{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T17:10:58Z","timestamp":1769101858957,"version":"3.49.0"},"reference-count":29,"publisher":"Proceedings of the National Academy of Sciences","issue":"18","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2009,5,5]]},"abstract":"<jats:p>\n            We have cultured\n            <jats:italic>Plasmodium falciparum<\/jats:italic>\n            directly from the blood of infected individuals to examine patterns of mature-stage gene expression in patient isolates. Analysis of the transcriptome of\n            <jats:italic>P. falciparum<\/jats:italic>\n            is complicated by the highly periodic nature of gene expression because small variations in the stage of parasite development between samples can lead to an apparent difference in gene expression values. To address this issue, we have developed statistical likelihood-based methods to estimate cell cycle progression and commitment to asexual or sexual development lineages in our samples based on microscopy and gene expression patterns. In cases subsequently matched for temporal development, we find that transcriptional patterns in ex vivo culture display little variation across patients with diverse clinical profiles and closely resemble transcriptional profiles that occur in vitro. These statistical methods, available to the research community, assist in the design and interpretation of\n            <jats:italic>P. falciparum<\/jats:italic>\n            expression profiling experiments where it is difficult to separate true differential expression from cell-cycle dependent expression. We reanalyze an existing dataset of in vivo patient expression profiles and conclude that previously observed discrete variation is consistent with the commitment of a varying proportion of the parasite population to the sexual development lineage.\n          <\/jats:p>","DOI":"10.1073\/pnas.0811829106","type":"journal-article","created":{"date-parts":[[2009,4,18]],"date-time":"2009-04-18T01:42:37Z","timestamp":1240018957000},"page":"7559-7564","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":98,"title":["Statistical estimation of cell-cycle progression and lineage commitment in\n            <i>Plasmodium falciparum<\/i>\n            reveals a homogeneous pattern of transcription in ex vivo culture"],"prefix":"10.1073","volume":"106","author":[{"given":"Jacob E.","family":"Lemieux","sequence":"first","affiliation":[{"name":"Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, United Kingdom;"}]},{"given":"Natalia","family":"Gomez-Escobar","sequence":"additional","affiliation":[{"name":"Medical Research Council Laboratories, P.O. Box 273, Fajara, The Gambia;"}]},{"given":"Avi","family":"Feller","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom;"}]},{"given":"Celine","family":"Carret","sequence":"additional","affiliation":[{"name":"The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom; and"}]},{"given":"Alfred","family":"Amambua-Ngwa","sequence":"additional","affiliation":[{"name":"Medical Research Council Laboratories, P.O. Box 273, Fajara, The Gambia;"}]},{"given":"Robert","family":"Pinches","sequence":"additional","affiliation":[{"name":"Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, United Kingdom;"}]},{"given":"Felix","family":"Day","sequence":"additional","affiliation":[{"name":"Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, United Kingdom;"}]},{"given":"Sue A.","family":"Kyes","sequence":"additional","affiliation":[{"name":"Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, United Kingdom;"}]},{"given":"David J.","family":"Conway","sequence":"additional","affiliation":[{"name":"Medical Research Council Laboratories, P.O. Box 273, Fajara, The Gambia;"}]},{"given":"Chris C.","family":"Holmes","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom;"},{"name":"Medical Research Council, Harwell, Oxon OX11 0RD, United Kingdom"}]},{"given":"Chris I.","family":"Newbold","sequence":"additional","affiliation":[{"name":"Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, United Kingdom;"}]}],"member":"341","published-online":{"date-parts":[[2009,5,5]]},"reference":[{"key":"e_1_3_3_1_2","doi-asserted-by":"publisher","DOI":"10.1086\/428289"},{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature06311"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1086\/522012"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0807404105"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0000005"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1087025"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkj517"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.2307\/3280287"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1084\/jem.169.1.357"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1080\/00034983.1978.11719283"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(81)90414-1"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2008-9-5-r88"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00394-06"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.2202\/1544-6115.1027"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.25.14863"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0308531101"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0030107"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1214\/aos\/1013699998"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.16.9333"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molbiopara.2005.05.007"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0801993105"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2004-5-10-r80"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.781840"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0408393102"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh205"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0031182001001202"},{"key":"e_1_3_3_27_2","first-page":"2031","article-title":"Large sample confidence intervals based on subsamples under minimal assumptions","author":"Politis DN","year":"1994","unstructured":"DN Politis, J.P Romano, Large sample confidence intervals based on subsamples under minimal assumptions. Annals of Statistics, pp. 2031\u20132050 (1994).","journal-title":"Annals of Statistics"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4612-1554-7"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0031182000061199"}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.0811829106","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,12]],"date-time":"2022-04-12T21:19:13Z","timestamp":1649798353000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/full\/10.1073\/pnas.0811829106"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,5,5]]},"references-count":29,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2009,5,5]]}},"alternative-id":["10.1073\/pnas.0811829106"],"URL":"https:\/\/doi.org\/10.1073\/pnas.0811829106","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,5,5]]},"assertion":[{"value":"2008-11-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2009-05-05","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}