{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:19:01Z","timestamp":1785424741943,"version":"3.56.0"},"posted":{"date-parts":[[2024,12,21]]},"group-title":"Genomics","reference-count":192,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2024,12,21]],"date-time":"2024-12-21T00:00:00Z","timestamp":1734739200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"award":["1R01AI150856"],"award-info":[{"award-number":["1R01AI150856"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["NRT-ROL 2021791"],"award-info":[{"award-number":["NRT-ROL 2021791"]}],"id":[{"id":"https:\/\/ror.org\/021nxhr62","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,9,29]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  Changes in the copy number of large genomic regions, termed copy number variations (CNVs), contribute to important phenotypes. CNVs are readily identified using conventional approaches when present in a large fraction of the cell population. However, CNVs in only a few genomes are often overlooked but important; if beneficial, a de novo CNV that arises in a single genome can expand during selection to create a population of cells with novel characteristics. While single cell methods for studying de novo CNVs are increasing, we continue to lack information about CNV dynamics in rapidly evolving microbial populations. Here, we investigated de novo CNVs in the genome of the\n                  <jats:italic>Plasmodium<\/jats:italic>\n                  parasite that causes human malaria. The highly AT-rich\n                  <jats:italic>P. falciparum<\/jats:italic>\n                  genome readily accumulates CNVs that facilitate rapid adaptation. We employed low-input genomics and specialized computational tools to evaluate the impact of sub-lethal stress on the de novo CNV rate. We observed a significant increase in genome-wide de novo CNVs following treatment with an antimalarial compound that inhibits replication. De novo CNVs encompassed genes from various cellular pathways participating in human infection. This snapshot of CNV dynamics emphasizes the connection between replication stress, DNA repair, and CNV generation in this important microbial pathogen.\n                <\/jats:p>","DOI":"10.1101\/2024.12.19.629492","type":"posted-content","created":{"date-parts":[[2024,12,24]],"date-time":"2024-12-24T05:45:20Z","timestamp":1735019120000},"source":"Crossref","is-referenced-by-count":3,"title":["Replication stress increases de novo CNVs across the malaria parasite genome"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-1284-0720","authenticated-orcid":false,"given":"Noah","family":"Brown","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aleksander","family":"Luniewski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5807-5716","authenticated-orcid":false,"given":"Xuanxuan","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4480-816X","authenticated-orcid":false,"given":"Michelle","family":"Warthan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiwei","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-9407-4640","authenticated-orcid":false,"given":"Julia","family":"Zulawinska","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Syed","family":"Ahmad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadia","family":"Prasad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Molly","family":"Congdon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Webster","family":"Santos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1597-4719","authenticated-orcid":false,"given":"Feifei","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6301-4563","authenticated-orcid":false,"given":"Jennifer L","family":"Guler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025100310301070000_2024.12.19.629492v3.1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2593"},{"key":"2025100310301070000_2024.12.19.629492v3.2","doi-asserted-by":"crossref","unstructured":"Lauer, S. and Gresham, D . (2019) An evolving view of copy number variants. Curr Genet.","DOI":"10.1007\/s00294-019-00980-0"},{"key":"2025100310301070000_2024.12.19.629492v3.3","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1016\/j.bj.2021.02.003","article-title":"DNA copy number variation: Main characteristics, evolutionary significance, and pathological aspects","volume":"44","year":"2021","journal-title":"Biomed J"},{"key":"2025100310301070000_2024.12.19.629492v3.4","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2010.07459.x"},{"key":"2025100310301070000_2024.12.19.629492v3.5","doi-asserted-by":"publisher","DOI":"10.1534\/g3.113.009365"},{"key":"2025100310301070000_2024.12.19.629492v3.6","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.05.049"},{"key":"2025100310301070000_2024.12.19.629492v3.7","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0808041105"},{"key":"2025100310301070000_2024.12.19.629492v3.8","doi-asserted-by":"publisher","DOI":"10.1038\/nature08822"},{"key":"2025100310301070000_2024.12.19.629492v3.9","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-1085-7"},{"key":"2025100310301070000_2024.12.19.629492v3.10","doi-asserted-by":"crossref","first-page":"926","DOI":"10.3390\/genes10110926","article-title":"CNV Detection from Circulating Tumor DNA in Late Stage Non-Small Cell Lung Cancer Patients","volume":"10","year":"2019","journal-title":"Genes (Basel"},{"key":"2025100310301070000_2024.12.19.629492v3.11","doi-asserted-by":"publisher","DOI":"10.1126\/science.1101160"},{"key":"2025100310301070000_2024.12.19.629492v3.12","doi-asserted-by":"publisher","DOI":"10.1126\/science.1138659"},{"key":"2025100310301070000_2024.12.19.629492v3.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2010.09.014"},{"key":"2025100310301070000_2024.12.19.629492v3.14","doi-asserted-by":"publisher","DOI":"10.1002\/eji.201242601"},{"key":"2025100310301070000_2024.12.19.629492v3.15","first-page":"7","article-title":"Copy Number Variations in the Survival Motor Neuron Genes: Implications for Spinal Muscular Atrophy and Other Neurodegenerative Diseases","volume":"3","year":"2016","journal-title":"Front Mol Biosci"},{"key":"2025100310301070000_2024.12.19.629492v3.16","doi-asserted-by":"publisher","DOI":"10.1038\/nature16549"},{"key":"2025100310301070000_2024.12.19.629492v3.17","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04668-w"},{"key":"2025100310301070000_2024.12.19.629492v3.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.bcmd.2017.09.004"},{"key":"2025100310301070000_2024.12.19.629492v3.19","doi-asserted-by":"publisher","DOI":"10.1007\/s13353-018-00480-w"},{"key":"2025100310301070000_2024.12.19.629492v3.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2009.01.024"},{"key":"2025100310301070000_2024.12.19.629492v3.21","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1109272108"},{"key":"2025100310301070000_2024.12.19.629492v3.22","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002981"},{"key":"2025100310301070000_2024.12.19.629492v3.23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000069"},{"key":"2025100310301070000_2024.12.19.629492v3.24","doi-asserted-by":"crossref","first-page":"391","DOI":"10.3390\/ijms25010391","article-title":"Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility","volume":"25","year":"2023","journal-title":"Int J Mol Sci"},{"key":"2025100310301070000_2024.12.19.629492v3.25","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1093\/bib\/bbad297","article-title":"Toward the functional interpretation of somatic structural variations: bulk- and single-cell approaches","volume":"24","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025100310301070000_2024.12.19.629492v3.26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004126"},{"key":"2025100310301070000_2024.12.19.629492v3.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.05.005"},{"key":"2025100310301070000_2024.12.19.629492v3.28","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2015.16"},{"key":"2025100310301070000_2024.12.19.629492v3.29","doi-asserted-by":"publisher","DOI":"10.1093\/BIB\/BBX004"},{"key":"2025100310301070000_2024.12.19.629492v3.30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0020057"},{"key":"2025100310301070000_2024.12.19.629492v3.31","doi-asserted-by":"publisher","DOI":"10.1016\/j.molbiopara.2007.05.005"},{"key":"2025100310301070000_2024.12.19.629492v3.32","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-10-353"},{"key":"2025100310301070000_2024.12.19.629492v3.33","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003293"},{"key":"2025100310301070000_2024.12.19.629492v3.34","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2018.09.009"},{"key":"2025100310301070000_2024.12.19.629492v3.35","doi-asserted-by":"publisher","DOI":"10.1016\/S0166-6851(02)00242-6"},{"key":"2025100310301070000_2024.12.19.629492v3.36","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms11187"},{"key":"2025100310301070000_2024.12.19.629492v3.37","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1016\/S0140-6736(04)16767-6","article-title":"Mefloquine resistance in Plasmodium falciparum and increased pfmdr1 gene copy number","volume":"364","year":"2004","journal-title":"The Lancet"},{"key":"2025100310301070000_2024.12.19.629492v3.38","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-44599-0"},{"key":"2025100310301070000_2024.12.19.629492v3.39","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.12162"},{"key":"2025100310301070000_2024.12.19.629492v3.40","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1268"},{"key":"2025100310301070000_2024.12.19.629492v3.41","doi-asserted-by":"publisher","DOI":"10.1038\/nature01097"},{"key":"2025100310301070000_2024.12.19.629492v3.42","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-021-00889-9"},{"key":"2025100310301070000_2024.12.19.629492v3.43","doi-asserted-by":"crossref","unstructured":"Brown, N. , Danis, C. , Ahmedjanova, V. and Guler, J.L. (2025) SVCROWS: A User-Defined Tool for Interpreting Significant Structural Variants in Heterogeneous Datasets. bioRxiv.","DOI":"10.1101\/2025.01.24.634734"},{"key":"2025100310301070000_2024.12.19.629492v3.44","doi-asserted-by":"crossref","unstructured":"Yu, X. , Qin, F. , Liu, S. , Brown, N.J. , Lu, Q. , Cai, G. , Guler, J.L. and Xiao, F. (2025) HapCNV: A Comprehensive Framework for CNV Detection in Low-input DNA Sequencing Data. bioRxiv.","DOI":"10.1101\/2024.12.19.629494"},{"key":"2025100310301070000_2024.12.19.629492v3.45","doi-asserted-by":"publisher","DOI":"10.1080\/10409230701648502"},{"key":"2025100310301070000_2024.12.19.629492v3.46","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2012.01.009"},{"key":"2025100310301070000_2024.12.19.629492v3.47","doi-asserted-by":"publisher","DOI":"10.1038\/nrc.2017.52"},{"key":"2025100310301070000_2024.12.19.629492v3.48","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.14624"},{"key":"2025100310301070000_2024.12.19.629492v3.49","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1186\/s12864-025-11859-5","article-title":"Direct long-read visualization reveals hidden variation in GCH1 gene copy number and precise expansion steps","volume":"26","year":"2025","journal-title":"BMC Genomics"},{"key":"2025100310301070000_2024.12.19.629492v3.50","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-61392-6"},{"key":"2025100310301070000_2024.12.19.629492v3.51","doi-asserted-by":"publisher","DOI":"10.1002\/cyto.a.22865"},{"key":"2025100310301070000_2024.12.19.629492v3.52","doi-asserted-by":"crossref","unstructured":"Nam, D. , Kim, S. , Kim, J.H. , Lee, S. , Kim, D. , Son, J. , Kim, D. , Cha, B.S. , Lee, E.S. and Park, K.S . (2023) Low-Temperature Loop-Mediated Isothermal Amplification Operating at Physiological Temperature. Biosensors (Basel ), 13.","DOI":"10.3390\/bios13030367"},{"key":"2025100310301070000_2024.12.19.629492v3.53","doi-asserted-by":"publisher","DOI":"10.1128\/aac.00346-24"},{"key":"2025100310301070000_2024.12.19.629492v3.54","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.05737-11"},{"key":"2025100310301070000_2024.12.19.629492v3.55","doi-asserted-by":"publisher","DOI":"10.1186\/s12936-021-03657-7"},{"key":"2025100310301070000_2024.12.19.629492v3.56","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.48.8.2924-2929.2004"},{"key":"2025100310301070000_2024.12.19.629492v3.57","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.3505","article-title":"SpeedSeq: ultra-fast personal genome analysis and interpretation","volume":"12","year":"2015","journal-title":"Nature methods"},{"key":"2025100310301070000_2024.12.19.629492v3.58","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","year":"2018","journal-title":"Wellcome Open Res"},{"key":"2025100310301070000_2024.12.19.629492v3.59","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"2025100310301070000_2024.12.19.629492v3.60","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts503"},{"key":"2025100310301070000_2024.12.19.629492v3.61","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genom-090413-025352"},{"key":"2025100310301070000_2024.12.19.629492v3.62","doi-asserted-by":"publisher","DOI":"10.1126\/science.aak9787"},{"key":"2025100310301070000_2024.12.19.629492v3.63","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1990.9999"},{"key":"2025100310301070000_2024.12.19.629492v3.64","doi-asserted-by":"publisher","DOI":"10.1101\/gr.107524.110"},{"key":"2025100310301070000_2024.12.19.629492v3.65","doi-asserted-by":"publisher","DOI":"10.1038\/ng.806"},{"key":"2025100310301070000_2024.12.19.629492v3.66","first-page":"1110","article-title":"From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline","volume":"43","year":"2013","journal-title":"Curr Protoc Bioinformatics"},{"key":"2025100310301070000_2024.12.19.629492v3.67","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","year":"2021","journal-title":"Wellcome Open Res"},{"key":"2025100310301070000_2024.12.19.629492v3.68","doi-asserted-by":"publisher","DOI":"10.1101\/gr.203711.115"},{"key":"2025100310301070000_2024.12.19.629492v3.69","doi-asserted-by":"publisher","DOI":"10.1101\/gr.114876.110"},{"key":"2025100310301070000_2024.12.19.629492v3.70","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-6-r84"},{"key":"2025100310301070000_2024.12.19.629492v3.71","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl646"},{"key":"2025100310301070000_2024.12.19.629492v3.72","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx212"},{"key":"2025100310301070000_2024.12.19.629492v3.73","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1578-y"},{"key":"2025100310301070000_2024.12.19.629492v3.74","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaa1106"},{"key":"2025100310301070000_2024.12.19.629492v3.75","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2022.821516"},{"key":"2025100310301070000_2024.12.19.629492v3.76","doi-asserted-by":"publisher","DOI":"10.1126\/science.aap7847"},{"key":"2025100310301070000_2024.12.19.629492v3.77","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn814"},{"key":"2025100310301070000_2024.12.19.629492v3.78","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijpara.2007.05.003"},{"key":"2025100310301070000_2024.12.19.629492v3.79","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-11-577"},{"key":"2025100310301070000_2024.12.19.629492v3.80","doi-asserted-by":"publisher","DOI":"10.1021\/jm8001026"},{"key":"2025100310301070000_2024.12.19.629492v3.81","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0030949"},{"key":"2025100310301070000_2024.12.19.629492v3.82","doi-asserted-by":"publisher","DOI":"10.1016\/0166-6851(84)90020-3"},{"key":"2025100310301070000_2024.12.19.629492v3.83","doi-asserted-by":"publisher","DOI":"10.1016\/0014-4894(84)90061-4"},{"key":"2025100310301070000_2024.12.19.629492v3.84","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.77.12.7049"},{"key":"2025100310301070000_2024.12.19.629492v3.85","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2010.01.021"},{"key":"2025100310301070000_2024.12.19.629492v3.86","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajpath.2012.09.011"},{"key":"2025100310301070000_2024.12.19.629492v3.87","doi-asserted-by":"publisher","DOI":"10.4269\/ajtmh.1978.27.743"},{"key":"2025100310301070000_2024.12.19.629492v3.88","doi-asserted-by":"publisher","DOI":"10.1172\/JCI114753"},{"key":"2025100310301070000_2024.12.19.629492v3.89","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-016-3045-z"},{"key":"2025100310301070000_2024.12.19.629492v3.90","doi-asserted-by":"publisher","DOI":"10.1101\/gr.262865.120"},{"key":"2025100310301070000_2024.12.19.629492v3.91","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-11146-4"},{"key":"2025100310301070000_2024.12.19.629492v3.92","doi-asserted-by":"crossref","unstructured":"Gabrielaite, M. , Torp, M.H. , Rasmussen, M.S. , Andreu-Sanchez, S. , Vieira, F.G. , Pedersen, C.B. , Kinalis, S. , Madsen, M.B. , Kodama, M. , Demircan, G.S. et al. (2021) A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data. Cancers (Basel ), 13.","DOI":"10.1101\/2021.04.30.442110"},{"key":"2025100310301070000_2024.12.19.629492v3.93","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1720-5"},{"key":"2025100310301070000_2024.12.19.629492v3.94","doi-asserted-by":"publisher","DOI":"10.1093\/emboj\/18.22.6221"},{"key":"2025100310301070000_2024.12.19.629492v3.95","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-5822.2008.01252.x"},{"key":"2025100310301070000_2024.12.19.629492v3.96","doi-asserted-by":"publisher","DOI":"10.1016\/j.molbiopara.2005.05.010"},{"key":"2025100310301070000_2024.12.19.629492v3.97","doi-asserted-by":"publisher","DOI":"10.1074\/mcp.M900479-MCP200"},{"key":"2025100310301070000_2024.12.19.629492v3.98","doi-asserted-by":"publisher","DOI":"10.1038\/nature03188"},{"key":"2025100310301070000_2024.12.19.629492v3.99","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000086"},{"key":"2025100310301070000_2024.12.19.629492v3.100","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.03582"},{"key":"2025100310301070000_2024.12.19.629492v3.101","first-page":"17","article-title":"Plasmodium UIS3 sequesters host LC3 to avoid elimination by autophagy in hepatocytes","volume":"3","year":"2018","journal-title":"Nat Microbiol"},{"key":"2025100310301070000_2024.12.19.629492v3.102","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aaz5629"},{"key":"2025100310301070000_2024.12.19.629492v3.103","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1038\/s41541-022-00558-x","article-title":"Creation and preclinical evaluation of genetically attenuated malaria parasites arresting growth late in the liver","volume":"7","year":"2022","journal-title":"NPJ Vaccines"},{"key":"2025100310301070000_2024.12.19.629492v3.104","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1001383"},{"key":"2025100310301070000_2024.12.19.629492v3.105","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1111\/mmi.15215","article-title":"The Plasmodium falciparum CCCH zinc finger protein MD3 regulates male gametocytogenesis through its interaction with RNA-binding proteins","volume":"121","year":"2024","journal-title":"Mol Microbiol"},{"key":"2025100310301070000_2024.12.19.629492v3.106","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000539"},{"key":"2025100310301070000_2024.12.19.629492v3.107","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000767"},{"key":"2025100310301070000_2024.12.19.629492v3.108","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms10403"},{"key":"2025100310301070000_2024.12.19.629492v3.109","first-page":"e03377","article-title":"Malaria Parasite Schizont Egress Antigen-1 Plays an Essential Role in Nuclear Segregation during Schizogony","volume":"12","year":"2021","journal-title":"mBio"},{"key":"2025100310301070000_2024.12.19.629492v3.110","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.gene.2008.05.005","article-title":"Characterization of replication fork and phosphorylation stimulated Plasmodium falciparum helicase 45","volume":"420","year":"2008","journal-title":"Gene"},{"key":"2025100310301070000_2024.12.19.629492v3.111","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.pep.2012.06.010","article-title":"Enhanced purification and characterization of the PfeIF4A (PfH45) helicase from Plasmodium falciparum using a codon-optimised clone","volume":"85","year":"2012","journal-title":"Protein Expr Purif"},{"key":"2025100310301070000_2024.12.19.629492v3.112","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2008.04.051"},{"key":"2025100310301070000_2024.12.19.629492v3.113","doi-asserted-by":"crossref","first-page":"16215","DOI":"10.1038\/s41598-021-95442-4","article-title":"In silico characterisation of putative Plasmodium falciparum vaccine candidates in African malaria populations","volume":"11","year":"2021","journal-title":"Sci Rep"},{"key":"2025100310301070000_2024.12.19.629492v3.114","doi-asserted-by":"publisher","DOI":"10.1126\/science.1254417"},{"key":"2025100310301070000_2024.12.19.629492v3.115","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20041392"},{"key":"2025100310301070000_2024.12.19.629492v3.116","doi-asserted-by":"publisher","DOI":"10.15698\/mic2016.10.534"},{"key":"2025100310301070000_2024.12.19.629492v3.117","doi-asserted-by":"publisher","DOI":"10.1126\/science.1254257"},{"key":"2025100310301070000_2024.12.19.629492v3.118","doi-asserted-by":"crossref","unstructured":"Xu, Q.H. , Chen, S.H. , Hu, Y.B. and Huang, W . (2021) Single-cell RNA transcriptome reveals the intra-tumoral heterogeneity and regulators underlying tumor progression in metastatic pancreatic ductal adenocarcinoma. Cell Death Discov, 7.","DOI":"10.1038\/s41420-021-00663-1"},{"key":"2025100310301070000_2024.12.19.629492v3.119","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-00795-2"},{"key":"2025100310301070000_2024.12.19.629492v3.120","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab413"},{"key":"2025100310301070000_2024.12.19.629492v3.121","doi-asserted-by":"publisher","DOI":"10.1038\/nature09807"},{"key":"2025100310301070000_2024.12.19.629492v3.122","doi-asserted-by":"publisher","DOI":"10.1126\/science.1243472"},{"key":"2025100310301070000_2024.12.19.629492v3.123","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2014.07.043"},{"key":"2025100310301070000_2024.12.19.629492v3.124","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-13-0879"},{"key":"2025100310301070000_2024.12.19.629492v3.125","doi-asserted-by":"publisher","DOI":"10.1038\/nature13952"},{"key":"2025100310301070000_2024.12.19.629492v3.126","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1812702115"},{"key":"2025100310301070000_2024.12.19.629492v3.127","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.51480"},{"key":"2025100310301070000_2024.12.19.629492v3.128","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab1203"},{"key":"2025100310301070000_2024.12.19.629492v3.129","doi-asserted-by":"publisher","DOI":"10.1101\/gr.168286.113"},{"key":"2025100310301070000_2024.12.19.629492v3.130","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evx256"},{"key":"2025100310301070000_2024.12.19.629492v3.131","doi-asserted-by":"publisher","DOI":"10.1016\/J.MOLCEL.2022.05.004"},{"key":"2025100310301070000_2024.12.19.629492v3.132","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003375"},{"key":"2025100310301070000_2024.12.19.629492v3.133","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.242624799"},{"key":"2025100310301070000_2024.12.19.629492v3.134","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000303"},{"key":"2025100310301070000_2024.12.19.629492v3.135","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2174"},{"key":"2025100310301070000_2024.12.19.629492v3.136","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-2-r21"},{"key":"2025100310301070000_2024.12.19.629492v3.137","doi-asserted-by":"publisher","DOI":"10.1126\/science.1193225"},{"key":"2025100310301070000_2024.12.19.629492v3.138","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M114.558353"},{"issue":"296r","key":"2025100310301070000_2024.12.19.629492v3.139","first-page":"a111","article-title":"A long-duration dihydroorotate dehydrogenase inhibitor (DSM265) for prevention and treatment of malaria","volume":"7","year":"2015","journal-title":"Sci Transl Med"},{"key":"2025100310301070000_2024.12.19.629492v3.140","doi-asserted-by":"crossref","unstructured":"Cowell, A. and Winzeler, E . (2018) Exploration of the Plasmodium falciparum Resistome and Druggable Genome Reveals New Mechanisms of Drug Resistance and Antimalarial Targets. Microbiol Insights, 11.","DOI":"10.1177\/1178636118808529"},{"key":"2025100310301070000_2024.12.19.629492v3.141","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1006930"},{"key":"2025100310301070000_2024.12.19.629492v3.142","doi-asserted-by":"publisher","DOI":"10.1126\/science.adk9893"},{"key":"2025100310301070000_2024.12.19.629492v3.143","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.12966"},{"key":"2025100310301070000_2024.12.19.629492v3.144","doi-asserted-by":"publisher","DOI":"10.1038\/nature09708"},{"key":"2025100310301070000_2024.12.19.629492v3.145","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-S11-S1"},{"key":"2025100310301070000_2024.12.19.629492v3.146","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2016.01.020"},{"key":"2025100310301070000_2024.12.19.629492v3.147","doi-asserted-by":"crossref","first-page":"6283","DOI":"10.3390\/cancers13246283","article-title":"A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data","volume":"13","year":"2021","journal-title":"Cancers (Basel"},{"key":"2025100310301070000_2024.12.19.629492v3.148","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijpara.2010.07.012"},{"key":"2025100310301070000_2024.12.19.629492v3.149","doi-asserted-by":"publisher","DOI":"10.1126\/science.1229164"},{"key":"2025100310301070000_2024.12.19.629492v3.150","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2523"},{"key":"2025100310301070000_2024.12.19.629492v3.151","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.10.026"},{"key":"2025100310301070000_2024.12.19.629492v3.152","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/s44259-025-00082-7","article-title":"Heteroresistance in Enterobacter cloacae complex caused by variation in transient gene amplification events","volume":"3","year":"2025","journal-title":"NPJ Antimicrob Resist"},{"key":"2025100310301070000_2024.12.19.629492v3.153","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt881"},{"key":"2025100310301070000_2024.12.19.629492v3.154","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.11.10.5244"},{"key":"2025100310301070000_2024.12.19.629492v3.155","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-018-2800-1"},{"key":"2025100310301070000_2024.12.19.629492v3.156","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.24.19.8504-8518.2004"},{"key":"2025100310301070000_2024.12.19.629492v3.157","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.25.16.7158-7169.2005"},{"key":"2025100310301070000_2024.12.19.629492v3.158","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0020048"},{"key":"2025100310301070000_2024.12.19.629492v3.159","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000327"},{"key":"2025100310301070000_2024.12.19.629492v3.160","doi-asserted-by":"publisher","DOI":"10.1038\/sj.onc.1206679"},{"key":"2025100310301070000_2024.12.19.629492v3.161","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)00176-8"},{"key":"2025100310301070000_2024.12.19.629492v3.162","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.7.3.1078"},{"key":"2025100310301070000_2024.12.19.629492v3.163","doi-asserted-by":"publisher","DOI":"10.1056\/NEJM199004193221607"},{"key":"2025100310301070000_2024.12.19.629492v3.164","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh842"},{"key":"2025100310301070000_2024.12.19.629492v3.165","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00287-13"},{"key":"2025100310301070000_2024.12.19.629492v3.166","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0708097105"},{"key":"2025100310301070000_2024.12.19.629492v3.167","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddu572"},{"key":"2025100310301070000_2024.12.19.629492v3.168","doi-asserted-by":"publisher","DOI":"10.2217\/17460913.2.3.309"},{"key":"2025100310301070000_2024.12.19.629492v3.169","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.13459"},{"key":"2025100310301070000_2024.12.19.629492v3.170","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00271-18"},{"key":"2025100310301070000_2024.12.19.629492v3.171","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1038\/s41564-018-0342-0","article-title":"The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification","volume":"4","year":"2019","journal-title":"Nat Microbiol"},{"key":"2025100310301070000_2024.12.19.629492v3.172","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23384-6"},{"key":"2025100310301070000_2024.12.19.629492v3.173","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/s42003-022-03884-x","article-title":"Genetic and microenvironmental intra-tumor heterogeneity impacts colorectal cancer evolution and metastatic development","volume":"5","year":"2022","journal-title":"Commun Biol"},{"key":"2025100310301070000_2024.12.19.629492v3.174","doi-asserted-by":"publisher","DOI":"10.1186\/s12936-017-1731-1"},{"key":"2025100310301070000_2024.12.19.629492v3.175","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003680"},{"key":"2025100310301070000_2024.12.19.629492v3.176","unstructured":"WHO. (2023) World Malaria Report 2023."},{"key":"2025100310301070000_2024.12.19.629492v3.177","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1038\/s41579-024-01099-x","article-title":"Towards next-generation treatment options to combat Plasmodium falciparum malaria","volume":"23","year":"2025","journal-title":"Nat Rev Microbiol"},{"key":"2025100310301070000_2024.12.19.629492v3.178","doi-asserted-by":"publisher","DOI":"10.1126\/science.2658061"},{"key":"2025100310301070000_2024.12.19.629492v3.179","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msl185"},{"key":"2025100310301070000_2024.12.19.629492v3.180","doi-asserted-by":"publisher","DOI":"10.1186\/s12936-016-1634-6"},{"key":"2025100310301070000_2024.12.19.629492v3.181","doi-asserted-by":"publisher","DOI":"10.1186\/s12936-019-2756-4"},{"key":"2025100310301070000_2024.12.19.629492v3.182","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-04104-z"},{"key":"2025100310301070000_2024.12.19.629492v3.183","doi-asserted-by":"publisher","DOI":"10.1006\/expr.2001.4618"},{"key":"2025100310301070000_2024.12.19.629492v3.184","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1011560108"},{"key":"2025100310301070000_2024.12.19.629492v3.185","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.17.9389"},{"key":"2025100310301070000_2024.12.19.629492v3.186","doi-asserted-by":"publisher","DOI":"10.1097\/MD.0000000000038565"},{"key":"2025100310301070000_2024.12.19.629492v3.187","doi-asserted-by":"crossref","first-page":"100602","DOI":"10.1016\/j.ijpddr.2025.100602","article-title":"Antimalarial drug resistance and drug discovery: learning from the past to innovate the future","volume":"28","year":"2025","journal-title":"Int J Parasitol Drugs Drug Resist"},{"key":"2025100310301070000_2024.12.19.629492v3.188","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2017.11.005"},{"key":"2025100310301070000_2024.12.19.629492v3.189","doi-asserted-by":"publisher","DOI":"10.1016\/j.critrevonc.2023.104192"},{"key":"2025100310301070000_2024.12.19.629492v3.190","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-22-0787"},{"key":"2025100310301070000_2024.12.19.629492v3.191","doi-asserted-by":"publisher","DOI":"10.1016\/s0140-6736(84)92057-9"},{"key":"2025100310301070000_2024.12.19.629492v3.192","doi-asserted-by":"publisher","DOI":"10.1016\/J.IJPDDR.2021.05.007"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2024.12.19.629492","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:03:41Z","timestamp":1782277421000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2024.12.19.629492"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,21]]},"references-count":192,"URL":"https:\/\/doi.org\/10.1101\/2024.12.19.629492","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1093\/nar\/gkaf1436","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2024,12,21]]},"subtype":"preprint"}}