{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T11:43:08Z","timestamp":1791546188258,"version":"4.3.4"},"reference-count":44,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2015,4,13]],"date-time":"2015-04-13T00:00:00Z","timestamp":1428883200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0124473","type":"journal-article","created":{"date-parts":[[2015,4,15]],"date-time":"2015-04-15T18:57:09Z","timestamp":1429124229000},"page":"e0124473","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":38,"title":["Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features"],"prefix":"10.1371","volume":"10","author":[{"given":"Abhinay","family":"Ramaprasad","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tobias","family":"Mourier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raeece","family":"Naeem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tareq B.","family":"Malas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ehab","family":"Moussa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aswini","family":"Panigrahi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah J.","family":"Vermont","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas D.","family":"Otto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Wastling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnab","family":"Pain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2015,4,13]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1093\/aje\/154.4.357","article-title":"Toxoplasma gondii infection in the United States: seroprevalence and risk factors","volume":"154","author":"JL Jones","year":"2001","journal-title":"Am J Epidemiol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.ijpara.2003.12.009","article-title":"Toxoplasma gondii: the model apicomplexan","volume":"34","author":"K Kim","year":"2004","journal-title":"Int J Parasitol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1016\/S0020-7519(99)00093-4","article-title":"Towards evaluating the economic impact of bovine neosporosis","volume":"29","author":"AJ Trees","year":"1999","journal-title":"Int J Parasitol"},{"key":"ref4","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1002567","article-title":"Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy","volume":"8","author":"A Reid","year":"2012","journal-title":"PLoS pathogens"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"D553","DOI":"10.1093\/nar\/gkm981","article-title":"ToxoDB: an integrated Toxoplasma gondii database resource","volume":"36","author":"B Gajria","year":"2008","journal-title":"Nucleic acids research"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.1093\/bioinformatics\/bth315","article-title":"TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders","volume":"20","author":"WH Majoros","year":"2004","journal-title":"Bioinformatics"},{"issue":"Suppl 1","key":"ref7","doi-asserted-by":"crossref","first-page":"S140","DOI":"10.1093\/bioinformatics\/17.suppl_1.S140","article-title":"Integrating genomic homology into gene structure prediction","volume":"17","author":"I Korf","year":"2001","journal-title":"Bioinformatics"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/1471-2105-5-59","article-title":"Gene finding in novel genomes","volume":"5","author":"I Korf","year":"2004","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 2","key":"ref9","doi-asserted-by":"crossref","first-page":"ii215","DOI":"10.1093\/bioinformatics\/btg1080","article-title":"Gene prediction with a hidden Markov model and a new intron submodel","volume":"19","author":"M Stanke","year":"2003","journal-title":"Bioinformatics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"3596","DOI":"10.1093\/bioinformatics\/bti609","article-title":"JIGSAW: integration of multiple sources of evidence for gene prediction","volume":"21","author":"JE Allen","year":"2005","journal-title":"Bioinformatics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/1471-2105-7-62","article-title":"Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources","volume":"7","author":"M Stanke","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"5654","DOI":"10.1093\/nar\/gkg770","article-title":"Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies","volume":"31","author":"BJ Haas","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1186\/1471-2164-13-696","article-title":"De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs","volume":"13","author":"MA Hassan","year":"2012","journal-title":"BMC Genomics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/S0020-7519(01)00308-3","article-title":"Characterisation of global protein expression by two-dimensional electrophoresis and mass spectrometry: proteomics of Toxoplasma gondii","volume":"32","author":"AM Cohen","year":"2002","journal-title":"Int J Parasitol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"R56","DOI":"10.1186\/gb-2012-13-6-r56","article-title":"Toward almost closed genomes with GapFiller","volume":"13","author":"M Boetzer","year":"2012","journal-title":"Genome biology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1704","DOI":"10.1093\/bioinformatics\/btq269","article-title":"Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology","volume":"26","author":"TD Otto","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"R47","DOI":"10.1186\/gb-2013-14-5-r47","article-title":"REAPR: a universal tool for genome assembly evaluation","volume":"14","author":"M Hunt","year":"2013","journal-title":"Genome biology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1093\/nar\/gkq1268","article-title":"RATT: Rapid Annotation Transfer Tool","volume":"39","author":"TD Otto","year":"2011","journal-title":"Nucleic acids research"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"D Kim","year":"2013","journal-title":"Genome Biol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with RNA-seq","volume":"31","author":"C Trapnell","year":"2013","journal-title":"Nat Biotechnol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"R116","DOI":"10.1186\/gb-2008-9-7-r116","article-title":"The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation","volume":"9","author":"D Xia","year":"2008","journal-title":"Genome Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1093\/bioinformatics\/16.10.944","article-title":"Artemis: sequence visualization and annotation","volume":"16","author":"K Rutherford","year":"2000","journal-title":"Bioinformatics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"3422","DOI":"10.1093\/bioinformatics\/bti553","article-title":"ACT: the Artemis Comparison Tool","volume":"21","author":"TJ Carver","year":"2005","journal-title":"Bioinformatics"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1093\/bioinformatics\/17.9.847","article-title":"InterProScan\u2014an integration platform for the signature-recognition methods in InterPro","volume":"17","author":"EM Zdobnov","year":"2001","journal-title":"Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"2529","DOI":"10.1101\/gr.140475.112","article-title":"Long noncoding RNAs in C. elegans","volume":"22","author":"JW Nam","year":"2012","journal-title":"Genome Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkm391","article-title":"CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine","volume":"35","author":"L Kong","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkt1223","article-title":"Pfam: the protein families database","volume":"42","author":"RD Finn","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"ref28","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2002-3-3-reviews0004","article-title":"Untranslated regions of mRNAs","volume":"3","author":"F Mignone","year":"2002","journal-title":"Genome Biol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"4607","DOI":"10.1093\/nar\/gkf600","article-title":"The malaria parasite Plasmodium falciparum encodes members of the Puf RNA-binding protein family with conserved RNA binding activity","volume":"30","author":"L Cui","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1016\/S0020-7519(02)00096-6","article-title":"Toxoplasma gondii eukaryotic translation initiation factor 4A associated with tachyzoite virulence is down-regulated in the bradyzoite stage","volume":"32","author":"MH Gastens","year":"2002","journal-title":"Int J Parasitol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1093\/nar\/gkm1142","article-title":"A conserved U-rich RNA region implicated in regulation of translation in Plasmodium female gametocytes","volume":"36","author":"JA Braks","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"R128","DOI":"10.1186\/gb-2013-14-11-r128","article-title":"Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum","volume":"14","author":"EM Bunnik","year":"2013","journal-title":"Genome Biol"},{"key":"ref33","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.04106","article-title":"Genome-wide regulatory dynamics of translation in the asexual blood stages","volume":"3","author":"F Caro","year":"2014","journal-title":"Elife"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1186\/1741-7007-3-26","article-title":"The transcriptome of Toxoplasma gondii","volume":"3","author":"JR Radke","year":"2005","journal-title":"BMC Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1645\/GE-2864.1","article-title":"Characterization of Toxoplasma gondii 5&apos; UTR with encyclopedic TSS information","volume":"98","author":"J Yamagishi","year":"2012","journal-title":"J Parasitol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"e77","DOI":"10.1371\/journal.ppat.0030077","article-title":"Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii","volume":"3","author":"M Gissot","year":"2007","journal-title":"PLoS Pathog"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.molbiopara.2004.02.007","article-title":"Widespread distribution of antisense transcripts in the Plasmodium falciparum genome","volume":"136","author":"AM Gunasekera","year":"2004","journal-title":"Mol Biochem Parasitol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nrg2521","article-title":"Long non-coding RNAs: insights into functions","volume":"10","author":"TR Mercer","year":"2009","journal-title":"Nat Rev Genet"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1093\/gbe\/evs020","article-title":"Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome","volume":"4","author":"RS Young","year":"2012","journal-title":"Genome Biol Evol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1101\/gr.133009.111","article-title":"Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis","volume":"22","author":"A Pauli","year":"2012","journal-title":"Genome Res"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"7529","DOI":"10.1093\/nar\/gkr501","article-title":"Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes","volume":"39","author":"S Jung","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1128\/EC.00147-06","article-title":"A novel class of developmentally regulated noncoding RNAs in Leishmania","volume":"5","author":"C Dumas","year":"2006","journal-title":"Eukaryot Cell"},{"key":"ref43","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":"ref44","doi-asserted-by":"crossref","first-page":"R56","DOI":"10.1186\/gb-2011-12-6-r56","article-title":"A global transcriptional analysis of Plasmodium falciparum malaria reveals a novel family of telomere-associated lncRNAs","volume":"12","author":"KM Broadbent","year":"2011","journal-title":"Genome Biol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0124473","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T00:38:50Z","timestamp":1588984730000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0124473"}},"subtitle":[],"editor":[{"given":"Ira J","family":"Blader","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2015,4,13]]},"references-count":44,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2015,4,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0124473","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,4,13]]}}}