{"id":"https://openalex.org/W4390101669","doi":"https://doi.org/10.7554/elife.87726.2.sa2","title":"Reviewer #1 (Public Review): 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","display_name":"Reviewer #1 (Public Review): 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","publication_year":2023,"publication_date":"2023-12-22","ids":{"openalex":"https://openalex.org/W4390101669","doi":"https://doi.org/10.7554/elife.87726.2.sa2"},"language":"en","primary_location":{"id":"doi:10.7554/elife.87726.2.sa2","doi":"https://doi.org/10.7554/elife.87726.2.sa2","is_oa":true,"landing_page_url":"https://doi.org/10.7554/elife.87726.2.sa2","pdf_url":null,"source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"peer-review"},"volume":null,"type":"peer-review","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.7554/elife.87726.2.sa2","any_repository_has_fulltext":false},"authorships":[],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3000,"currency":"USD","value_usd":2500},"apc_paid":{"value":3000,"currency":"USD","value_usd":2500},"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10091","display_name":"Malaria Research and Control","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10091","display_name":"Malaria Research and Control","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12178","display_name":"Bird parasitology and diseases","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2405","display_name":"Parasitology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/plasmodium-falciparum","display_name":"Plasmodium falciparum","score":0.9929999709129333},{"id":"https://openalex.org/keywords/var-genes","display_name":"var genes","score":0.8389999866485596},{"id":"https://openalex.org/keywords/pfemp1","display_name":"PfEMP1","score":0.9309999942779541},{"id":"https://openalex.org/keywords/var-gene-expression","display_name":"var gene expression","score":0.7350000143051147},{"id":"https://openalex.org/keywords/var-gene-switching","display_name":"var gene switching","score":0.7149999737739563},{"id":"https://openalex.org/keywords/var2csa","display_name":"VAR2CSA","score":0.9589999914169312},{"id":"https://openalex.org/keywords/in-vitro-culture","display_name":"in vitro culture","score":0.6320000290870667},{"id":"https://openalex.org/keywords/transcriptome","display_name":"transcriptome","score":0.6759999990463257},{"id":"https://openalex.org/keywords/malaria-pathogenesis","display_name":"malaria pathogenesis","score":0.7770000100135803},{"id":"https://openalex.org/keywords/cytoadhesion","display_name":"cytoadhesion","score":0.8029999732971191}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.8796913623809814},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8459764719009399},{"id":"https://openalex.org/C2778371730","wikidata":"https://www.wikidata.org/wiki/Q311383","display_name":"Plasmodium falciparum","level":3,"score":0.7334040999412537},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6582019329071045},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.6111002564430237},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5775268077850342},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5583544969558716},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5238929986953735},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5147664546966553},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4877193868160248},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.48447751998901367},{"id":"https://openalex.org/C207001950","wikidata":"https://www.wikidata.org/wiki/Q141124","display_name":"In vivo","level":2,"score":0.42320355772972107},{"id":"https://openalex.org/C2778048844","wikidata":"https://www.wikidata.org/wiki/Q12156","display_name":"Malaria","level":2,"score":0.29621589183807373},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.1822504997253418},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.7554/elife.87726.2.sa2","doi":"https://doi.org/10.7554/elife.87726.2.sa2","is_oa":true,"landing_page_url":"https://doi.org/10.7554/elife.87726.2.sa2","pdf_url":null,"source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"peer-review"}],"best_oa_location":{"id":"doi:10.7554/elife.87726.2.sa2","doi":"https://doi.org/10.7554/elife.87726.2.sa2","is_oa":true,"landing_page_url":"https://doi.org/10.7554/elife.87726.2.sa2","pdf_url":null,"source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"peer-review"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8199999928474426}],"sustainable_development_goals_aurora":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.800000011920929}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W6889906993","https://openalex.org/W6945742208","https://openalex.org/W2102684392","https://openalex.org/W2088459771","https://openalex.org/W2342129779","https://openalex.org/W2912605962","https://openalex.org/W2186155429","https://openalex.org/W2163850237","https://openalex.org/W2120295632","https://openalex.org/W1679367724"],"abstract_inverted_index":{"The":[0],"pathogenesis":[1],"of":[2,11,32,37,56,95,105,120,131,134,155,165,207,209,228,232],"severe":[3],"Plasmodium":[4],"falciparum":[5,17,63],"malaria":[6,138],"involves":[7],"cytoadhesive":[8],"microvascular":[9],"sequestration":[10],"infected":[12],"erythrocytes,":[13],"mediated":[14],"by":[15,27],"P.":[16,62],"erythrocyte":[18],"membrane":[19],"protein":[20],"1":[21,219],"(PfEMP1).":[22],"PfEMP1":[23],"variants":[24],"are":[25,39],"encoded":[26],"the":[28,35,92,108,112,118,121,132,210,226,229],"highly":[29],"polymorphic":[30],"family":[31],"var":[33,51,82,113,135,149,192],"genes,":[34],"sequences":[36],"which":[38,66],"largely":[40],"unknown":[41],"in":[42,60,115,137,148,159,182,201,241],"clinical":[43,61,100],"samples.":[44,220],"Previously,":[45],"we":[46,75],"published":[47],"new":[48,143],"approaches":[49],"for":[50,81,174],"gene":[52,83,150,185,193],"profiling":[53],"and":[54,85,99,123,195,217,244],"classification":[55],"predicted":[57],"binding":[58],"phenotypes":[59],"isolates":[64,101,157],"(),":[65],"represented":[67],"a":[68,78,103],"major":[69],"technical":[70],"advance.":[71],"Building":[72],"on":[73,96,225],"this,":[74],"report":[76],"here":[77],"novel":[79],"method":[80,144],"assembly":[84],"multidimensional":[86],"quantification":[87],"from":[88,169],"RNA-sequencing":[89],"that":[90],"outperforms":[91],"earlier":[93],"approach":[94],"both":[97],"laboratory":[98],"across":[102],"combination":[104],"metrics.":[106],"Importantly,":[107],"tool":[109],"can":[110,124],"interrogate":[111],"transcriptome":[114,122,212],"context":[116],"with":[117,204],"rest":[119],"be":[125],"applied":[126,141],"to":[127,145,158,176,237],"enhance":[128],"our":[129,170],"understanding":[130],"role":[133],"genes":[136],"pathogenesis.":[139],"We":[140],"this":[142],"investigate":[146],"changes":[147,181],"expression":[151,186,206],"through":[152],"early":[153],"transition":[154],"parasite":[156],"vitro":[160],"culture,":[161,202],"using":[162,233],"paired":[163,214],"sets":[164],"ex":[166,215],"vivo":[167,216,242],"samples":[168],"previous":[171],"study,":[172],"cultured":[173,235],"up":[175],"three":[177],"generations.":[178],"In":[179],"parallel,":[180],"non-polymorphic":[183],"core":[184,211],"were":[187,199],"investigated.":[188],"Modest":[189],"but":[190],"unpredictable":[191],"switching":[194],"convergence":[196],"towards":[197],"var2csa":[198],"observed":[200],"along":[203],"differential":[205],"19%":[208],"between":[213],"generation":[218],"Our":[221],"results":[222],"cast":[223],"doubt":[224],"validity":[227],"common":[230],"practice":[231],"short-term":[234],"parasites":[236],"make":[238],"inferences":[239],"about":[240],"phenotype":[243],"behaviour.":[245]},"counts_by_year":[],"updated_date":"2026-10-29T09:56:32.521200","created_date":"2023-12-23T00:00:00"}