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Notes"},{"key":"pgen.1008917.ref072","doi-asserted-by":"crossref","first-page":"e1003118","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for Computing and Annotating Genomic Ranges","volume":"9","author":"M Lawrence","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"pgen.1008917.ref073","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1093\/bioinformatics\/btp328","article-title":"rtracklayer: an R package for interfacing with genome browsers","volume":"25","author":"M Lawrence","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1008917.ref074","doi-asserted-by":"crossref","first-page":"2110","DOI":"10.1093\/nar\/gkv1214","article-title":"The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences","volume":"44","author":"PR Kensche","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"pgen.1008917.ref075","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1093\/bioinformatics\/btt756","article-title":"CGAT: Computational genomics analysis toolkit","volume":"30","author":"D Sims","year":"2014","journal-title":"Bioinformatics"},{"key":"pgen.1008917.ref076","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.exppara.2004.11.012","article-title":"An alternative method for Plasmodium culture synchronization","volume":"109","author":"J Leli\u00e8vre","year":"2005","journal-title":"Exp Parasitol"},{"key":"pgen.1008917.ref077","doi-asserted-by":"crossref","first-page":"418","DOI":"10.2307\/3280287","article-title":"Synchronization of Plasmodium falciparum erythrocytic stages in culture","volume":"65","author":"C Lambros","year":"1979","journal-title":"J Parasitol"},{"key":"pgen.1008917.ref078","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1073\/pnas.92.4.973","article-title":"Transfection of Plasmodium falciparum within human red blood cells","volume":"92","author":"Y Wu","year":"1995","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pgen.1008917.ref079","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1261\/rna.1080109","article-title":"Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum","volume":"15","author":"C Epp","year":"2009","journal-title":"RNA"},{"key":"pgen.1008917.ref080","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1046\/j.1365-2958.2003.03570.x","article-title":"Selective upregulation of a single distinctly structured var gene in chondroitin sulphate A-adhering Plasmodium falciparum involved in pregnancy-associated malaria","volume":"49","author":"A Salanti","year":"2003","journal-title":"Mol Microbiol"},{"key":"pgen.1008917.ref081","doi-asserted-by":"crossref","first-page":"e22","DOI":"10.1371\/journal.ppat.0020022","article-title":"Mutually Exclusive Expression of Virulence Genes by Malaria Parasites Is Regulated Independently of Antigen Production","volume":"2","author":"R Dzikowski","year":"2006","journal-title":"PLoS Pathog"},{"key":"pgen.1008917.ref082","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1186\/1471-2164-15-150","article-title":"Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum","volume":"15","author":"TN Siegel","year":"2014","journal-title":"BMC Genomics"},{"key":"pgen.1008917.ref083","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1008917.ref084","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion 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