{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T23:29:24Z","timestamp":1791934164790,"version":"4.3.4"},"reference-count":35,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T00:00:00Z","timestamp":1751241600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["204911"],"award-info":[{"award-number":["204911"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["206194"],"award-info":[{"award-number":["206194"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Gates Foundation","doi-asserted-by":"publisher","award":["INV-007590"],"award-info":[{"award-number":["INV-007590"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Gates Foundation","doi-asserted-by":"publisher","award":["INV-001927"],"award-info":[{"award-number":["INV-001927"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000865","name":"Gates Foundation","doi-asserted-by":"publisher","award":["INV-068808"],"award-info":[{"award-number":["INV-068808"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["wellcomeopenresearch.org"],"crossmark-restriction":false},"short-container-title":["Wellcome Open Res"],"abstract":"<ns3:p>\n                    We describe the Pf8 data resource, the latest MalariaGEN release of curated genome variation data on over 33,000\n                    <ns3:italic>Plasmodium falciparum<\/ns3:italic>\n                    samples from 99 partner studies and 122 locations over more than 50 years. This release provides open access to raw sequencing data and genotypes at over 12 million genomic positions. For the first time, it includes copy-number variation (CNV) calls in the drug-resistance associated genes\n                    <ns3:italic>gch1<\/ns3:italic>\n                    and\n                    <ns3:italic>crt<\/ns3:italic>\n                    . As in Pf7, CNV calls are provided for\n                    <ns3:italic>mdr1<\/ns3:italic>\n                    and\n                    <ns3:italic>plasmepsin2\/3<\/ns3:italic>\n                    , along with calls for deletion in\n                    <ns3:italic>hrp2<\/ns3:italic>\n                    and\n                    <ns3:italic>hrp3,<\/ns3:italic>\n                    genes associated with rapid diagnostic test failures. This data resource additionally features derived datasets, interactive web applications for exploring patterns of drug resistance and variation in over 5,000 genes, an updated Python package providing methods for accessing and analysing the data, and open access analysis notebooks that can be used as starting points for further analyses. In addition, informative example analyses show contrasting profiles of the decline of chloroquine resistance-associated mutations in Africa, and variation in copy number variation across 10 distinct sub-populations. To the best of our knowledge, Pf8 is the largest open data set of genome variation in any eukaryotic species, making it an invaluable foundational resource for understanding evolution, including that of pathogens.\n                  <\/ns3:p>","DOI":"10.12688\/wellcomeopenres.24031.1","type":"journal-article","created":{"date-parts":[[2025,6,30]],"date-time":"2025-06-30T11:30:09Z","timestamp":1751283009000},"page":"325","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":28,"title":["Pf8: an open dataset of Plasmodium falciparum\u00a0genome variation in 33,325 worldwide samples"],"prefix":"10.12688","volume":"10","author":[{"name":"Malaria Genomic Epidemiology Network (MalariaGEN)","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muzamil Mahdi","family":"Abdel Hamid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed Hassan","family":"Abdelraheem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8197-2618","authenticated-orcid":false,"given":"Desmond Omane","family":"Acheampong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ishag","family":"Adam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro","family":"Aide","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3888-2366","authenticated-orcid":false,"given":"Olusola","family":"Ajibaye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mozam","family":"Ali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob","family":"Almagro-Garcia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfred","family":"Amambua-Ngwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4468-0506","authenticated-orcid":false,"given":"Lucas","family":"Amenga-Etego","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ifeyinwa","family":"Aniebo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6489-167X","authenticated-orcid":false,"given":"Enoch","family":"Aninagyei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Felix","family":"Ansah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias O","family":"Apinjoh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina V","family":"Ariani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Auburn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gordon A","family":"Awandare","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Balmer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2135-7549","authenticated-orcid":false,"given":"Philip","family":"Bejon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8323-9863","authenticated-orcid":false,"given":"Simone","family":"Boene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Bwire","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baltazar","family":"Candrinho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arlindo","family":"Chidimatembue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keobouphaphone","family":"Chindavongsa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiba","family":"Comiche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8711-3037","authenticated-orcid":false,"given":"David","family":"Conway","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7739-4437","authenticated-orcid":false,"given":"Antoine","family":"Dara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4268-8857","authenticated-orcid":false,"given":"Mahamadou","family":"Diakite","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0062-2283","authenticated-orcid":false,"given":"Abdoulaye","family":"Djimde","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5190-2395","authenticated-orcid":false,"given":"Arjen","family":"Dondorp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seydou","family":"Doumbia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleanor","family":"Drury","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1932-9562","authenticated-orcid":false,"given":"Caterina A","family":"Fanello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike","family":"Ferdig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Figueroa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dionicia","family":"Gamboa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lemu","family":"Golassa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00f3nia","family":"Gon\u00e7alves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Merepen dite Agnes","family":"Guindo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0266-1414","authenticated-orcid":false,"given":"Mainga","family":"Hamaluba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Borimas","family":"Hanboonkunupakarn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Howe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maazza","family":"Hussien","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mallika","family":"Imwong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deus","family":"Ishengoma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Jeans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alinune","family":"Kabaghe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Appolinary","family":"Kamuhabwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Marie","family":"Kindermans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4177-9642","authenticated-orcid":false,"given":"Drissa S","family":"Konate","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominic P","family":"Kwiatkowski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiyun","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel K","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8409-4248","authenticated-orcid":false,"given":"Sue J","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5734-0845","authenticated-orcid":false,"given":"Benedikt","family":"Ley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7567-5534","authenticated-orcid":false,"given":"Alejandro","family":"Llanos-Cuentas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jutta","family":"Marfurt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gl\u00f3ria","family":"Matambisso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rapeephan Rattanawongnara","family":"Maude","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5355-0562","authenticated-orcid":false,"given":"Richard James","family":"Maude","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfredo","family":"Mayor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6056-4516","authenticated-orcid":false,"given":"Mayfong","family":"Mayxay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oumou","family":"Ma\u00efga-Ascofar\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert S","family":"McCann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alistair","family":"Miles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivo","family":"Miotto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0840-1637","authenticated-orcid":false,"given":"Abdelrahim Osman","family":"Mohamed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6988-150X","authenticated-orcid":false,"given":"Collins Misita","family":"Morang\u2019a","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn","family":"Murie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9300-7719","authenticated-orcid":false,"given":"Billy Ephraim","family":"Ngasala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4101-5706","authenticated-orcid":false,"given":"Thuy-Nhien","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar","family":"Nolasco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7951-0745","authenticated-orcid":false,"given":"Francois","family":"Nosten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rintis","family":"Noviyanti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00cdsla","family":"O'Connor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary","family":"Oboh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lynette Isabella","family":"Ochola-Oyier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Olufunke Falade","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adeola","family":"Olukosi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ajibola","family":"Olumide","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fiyinfoluwa I","family":"Olusola","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7501-5931","authenticated-orcid":false,"given":"Marie A","family":"Onyamboko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eniyou Cheryll","family":"Oriero","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wellington Aghoghovwia","family":"Oyibo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danielle","family":"Pannebaker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7386-3566","authenticated-orcid":false,"given":"Richard D","family":"Pearson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1753-2727","authenticated-orcid":false,"given":"Kamija","family":"Phiri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rob W","family":"van der Pluijm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2000-2874","authenticated-orcid":false,"given":"Ric N","family":"Price","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huynh Hong","family":"Quang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vinoth","family":"Rajkumar Devaraju","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2767-0349","authenticated-orcid":false,"given":"Milijaona","family":"Randrianarivelojosia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1992-3940","authenticated-orcid":false,"given":"Lisa","family":"Ranford-Cartwright","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9835-1014","authenticated-orcid":false,"given":"Julian C","family":"Rayner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4765-1076","authenticated-orcid":false,"given":"Eduard","family":"Rovira-Vallbona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine","family":"Rowlands","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentin","family":"Ruano-Rubio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan F","family":"Sanchez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco","family":"Sa\u00fate","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuwaram","family":"Shettima","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clemente","family":"da Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria J","family":"Simpson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Suddaby","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Willem","family":"Takken","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aung Myint","family":"Thu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahamoudou","family":"Toure","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eyyub","family":"Unlu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2159-5667","authenticated-orcid":false,"given":"Hugo O","family":"Valdivia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michele","family":"van Vugt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2267-9347","authenticated-orcid":false,"given":"Naomi","family":"Waithira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3899-8454","authenticated-orcid":false,"given":"Thomas","family":"Wellems","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason","family":"Wendler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7110-7874","authenticated-orcid":false,"given":"Nina","family":"White","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Wuendrich Ogidan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2025,6,30]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"50-55","DOI":"10.1038\/nature12876","article-title":"A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.","volume":"505","author":"F Ariey","year":"2014","journal-title":"Nature."},{"key":"ref-2","doi-asserted-by":"publisher","first-page":"337-345","DOI":"10.1016\/S1473-3099(18)30068-9","article-title":"Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study.","volume":"18","author":"R Amato","year":"2018","journal-title":"Lancet Infect Dis."},{"key":"ref-3","doi-asserted-by":"publisher","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":"C Jacob","year":"2021","journal-title":"eLife."},{"key":"ref-4","article-title":"World malaria report 2024: addressing inequity in the global malaria response","year":"2024"},{"key":"ref-5","doi-asserted-by":"publisher","first-page":"964-969","DOI":"10.1016\/j.pt.2024.09.005","article-title":"Towards integrated Malaria Molecular Surveillance in Africa.","volume":"40","author":"N Dada","year":"2024","journal-title":"Trends Parasitol."},{"key":"ref-6","doi-asserted-by":"publisher","first-page":"136","DOI":"10.12688\/wellcomeopenres.17795.1","article-title":"An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples [version 1; peer review: 2 approved].","volume":"7","author":"G Malaria","year":"2022","journal-title":"Wellcome Open Res."},{"key":"ref-7","doi-asserted-by":"publisher","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 [version 1; peer review: 3 approved].","volume":"8","author":"G Malaria","year":"2023","journal-title":"Wellcome Open Res."},{"key":"ref-8","doi-asserted-by":"publisher","first-page":"1213-1226","DOI":"10.1038\/s41564-023-01377-z","article-title":"Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative Amino Acid Transporter AAT1.","volume":"8","author":"A Amambua-Ngwa","year":"2023","journal-title":"Nat Microbiol."},{"key":"ref-9","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36921-2","article-title":"Potent acyl-CoA synthetase 10 inhibitors kill Plasmodium falciparum by disrupting triglyceride formation.","volume":"14","author":"S Bopp","year":"2023","journal-title":"Nat Commun."},{"key":"ref-10","doi-asserted-by":"publisher","DOI":"10.1128\/aac.01203-24","article-title":"Geo-classification of drug-resistant travel-associated Plasmodium falciparum using Pfs47 and Pfcpmp gene sequences (USA, 2018\u20132021).","volume":"68","author":"E Pierre-Louis","year":"2024","journal-title":"Antimicrob Agents Chemother."},{"key":"ref-11","doi-asserted-by":"publisher","first-page":"125-133","DOI":"10.1038\/s41586-024-07546-2","article-title":"Ancient Plasmodium genomes shed light on the history of human malaria.","volume":"631","author":"M Michel","year":"2024","journal-title":"Nature."},{"key":"ref-12","doi-asserted-by":"publisher","DOI":"10.1101\/2024.03.08.584049","article-title":"Regional Plasmodium falciparum subpopulations and malaria transmission connectivity in Africa detected with an enlarged panel of genome-wide microsatellite loci","author":"M Demba","year":"2024"},{"key":"ref-13","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.87726","article-title":"A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture.","volume":"12","author":"C Andradi-Brown","year":"2024","journal-title":"eLife."},{"key":"ref-14","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-03063-z","article-title":"MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites.","volume":"24","author":"C Wang","year":"2023","journal-title":"Genome Biol."},{"key":"ref-15","doi-asserted-by":"publisher","DOI":"10.1016\/j.lanmic.2024.07.004","article-title":"Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis.","volume":"5","author":"O Miotto","year":"2024","journal-title":"Lancet Microbe."},{"key":"ref-16","doi-asserted-by":"publisher","DOI":"10.1038\/s41541-023-00709-8","article-title":"A potent and durable malaria Transmission-Blocking Vaccine designed from a single-component 60\u2013copy Pfs230D1 nanoparticle.","volume":"8","author":"N Salinas","year":"2023","journal-title":"NPJ Vaccines."},{"key":"ref-17","doi-asserted-by":"publisher","DOI":"10.1101\/2024.09.20.24314052","article-title":"Genetic diversity of the Plasmodium falciparum reticulocyte binding protein homologue-5 which is a potential malaria vaccine candidate: baseline data from areas of varying malaria endemicity in Mainland Tanzania","author":"A Kisambale","year":"2024"},{"key":"ref-18","doi-asserted-by":"publisher","first-page":"420-432","DOI":"10.1016\/j.immuni.2023.01.013","article-title":"Potent transmission-blocking monoclonal antibodies from naturally exposed individuals target a conserved epitope on Plasmodium falciparum Pfs230.","volume":"56","author":"D Ivanochko","year":"2023","journal-title":"Immunity."},{"key":"ref-19","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2213626120","article-title":"Role of Pfs47 in the dispersal of ancestral Plasmodium falciparum malaria through adaptation to different anopheline vectors","volume":"120","author":"A Molina-Cruz","year":"2023","journal-title":"Proc Natl Acad Sci U S A."},{"key":"ref-20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002507","article-title":"Role for gene conversion in the evolution of cell-surface antigens of the malaria parasite Plasmodium falciparum.","volume":"22","author":"B Letcher","year":"2024","journal-title":"PLoS Biol."},{"key":"ref-21","doi-asserted-by":"publisher","first-page":"215","DOI":"10.12688\/wellcomeopenres.19092.1","article-title":"Modelling transmission dynamics and genomic diversity in a recombining parasite population [version 1; peer review: 1 approved, 2 approved with reservations].","volume":"9","author":"D Kwiatkowski","year":"2024","journal-title":"Wellcome Open Res."},{"key":"ref-22","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000243","article-title":"Adaptive copy number evolution in malaria parasites.","volume":"4","author":"S Nair","year":"2008","journal-title":"PLoS Genet."},{"key":"ref-23","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-44599-0","article-title":"An analysis of large structural variation in global Plasmodium falciparum isolates identifies a novel duplication of the chloroquine resistance associated gene.","volume":"9","author":"M Ravenhall","year":"2019","journal-title":"Sci Rep."},{"key":"ref-24","doi-asserted-by":"publisher","first-page":"550-557","DOI":"10.1016\/j.jiph.2022.03.015","article-title":"Molecular surveillance of chloroquine-resistant Plasmodium falciparum in sub-Saharan African countries after withdrawal of chloroquine for treatment of uncomplicated malaria: a systematic review.","volume":"15","author":"B Njiro","year":"2022","journal-title":"J Infect Public Health."},{"key":"ref-25","doi-asserted-by":"publisher","DOI":"10.1101\/2024.06.06.24308535","article-title":"Genetic surveillance of Plasmodium falciparum reveals rapid population changes following first-line treatment policy revisions in the Greater Mekong Subregion.","author":"V Wasakul","year":"2024"},{"key":"ref-26","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae673","article-title":"Pf-HaploAtlas: an interactive web app for spatiotemporal analysis of Plasmodium falciparum genes.","volume":"40","author":"C Lee","year":"2024","journal-title":"Bioinformatics."},{"key":"ref-27","doi-asserted-by":"publisher","first-page":"375-379","DOI":"10.1038\/nature11174","article-title":"Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.","volume":"487","author":"M Manske","year":"2012","journal-title":"Nature."},{"key":"ref-28","doi-asserted-by":"publisher","first-page":"1288-1299","DOI":"10.1101\/gr.203711.115","article-title":"Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum.","volume":"26","author":"A Miles","year":"2016","journal-title":"Genome Res."},{"key":"ref-29","doi-asserted-by":"publisher","first-page":"1754-1760","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform.","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics."},{"key":"ref-30","doi-asserted-by":"publisher","first-page":"2078-2079","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools.","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics."},{"key":"ref-31","doi-asserted-by":"publisher","first-page":"11.10.1-11.10.33","DOI":"10.1002\/0471250953.bi1110s43","article-title":"From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline.","volume":"43","author":"G Van der Auwera","year":"2013","journal-title":"Curr Protoc Bioinformatics."},{"key":"ref-32","doi-asserted-by":"publisher","first-page":"80-92","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.","volume":"6","author":"P Cingolani","year":"2012","journal-title":"Fly (Austin)."},{"key":"ref-33","doi-asserted-by":"publisher","first-page":"2987-2993","DOI":"10.1093\/bioinformatics\/btr509","article-title":"A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.","volume":"27","author":"H Li","year":"2011","journal-title":"Bioinformatics."},{"key":"ref-34","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.11206451","article-title":"zarr-developers\/zarr-python: v2.18.1.","author":"A Miles","year":"2024","journal-title":"Zenodo."},{"key":"ref-35","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.10876220","article-title":"cggh\/scikit-allel: v1.3.8.","author":"A Miles","year":"2024","journal-title":"Zenodo."}],"container-title":["Wellcome Open Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-325\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-325\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-325\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T08:54:08Z","timestamp":1774256048000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-325\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,30]]},"references-count":35,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.24031.1","relation":{"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.26513.r137754","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26513.r127191","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26513.r137757","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26513.r127191","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26513.r137754","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.26513.r137757","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,30]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-325\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.26513.r127191, Qixin He, Purdue University, West Lafayette, Indiana, 27 Aug 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-325\/v1#referee-response-127191","order":0,"name":"referee-response-127191","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.26513.r137754, Daniel Jeffares, University of York, York, England, 18 Nov 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-325\/v1#referee-response-137754","order":1,"name":"referee-response-137754","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.26513.r137757, Wim L Cuypers, University of Antwerp, Antwerp, Flanders, 19 Dec 2025, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/10-325\/v1#referee-response-137757","order":2,"name":"referee-response-137757","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by Wellcome [204911] [206194]; Bill and Melinda Gates Foundation [INV-007590] [INV-001927] [INV-068808]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}