserted-by":"crossref","first-page":"D539","DOI":"10.1093\/nar\/gkn814","article-title":"PlasmoDB: a functional genomic database for malaria parasites","volume":"37","author":"Aurrecoechea","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.pt.2023.11.006_bb0240","article-title":"Real time, field-deployable whole genome sequencing of malaria parasites using nanopore technology","author":"Razook","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.pt.2023.11.006_bb0470","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1093\/dnares\/dsu028","article-title":"Optimized whole-genome amplification strategy for extremely AT-biased template","volume":"21","author":"Oyola","year":"2014","journal-title":"DNA Res."},{"key":"10.1016\/j.pt.2023.11.006_bb0475","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1186\/s12936-016-1641-7","article-title":"Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification","volume":"15","author":"Oyola","year":"2016","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0480","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.02257-16","article-title":"Selective whole-genome amplification is a robust method that enables scalable whole-genome sequencing of Plasmodium vivax from unprocessed clinical samples","volume":"8","author":"Cowell","year":"2017","journal-title":"mBio"},{"key":"10.1016\/j.pt.2023.11.006_bb0485","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1186\/s12936-021-03630-4","article-title":"Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples","volume":"20","author":"Teyssier","year":"2021","journal-title":"Malar. J."},{"key":"10.1016\/j.pt.2023.11.006_bb0490","doi-asserted-by":"crossref","DOI":"10.1016\/S2666-5247(20)30206-8","article-title":"Africa's $100-million Pathogen Genomics Initiative","volume":"1","author":"Makoni","year":"2020","journal-title":"Lancet Microbe"},{"key":"10.1016\/j.pt.2023.11.006_bb0495","doi-asserted-by":"crossref","DOI":"10.3389\/fpara.2023.1067966","article-title":"Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high transmission","author":"Ghansah","year":"2023","journal-title":"Front. Parasitol."}],"container-title":["Trends in Parasitology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1471492223002866?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1471492223002866?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T19:53:46Z","timestamp":1778615626000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1471492223002866"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2]]},"references-count":100,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,2]]}},"alternative-id":["S1471492223002866"],"URL":"https:\/\/doi.org\/10.1016\/j.pt.2023.11.006","relation":{},"ISSN":["1471-4922"],"issn-type":[{"value":"1471-4922","type":"print"}],"subject":[],"published":{"date-parts":[[2024,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Molecular markers for malaria genetic epidemiology: progress and pitfalls","name":"articletitle","label":"Article Title"},{"value":"Trends in Parasitology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.pt.2023.11.006","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}]}}