{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T04:22:07Z","timestamp":1781756527933,"version":"3.54.5"},"reference-count":45,"publisher":"Oxford University Press (OUP)","funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["10.13039\/100000002"],"award-info":[{"award-number":["10.13039\/100000002"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1542597"],"award-info":[{"award-number":["1542597"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Following the completion of the genome sequencing and gene prediction of Mnemiopsis leidyi, a lobate ctenophore that is native to the coastal waters of the western Atlantic Ocean, we developed and implemented the Mnemiopsis Genome Project Portal (MGP Portal), a comprehensive Web-based data portal for navigating the genome sequence and gene annotations. In the years following the first release of the MGP Portal, it has become evident that the inclusion of data from significant published studies on Mnemiopsis has been critical to its adoption as the centralized resource for this emerging model organism. With this most recent update, the Portal has significantly expanded to include in situ images, temporal developmental expression profiles and single-cell expression data. Recent enhancements also include implementations of an updated BLAST interface, new graphical visualization tools and updates to gene pages that integrate all new data types.<\/jats:p>\n               <jats:p>Database URL: https:\/\/research.nhgri.nih.gov\/mnemiopsis\/<\/jats:p>","DOI":"10.1093\/database\/baaa029","type":"journal-article","created":{"date-parts":[[2020,3,31]],"date-time":"2020-03-31T19:13:17Z","timestamp":1585681997000},"source":"Crossref","is-referenced-by-count":27,"title":["The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization"],"prefix":"10.1093","volume":"2020","author":[{"given":"R Travis","family":"Moreland","sequence":"first","affiliation":[{"name":"Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anh-Dao","family":"Nguyen","sequence":"first","affiliation":[{"name":"Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph F","family":"Ryan","sequence":"first","affiliation":[{"name":"Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL 32080, USA"},{"name":"Department of Biology, University of Florida, Gainesville, FL 32611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas D","family":"Baxevanis","sequence":"first","affiliation":[{"name":"Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,5,9]]},"reference":[{"issue":"6164","key":"2020050912375052900_ref1","doi-asserted-by":"crossref","first-page":"1242592","DOI":"10.1126\/science.1242592","article-title":"The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution","volume":"342","author":"Ryan","year":"2013","journal-title":"Science"},{"issue":"7188","key":"2020050912375052900_ref2","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/nature06614","article-title":"Broad phylogenomic sampling improves resolution of the animal tree of life","volume":"452","author":"Dunn","year":"2008","journal-title":"Nature"},{"issue":"1677","key":"2020050912375052900_ref3","doi-asserted-by":"crossref","first-page":"4261","DOI":"10.1098\/rspb.2009.0896","article-title":"Assessing the root of bilaterian animals with scalable phylogenomic methods","volume":"276","author":"Hejnol","year":"2009","journal-title":"Proc. Biol. Sci."},{"issue":"7503","key":"2020050912375052900_ref4","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/nature13400","article-title":"The ctenophore genome and the evolutionary origins of neural systems","volume":"510","author":"Moroz","year":"2014","journal-title":"Nature"},{"issue":"48","key":"2020050912375052900_ref5","doi-asserted-by":"crossref","first-page":"14912","DOI":"10.1073\/pnas.1511468112","article-title":"Genomic insights into the evolutionary origin of Myxozoa with Cnidaria","volume":"112","author":"Chang","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"issue":"18","key":"2020050912375052900_ref6","doi-asserted-by":"crossref","first-page":"5773","DOI":"10.1073\/pnas.1503453112","article-title":"Error, signal, and the placement of Ctenophora sister to all other animals","volume":"112","author":"Whelan","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020050912375052900_ref7","first-page":"1","article-title":"Phylotranscriptomics reveals ancient and convergent features in Corallochytrium and Ministeria (Holozoa, Opisthokonta)!","volume":"75","author":"Torruella","year":"2014","journal-title":"Phylogeny and evolutionary perspective of Opisthokonta protists"},{"key":"2020050912375052900_ref8","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1186\/s12864-015-2146-4","article-title":"Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa","volume":"16","author":"Borowiec","year":"2015","journal-title":"BMC Genom."},{"issue":"2","key":"2020050912375052900_ref9","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/s41559-016-0020","article-title":"Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life","volume":"1","author":"Arcila","year":"2017","journal-title":"Nat. Ecol. Evol."},{"issue":"11","key":"2020050912375052900_ref10","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1038\/s41559-017-0331-3","article-title":"Ctenophore relationships and their placement as the sister group to all other animals","volume":"1","author":"Whelan","year":"2017","journal-title":"Nat. Ecol. Evol."},{"issue":"5","key":"2020050912375052900_ref11","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/s41559-017-0126","article-title":"Contentious relationships in phylogenomic studies can be driven by a handful of genes","volume":"1","author":"Shen","year":"2017","journal-title":"Nat. Ecol. Evol."},{"issue":"1906","key":"2020050912375052900_ref12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1098\/rspb.2019.0831","article-title":"Revisiting metazoan phylogeny with genomic sampling of all phyla","volume":"286","author":"Laumer","year":"2019","journal-title":"Proc. Biol. Sci."},{"issue":"3","key":"2020050912375052900_ref13","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1093\/gbe\/evz043","article-title":"The draft genome of an Octocoral, Dendronephthya gigantea","volume":"11","author":"Jeon","year":"2019","journal-title":"Genome. Biol. Evol."},{"issue":"1","key":"2020050912375052900_ref14","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/s12915-019-0643-7","article-title":"The genome of the giant Nomura\u2019s jellyfish sheds light on the early evolution of active predation","volume":"17","author":"Kim","year":"2019","journal-title":"BMC Biol"},{"issue":"8","key":"2020050912375052900_ref15","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1016\/j.cub.2009.02.052","article-title":"Phylogenomics revives traditional views on deep animal relationships","volume":"19","author":"Philippe","year":"2009","journal-title":"Curr. Biol."},{"issue":"9","key":"2020050912375052900_ref16","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1093\/molbev\/msq089","article-title":"Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships","volume":"27","author":"Pick","year":"2010","journal-title":"Mol. Biol. Evol."},{"issue":"1","key":"2020050912375052900_ref17","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.ympev.2013.01.010","article-title":"Deep metazoan phylogeny: when different genes tell different stories","volume":"67","author":"Nosenko","year":"2013","journal-title":"Mol. Phylogenet. Evol."},{"issue":"50","key":"2020050912375052900_ref18","doi-asserted-by":"crossref","first-page":"15402","DOI":"10.1073\/pnas.1518127112","article-title":"Genomic data do not support comb jellies as the sister group to all other animals","volume":"112","author":"Pisani","year":"2015","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"7","key":"2020050912375052900_ref19","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1016\/j.cub.2017.02.031","article-title":"A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals","volume":"27","author":"Simion","year":"2017","journal-title":"Curr. Biol."},{"issue":"24","key":"2020050912375052900_ref20","doi-asserted-by":"crossref","first-page":"3864","DOI":"10.1016\/j.cub.2017.11.008","article-title":"Improved modeling of compositional heterogeneity supports sponges as sister to all other animals","volume":"27","author":"Feuda","year":"2017","journal-title":"Curr. Biol."},{"issue":"5","key":"2020050912375052900_ref21","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1038\/s41559-019-0833-2","article-title":"The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle","volume":"3","author":"Leclere","year":"2019","journal-title":"Nat. Ecol. Evol."},{"issue":"4","key":"2020050912375052900_ref22","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1093\/molbev\/msz013","article-title":"The role of homology and orthology in the phylogenomic analysis of metazoan gene content","volume":"36","author":"Pett","year":"2019","journal-title":"Mol. Biol. Evol."},{"issue":"212","key":"2020050912375052900_ref23","first-page":"1","article-title":"Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals","volume":"14","author":"Maxwell","year":"2014","journal-title":"BMC Evol. Biol."},{"issue":"5","key":"2020050912375052900_ref24","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1186\/gb-2011-12-5-115","article-title":"In praise of model organisms","volume":"12","author":"Petsko","year":"2011","journal-title":"Genome. Biol."},{"key":"2020050912375052900_ref25","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1186\/1471-2164-15-316","article-title":"A customized web portal for the genome of the ctenophore Mnemiopsis leidyi","volume":"15","author":"Moreland","year":"2014","journal-title":"BMC Genomics."},{"issue":"1","key":"2020050912375052900_ref26","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s12862-019-1360-0","article-title":"Taxon-specific expansion and loss of tektins inform metazoan ciliary diversity","volume":"19","author":"Bastin","year":"2019","journal-title":"BMC Evol. Biol"},{"key":"2020050912375052900_ref27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7717\/peerj.5067","article-title":"Horizontally transferred genes in the ctenophore Mnemiopsis leidyi","volume":"6","author":"Hernandez","year":"2018","journal-title":"PeerJ."},{"issue":"11","key":"2020050912375052900_ref28","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1002\/mrd.22926","article-title":"The maternal-zygotic transition and zygotic activation of the Mnemiopsis leidyi genome occurs within the first three cleavage cycles","volume":"84","author":"Davidson","year":"2017","journal-title":"Mol. Reprod. Dev."},{"issue":"6","key":"2020050912375052900_ref29","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/gbe\/evx106","article-title":"Evolution of miRNA tailing by 3\u2019 terminal uridylyl transferases in metazoa","volume":"9","author":"Modepalli","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"2020050912375052900_ref30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7717\/peerj.1846","article-title":"The sex lives of ctenophores: the influence of light, body size, and self-fertilization on the reproductive output of the sea walnut, Mnemiopsis leidyi","volume":"4","author":"Sasson","year":"2016","journal-title":"PeerJ."},{"issue":"9","key":"2020050912375052900_ref31","doi-asserted-by":"crossref","first-page":"2367","DOI":"10.1093\/molbev\/msv117","article-title":"Dynamic and widespread lncRNA expression in a sponge and the origin of animal complexity","volume":"32","author":"Gaiti","year":"2015","journal-title":"Mol. Biol. Evol."},{"issue":"7596","key":"2020050912375052900_ref32","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nature16994","article-title":"The mid-developmental transition and the evolution of animal body plans","volume":"531","author":"Levin","year":"2016","journal-title":"Nature"},{"issue":"1","key":"2020050912375052900_ref33","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene expression omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"2020050912375052900_ref34","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1016\/j.celrep.2012.08.003","article-title":"CEL-Seq: single-cell RNA-seq by multiplexed linear amplification","volume":"2","author":"Hashimshony","year":"2012","journal-title":"Cell Rep."},{"key":"2020050912375052900_ref35","author":"Sielen","year":"2018"},{"issue":"7","key":"2020050912375052900_ref36","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1038\/s41559-018-0575-6","article-title":"Early metazoan cell type diversity and the evolution of multicellular gene regulation","volume":"2","author":"Sebe-Pedros","year":"2018","journal-title":"Nat. Ecol. Evol."},{"key":"2020050912375052900_ref37","first-page":"206, 1","article-title":"MetaCell: analysis of single cell RNA-seq data using K-nn graph partitions","volume-title":"Genome Biology","author":"Baran","year":"2019"},{"issue":"12","key":"2020050912375052900_ref38","first-page":"2940","article-title":"Integrating embryonic development and evolutionary history to characterize tentacle-specific cell types in a ctenophore","volume":"35","author":"Babonis","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"2020050912375052900_ref39","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/s13227-016-0051-9","article-title":"Developmental expression of \u201cgermline\u201d - and \u201csex determination\u201d-related genes in the ctenophore Mnemiopsis leidyi","volume":"7","author":"Reitzel","year":"2016","journal-title":"Evodevo."},{"key":"2020050912375052900_ref40","first-page":"2922","article-title":"Sequenceserver: a modern graphical user interface for custom BLAST databases","volume-title":"Mol. Biol. Evol.","author":"Priyam","year":"2019"},{"key":"2020050912375052900_ref41","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/s","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol."},{"issue":"4","key":"2020050912375052900_ref42","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. Methods."},{"issue":"3","key":"2020050912375052900_ref43","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"2020050912375052900_ref44","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.24176.029","article-title":"Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues","author":"Fidler","year":"2017","journal-title":"elife"},{"issue":"6","key":"2020050912375052900_ref45","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1007\/s00427-008-0222-3","article-title":"Developmental expression of homeobox genes in the ctenophore Mnemiopsis leidyi","volume":"218","author":"Pang","year":"2008","journal-title":"Dev. Genes Evol."}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa029\/33195662\/baaa029.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baaa029\/33195662\/baaa029.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T16:38:34Z","timestamp":1589042314000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baaa029\/5834871"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,1]]},"references-count":45,"URL":"https:\/\/doi.org\/10.1093\/database\/baaa029","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020]]},"published":{"date-parts":[[2020,1,1]]},"article-number":"baaa029"}}