{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T21:00:23Z","timestamp":1791234023175,"version":"4.1.0"},"reference-count":56,"publisher":"Frontiers Media SA","content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2017.01418","type":"journal-article","created":{"date-parts":[[2017,8,1]],"date-time":"2017-08-01T23:41:32Z","timestamp":1501630892000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":52,"title":["Human Retrotransposon Insertion Polymorphisms Are Associated with Health and Disease via Gene Regulatory Phenotypes"],"prefix":"10.3389","volume":"8","author":[{"given":"Lu","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily T.","family":"Norris","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I. K.","family":"Jordan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2017,8,2]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1016\/j.molmet.2016.01.002","article-title":"Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes.","volume":"5","author":"Ackermann","year":"2016","journal-title":"Mol. Metab."},{"key":"B2","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation.","volume":"526","author":"Altshuler","year":"2015","journal-title":"Nature"},{"key":"B3","doi-asserted-by":"publisher","first-page":"S9","DOI":"10.1007\/s10875-010-9405-6","article-title":"A novel role for the IgG Fc glycan: the anti-inflammatory activity of sialylated IgG Fcs.","author":"Anthony","year":"2010","journal-title":"J. Clin. Immunol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1016\/0888-7543(91)90414-A","article-title":"A human-specific subfamily of Alu sequences.","volume":"9","author":"Batzer","year":"1991","journal-title":"Genomics"},{"key":"B5","doi-asserted-by":"publisher","first-page":"3619","DOI":"10.1093\/nar\/19.13.3619","article-title":"Amplification dynamics of human-specific (HS) Alu family members.","volume":"19","author":"Batzer","year":"1991","journal-title":"Nucleic Acids Res."},{"key":"B6","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1038\/nature04696","article-title":"A distal enhancer and an ultraconserved exon are derived from a novel retroposon.","volume":"441","author":"Bejerano","year":"2006","journal-title":"Nature"},{"key":"B7","doi-asserted-by":"publisher","first-page":"5280","DOI":"10.1073\/pnas.0831042100","article-title":"Hot L1s account for the bulk of retrotransposition in the human population.","volume":"100","author":"Brouha","year":"2003","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1126\/science.aad5497","article-title":"Regulatory evolution of innate immunity through co-option of endogenous retroviruses.","volume":"351","author":"Chuong","year":"2016","journal-title":"Science"},{"key":"B9","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/nrg.2016.139","article-title":"Regulatory activities of transposable elements: from conflicts to benefits.","volume":"18","author":"Chuong","year":"2017","journal-title":"Nat. Rev. Genet."},{"key":"B10","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1038\/ng.2553","article-title":"Endogenous retroviruses function as species-specific enhancer elements in the placenta.","volume":"45","author":"Chuong","year":"2013","journal-title":"Nat. Genet."},{"key":"B11","doi-asserted-by":"publisher","DOI":"10.3389\/fmolb.2016.00076","article-title":"Patterns of transposable element expression and insertion in cancer.","volume":"3","author":"Clayton","year":"2016","journal-title":"Front. Mol. Biosci."},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1186\/1759-8753-3-15","article-title":"Cell type-specific termination of transcription by transposable element sequences.","volume":"3","author":"Conley","year":"2012","journal-title":"Mob. DNA"},{"key":"B13","doi-asserted-by":"publisher","first-page":"1563","DOI":"10.1093\/bioinformatics\/btn243","article-title":"Retroviral promoters in the human genome.","volume":"24","author":"Conley","year":"2008","journal-title":"Bioinformatics"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002384","article-title":"Repetitive elements may comprise over two-thirds of the human genome.","volume":"7","author":"de Koning","year":"2011","journal-title":"PLoS Genet."},{"key":"B15","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/nmeth.1906","article-title":"ChromHMM: automating chromatin-state discovery and characterization.","volume":"9","author":"Ernst","year":"2012","journal-title":"Nat. Methods"},{"key":"B16","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1038\/nrg2337","article-title":"Transposable elements and the evolution of regulatory networks.","volume":"9","author":"Feschotte","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"B17","doi-asserted-by":"publisher","first-page":"D48","DOI":"10.1093\/nar\/gks1236","article-title":"Ensembl 2013.","volume":"41","author":"Flicek","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-016-0065-9","article-title":"Roles for retrotransposon insertions in human disease.","volume":"7","author":"Hancks","year":"2016","journal-title":"Mob. DNA"},{"key":"B19","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/j.gde.2012.02.006","article-title":"Active human retrotransposons: variation and disease.","volume":"22","author":"Hancks","year":"2012","journal-title":"Curr. Opin. Genet. Dev."},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003504","article-title":"The majority of primate-specific regulatory sequences are derived from transposable elements.","volume":"9","author":"Jacques","year":"2013","journal-title":"PLoS Genet."},{"key":"B21","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1016\/S0168-9525(02)00006-9","article-title":"Origin of a substantial fraction of human regulatory sequences from transposable elements.","volume":"19","author":"Jordan","year":"2003","journal-title":"Trends Genet."},{"key":"B22","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1126\/science.1129594","article-title":"Anti-inflammatory activity of immunoglobulin G resulting from Fc sialylation.","volume":"313","author":"Kaneko","year":"2006","journal-title":"Science"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003470","article-title":"Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.","volume":"9","author":"Kapusta","year":"2013","journal-title":"PLoS Genet."},{"key":"B24","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1038\/332164a0","article-title":"Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man.","volume":"332","author":"Kazazian","year":"1988","journal-title":"Nature"},{"key":"B25","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/ng.600","article-title":"Transposable elements have rewired the core regulatory network of human embryonic stem cells.","volume":"42","author":"Kunarso","year":"2010","journal-title":"Nat. Genet."},{"key":"B26","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome.","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"B27","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/nature12531","article-title":"Transcriptome and genome sequencing uncovers functional variation in humans.","volume":"501","author":"Lappalainen","year":"2013","journal-title":"Nature"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1003225","article-title":"Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.","volume":"9","author":"Lauc","year":"2013","journal-title":"PLoS Genet."},{"key":"B29","doi-asserted-by":"publisher","first-page":"D896","DOI":"10.1093\/nar\/gkw1133","article-title":"The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).","volume":"45","author":"MacArthur","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B30","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1159\/000084965","article-title":"Transposable elements donate lineage-specific regulatory sequences to host genomes.","volume":"110","author":"Marino-Ramirez","year":"2005","journal-title":"Cytogenet. Genome Res."},{"key":"B31","doi-asserted-by":"publisher","first-page":"660","DOI":"10.1126\/science.aaa0355","article-title":"Human genomics. The human transcriptome across tissues and individuals.","volume":"348","author":"Mele","year":"2015","journal-title":"Science"},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms7644","article-title":"A family of transposable elements co-opted into developmental enhancers in the mouse neocortex.","volume":"6","author":"Notwell","year":"2015","journal-title":"Nat. Commun."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1444","DOI":"10.1086\/380207","article-title":"SVA elements are nonautonomous retrotransposons that cause disease in humans.","volume":"73","author":"Ostertag","year":"2003","journal-title":"Am. J. Hum. Genet."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1853","DOI":"10.2337\/db14-0732","article-title":"Genetic variants associated with quantitative glucose homeostasis traits translate to type 2 diabetes in Mexican Americans: the GUARDIAN (genetics underlying diabetes in Hispanics) consortium.","volume":"64","author":"Palmer","year":"2015","journal-title":"Diabetes"},{"key":"B35","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/S0378-1119(01)00645-X","article-title":"Similar integration but different stability of Alus and LINEs in the human genome.","volume":"276","author":"Pavlicek","year":"2001","journal-title":"Gene"},{"key":"B36","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1534\/genetics.107.072553","article-title":"Origin and evolution of human microRNAs from transposable elements.","volume":"176","author":"Piriyapongsa","year":"2007","journal-title":"Genetics"},{"key":"B37","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1677\/JOE-08-0290","article-title":"Physiology of the pancreatic alpha-cell and glucagon secretion: role in glucose homeostasis and diabetes.","volume":"199","author":"Quesada","year":"2008","journal-title":"J. Endocrinol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1146\/annurev-genet-110711-155621","article-title":"Transposable elements: an abundant and natural source of regulatory sequences for host genes.","volume":"46","author":"Rebollo","year":"2012","journal-title":"Annu. Rev. Genet."},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbw072","article-title":"Benchmarking computational tools for polymorphic transposable element detection.","author":"Rishishwar","year":"2016","journal-title":"Brief. Bioinform."},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1186\/s13100-015-0052-6","article-title":"Transposable element polymorphisms recapitulate human evolution.","volume":"6","author":"Rishishwar","year":"2015","journal-title":"Mob. DNA"},{"key":"B41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1080\/2159256X.2017.1280116","article-title":"Population and clinical genetics of human transposable elements in the (post) genomic era.","volume":"7","author":"Rishishwar","year":"2017","journal-title":"Mob. Genet. Elements"},{"key":"B42","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1126\/science.1261877","article-title":"Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.","volume":"348","author":"Rivas","year":"2015","journal-title":"Science"},{"key":"B43","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1038\/nature14248","article-title":"Integrative analysis of 111 reference human epigenomes.","volume":"518","author":"Roadmap Epigenomics","year":"2015","journal-title":"Nature"},{"key":"B44","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1016\/j.cell.2011.11.058","article-title":"Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.","volume":"148","author":"Schmidt","year":"2012","journal-title":"Cell"},{"key":"B45","doi-asserted-by":"publisher","first-page":"1353","DOI":"10.1093\/bioinformatics\/bts163","article-title":"Matrix eQTL: ultra fast eQTL analysis via large matrix operations.","volume":"28","author":"Shabalin","year":"2012","journal-title":"Bioinformatics"},{"key":"B46","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1038\/nprot.2011.457","article-title":"Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.","volume":"7","author":"Stegle","year":"2012","journal-title":"Nat. Protoc."},{"key":"B47","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2,504 human genomes.","volume":"526","author":"Sudmant","year":"2015","journal-title":"Nature"},{"key":"B48","doi-asserted-by":"publisher","first-page":"1963","DOI":"10.1101\/gr.168872.113","article-title":"Widespread contribution of transposable elements to the innovation of gene regulatory networks.","volume":"24","author":"Sundaram","year":"2014","journal-title":"Genome Res."},{"key":"B49","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1038\/nbt.2702","article-title":"Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.","volume":"31","author":"t Hoen","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"994","DOI":"10.1016\/j.jmb.2005.09.085","article-title":"SVA elements: a hominid-specific retroposon family.","volume":"354","author":"Wang","year":"2005","journal-title":"J. Mol. Biol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"E4428","DOI":"10.1073\/pnas.1507253112","article-title":"MIR retrotransposon sequences provide insulators to the human genome.","volume":"112","author":"Wang","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B52","doi-asserted-by":"publisher","first-page":"2318","DOI":"10.1093\/nar\/gkw1286","article-title":"Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements.","volume":"45","author":"Wang","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B53","doi-asserted-by":"publisher","first-page":"3028","DOI":"10.2337\/db16-0405","article-title":"Single-Cell transcriptomics of the human endocrine pancreas.","volume":"65","author":"Wang","year":"2016","journal-title":"Diabetes"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.0020205","article-title":"Mammalian small nucleolar RNAs are mobile genetic elements.","volume":"2","author":"Weber","year":"2006","journal-title":"PLoS Genet."},{"key":"B55","doi-asserted-by":"publisher","first-page":"E2326","DOI":"10.1073\/pnas.1602336113","article-title":"Discovery of unfixed endogenous retrovirus insertions in diverse human populations.","volume":"113","author":"Wildschutte","year":"2016","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bav124","article-title":"CCSI: a database providing chromatin-chromatin spatial interaction information.","volume":"2016","author":"Xie","year":"2016","journal-title":"Database"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fmicb.2017.01418\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,8,1]],"date-time":"2017-08-01T23:41:35Z","timestamp":1501630895000},"score":1,"resource":{"primary":{"URL":"http:\/\/journal.frontiersin.org\/article\/10.3389\/fmicb.2017.01418\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,2]]},"references-count":56,"alternative-id":["10.3389\/fmicb.2017.01418"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2017.01418","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,8,2]]},"article-number":"1418"}}