{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T09:44:59Z","timestamp":1789465499445,"version":"build-2803163510"},"reference-count":152,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":80,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R03AG070474"],"award-info":[{"award-number":["R03AG070474"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R21AG077643"],"award-info":[{"award-number":["R21AG077643"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R21AG089851"],"award-info":[{"award-number":["R21AG089851"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R21NS133823"],"award-info":[{"award-number":["R21NS133823"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01NS123571"],"award-info":[{"award-number":["R01NS123571"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1U19NS130607"],"award-info":[{"award-number":["1U19NS130607"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 NS041021"],"award-info":[{"award-number":["R01 NS041021"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Franklin College of Art and Sciences and the Cellular Biology Department"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Genomic DNA encodes regulatory information that determines where, when, and to what extent genes are expressed. Theoretically, we should be able to identify these transcriptional \u201cinstructions\u201d by examining genomic DNA sequence alone, yet this has remained challenging. Here we present the\u00a0Vertebrate Regulatory MOdule Detector (VRMOD), a method that accurately predicts gene regulatory sequences using only the query genomic sequences. We applied VRMOD to 309 Ensembl genomes, generating a compendium of high-resolution, genome-position-fixed cis-regulatory modules without parameter tuning. We performed extensive computational evaluation and experimental validation of VRMOD predictions. Notably, VRMOD predicted three sub-enhancers within the human hs52 enhancer at the FTO locus from the VISTA database, including one missed by existing methods. Using a chicken embryo system and 3D tissue imaging, we showed that each sub-enhancer exhibits restricted spatiotemporal activity within specific subsets of tissues where the full enhancer is active. We further demonstrated VRMOD\u2019s utility for identifying evolutionarily non-conserved enhancers, annotating regulatory sequences in non-model organisms, and identifying candidate disease-causal variants. Collectively, VRMOD provides a universal coordinate reference system for regulatory sequences across 309 vertebrate genomes and enables genome-wide annotation of non-coding regulatory elements in any vertebrate species using genomic sequence alone.<\/jats:p>","DOI":"10.1093\/nargab\/lqag107","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T08:25:01Z","timestamp":1789460701000},"source":"Crossref","is-referenced-by-count":0,"title":["Unlocking\n                    <i>cis<\/i>\n                    -regulatory landscapes across 500 million years of evolution and disease mechanisms"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2929-9686","authenticated-orcid":false,"given":"T\u00e1ssia","family":"Mangetti\u00a0Gon\u00e7alves","sequence":"first","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-9409-218X","authenticated-orcid":false,"given":"Casey L","family":"Stewart","sequence":"additional","affiliation":[{"name":"Department of Cellular Biology, University of Georgia , Athens, GA 30602 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha D","family":"Baxley","sequence":"additional","affiliation":[{"name":"Department of Cellular Biology, University of Georgia , Athens, GA 30602 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Missouri University of Science & Technology , Rolla, MO 65409 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin","family":"Boyer","sequence":"additional","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2591-5533","authenticated-orcid":false,"given":"Bijesh","family":"George","sequence":"additional","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7492-3703","authenticated-orcid":false,"given":"Daofeng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4577-5590","authenticated-orcid":false,"given":"Chengran","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harrison W","family":"Gabel","sequence":"additional","affiliation":[{"name":"Department of Neuroscience, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianhua","family":"Piao","sequence":"additional","affiliation":[{"name":"Division of Neonatology, Department of Pediatrics, University of California , San Francisco, CA 94143,","place":["United States"]},{"name":"Newborn Brain Research Institute, University of California , San Francisco, CA 94143,","place":["United States"]},{"name":"Weill Institute for Neuroscience, University of California , San Francisco, CA 94143,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5261-689X","authenticated-orcid":false,"given":"Carlos","family":"Cruchaga","sequence":"additional","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]},{"name":"Department of Psychiatry, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]},{"name":"Department of Neurology, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6997-6018","authenticated-orcid":false,"given":"Yang E","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]},{"name":"Department of Neurosurgery, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]},{"name":"The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5826-0134","authenticated-orcid":false,"given":"Oshri","family":"Avraham","sequence":"additional","affiliation":[{"name":"Department of Cellular Biology, University of Georgia , Athens, GA 30602 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5615-6774","authenticated-orcid":false,"given":"Guoyan","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Genetics, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]},{"name":"Department of Neurology, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]},{"name":"Department of Pathology and Immunology, Washington University School of Medicine , St. Louis, MO 63110 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,15]]},"reference":[{"key":"2026091504194087300_B1","volume-title":"Molecular Biology of the Gene.","author":"Watson","year":"2008"},{"key":"2026091504194087300_B2","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1002\/wdev.168","article-title":"Identifying transcriptional cis-regulatory modules in animal genomes","volume":"4","author":"Suryamohan","year":"2015","journal-title":"Wiley Interdiscip Rev Dev Biol"},{"key":"2026091504194087300_B3","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.tig.2018.11.004","article-title":"Studying transcriptional enhancers: the founder fallacy, validation creep, and other biases","volume":"35","author":"Halfon","year":"2019","journal-title":"Trends Genet"},{"key":"2026091504194087300_B4","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1038\/s41576-022-00509-1","article-title":"Characterizing cis-regulatory elements using single-cell epigenomics","volume":"24","author":"Preissl","year":"2023","journal-title":"Nat Rev Genet"},{"key":"2026091504194087300_B5","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1146\/annurev.biophys.35.040405.102002","article-title":"Gene regulation: gene control network in development","volume":"36","author":"Ben-Tabou\u00a0de-Leon","year":"2007","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"2026091504194087300_B6","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1242\/dev.124.10.1851","article-title":"The hardwiring of development: organization and function of genomic regulatory systems","volume":"124","author":"Arnone","year":"1997","journal-title":"Development"},{"key":"2026091504194087300_B7","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1016\/0092-8674(95)90136-1","article-title":"Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome","volume":"83","author":"Thanos","year":"1995","journal-title":"Cell"},{"key":"2026091504194087300_B8","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1016\/j.devcel.2021.02.016","article-title":"Enhancer grammar in development, evolution, and disease: dependencies and interplay","volume":"56","author":"Jindal","year":"2021","journal-title":"Dev Cell"},{"key":"2026091504194087300_B9","doi-asserted-by":"publisher","first-page":"1134","DOI":"10.1126\/science.8178172","article-title":"Short-range DNA looping by the Xenopus HMG-box transcription factor, xUBF","volume":"264","author":"Bazett-Jones","year":"1994","journal-title":"Science"},{"key":"2026091504194087300_B10","doi-asserted-by":"publisher","first-page":"6569","DOI":"10.1242\/dev.00890","article-title":"Information display by transcriptional enhancers","volume":"130","author":"Kulkarni","year":"2003","journal-title":"Development"},{"key":"2026091504194087300_B11","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1016\/j.cell.2012.01.030","article-title":"A transcription factor collective defines cardiac cell fate and reflects lineage history","volume":"148","author":"Junion","year":"2012","journal-title":"Cell"},{"key":"2026091504194087300_B12","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1038\/nrg3682","article-title":"Transcriptional enhancers: from properties to genome-wide predictions","volume":"15","author":"Shlyueva","year":"2014","journal-title":"Nat Rev Genet"},{"key":"2026091504194087300_B13","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1038\/nrg3684","article-title":"In pursuit of design principles of regulatory sequences","volume":"15","author":"Levo","year":"2014","journal-title":"Nat Rev Genet"},{"key":"2026091504194087300_B14","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1016\/j.tibs.2014.07.002","article-title":"Absence of a simple code: how transcription factors read the genome","volume":"39","author":"Slattery","year":"2014","journal-title":"Trends Biochem Sci"},{"key":"2026091504194087300_B15","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1016\/j.molcel.2022.12.032","article-title":"Deciphering the multi-scale, quantitative cis-regulatory code","volume":"83","author":"Kim","year":"2023","journal-title":"Mol Cell"},{"key":"2026091504194087300_B16","doi-asserted-by":"publisher","first-page":"D88","DOI":"10.1093\/nar\/gkl822","article-title":"VISTA Enhancer Browser: a database of tissue-specific human enhancers","volume":"35","author":"Visel","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B17","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/bs.adgen.2016.08.004","article-title":"The functionality and evolution of eukaryotic transcriptional enhancers","volume":"96","author":"Buffry","year":"2016","journal-title":"Adv Genet"},{"key":"2026091504194087300_B18","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/nrg1315","article-title":"Applied bioinformatics for the identification of regulatory elements","volume":"5","author":"Wasserman","year":"2004","journal-title":"Nat Rev Genet"},{"key":"2026091504194087300_B19","doi-asserted-by":"publisher","first-page":"2847","DOI":"10.4161\/15384101.2014.949201","article-title":"Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond","volume":"13","author":"Mundade","year":"2014","journal-title":"Cell Cycle"},{"key":"2026091504194087300_B20","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/nature11232","article-title":"The accessible chromatin landscape of the human genome","volume":"489","author":"Thurman","year":"2012","journal-title":"Nature"},{"key":"2026091504194087300_B21","doi-asserted-by":"publisher","first-page":"21.29.1","DOI":"10.1002\/0471142727.mb2129s109","article-title":"ATAC-seq: a method for assaying chromatin accessibility genome-wide","volume":"109","author":"Buenrostro","year":"2015","journal-title":"Curr Protoc Mol Biol"},{"key":"2026091504194087300_B22","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1126\/science.1232542","article-title":"Genome-wide quantitative enhancer activity maps identified by STARR-seq","volume":"339","author":"Arnold","year":"2013","journal-title":"Science"},{"key":"2026091504194087300_B23","doi-asserted-by":"publisher","first-page":"11952","DOI":"10.1073\/pnas.1307449110","article-title":"Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks","volume":"110","author":"White","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091504194087300_B24","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1016\/j.tig.2015.11.004","article-title":"Enhanced identification of transcriptional enhancers provides mechanistic insights into diseases","volume":"32","author":"Murakawa","year":"2016","journal-title":"Trends Genet"},{"key":"2026091504194087300_B25","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1038\/s41576-019-0209-0","article-title":"Towards a comprehensive catalogue of validated and target-linked human enhancers","volume":"21","author":"Gasperini","year":"2020","journal-title":"Nat Rev Genet"},{"key":"2026091504194087300_B26","doi-asserted-by":"publisher","first-page":"1516","DOI":"10.1016\/j.cell.2019.02.027","article-title":"A genome-wide framework for mapping gene regulation via cellular genetic screens","volume":"176","author":"Gasperini","year":"2019","journal-title":"Cell"},{"key":"2026091504194087300_B27","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1101\/gad.309351.117","article-title":"Widespread transcriptional pausing and elongation control at enhancers","volume":"32","author":"Henriques","year":"2018","journal-title":"Genes Dev"},{"key":"2026091504194087300_B28","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1038\/ng.1064","article-title":"Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development","volume":"44","author":"Bonn","year":"2012","journal-title":"Nat Genet"},{"key":"2026091504194087300_B29","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1038\/ng.3550","article-title":"Histone H3 globular domain acetylation identifies a new class of enhancers","volume":"48","author":"Pradeepa","year":"2016","journal-title":"Nat Genet"},{"key":"2026091504194087300_B30","doi-asserted-by":"publisher","first-page":"2053","DOI":"10.1101\/gr.155028.113","article-title":"H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction","volume":"23","author":"Taylor","year":"2013","journal-title":"Genome Res"},{"key":"2026091504194087300_B31","doi-asserted-by":"publisher","first-page":"897","DOI":"10.1038\/ng.154","article-title":"Combinatorial patterns of histone acetylations and methylations in the human genome","volume":"40","author":"Wang","year":"2008","journal-title":"Nat Genet"},{"key":"2026091504194087300_B32","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1038\/nrg3242","article-title":"Genomic approaches towards finding cis-regulatory modules in animals","volume":"13","author":"Hardison","year":"2012","journal-title":"Nat Rev Genet"},{"key":"2026091504194087300_B33","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1038\/s41592-022-01716-8","article-title":"Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing","volume":"20","author":"Kovaka","year":"2023","journal-title":"Nat Methods"},{"key":"2026091504194087300_B34","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1038\/s41586-024-08070-z","article-title":"Machine-guided design of cell-type-targeting cis-regulatory elements","volume":"634","author":"Gosai","year":"2024","journal-title":"Nature"},{"key":"2026091504194087300_B35","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1093\/bib\/bbv101","article-title":"Progress and challenges in bioinformatics approaches for enhancer identification","volume":"17","author":"Kleftogiannis","year":"2016","journal-title":"Brief Bioinform"},{"key":"2026091504194087300_B36","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1101\/gr.227819.117","article-title":"Sequential regulatory activity prediction across chromosomes with convolutional neural networks","volume":"28","author":"Kelley","year":"2018","journal-title":"Genome Res"},{"key":"2026091504194087300_B37","doi-asserted-by":"publisher","first-page":"990","DOI":"10.1101\/gr.200535.115","article-title":"Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks","volume":"26","author":"Kelley","year":"2016","journal-title":"Genome Res"},{"key":"2026091504194087300_B38","doi-asserted-by":"publisher","first-page":"1564","DOI":"10.1038\/s41588-021-00947-3","article-title":"The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation","volume":"53","author":"Kim","year":"2021","journal-title":"Nat Genet"},{"key":"2026091504194087300_B39","doi-asserted-by":"publisher","first-page":"1815","DOI":"10.1101\/gr.260844.120","article-title":"Cross-species analysis of enhancer logic using deep learning","volume":"30","author":"Minnoye","year":"2020","journal-title":"Genome Res"},{"key":"2026091504194087300_B40","doi-asserted-by":"publisher","first-page":"e1006484","DOI":"10.1371\/journal.pcbi.1006484","article-title":"Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties","volume":"14","author":"Chen","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2026091504194087300_B41","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1186\/s12864-022-08450-7","article-title":"Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin","volume":"23","author":"Kaplow","year":"2022","journal-title":"BMC Genomics"},{"key":"2026091504194087300_B42","doi-asserted-by":"publisher","first-page":"723","DOI":"10.1016\/j.tcb.2015.10.007","article-title":"Theory in biology: figure 1 or figure 7?","volume":"25","author":"Phillips","year":"2015","journal-title":"Trends Cell Biol"},{"key":"2026091504194087300_B43","doi-asserted-by":"publisher","first-page":"e08445","DOI":"10.7554\/eLife.08445","article-title":"Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo","volume":"5","author":"Sayal","year":"2016","journal-title":"eLife"},{"key":"2026091504194087300_B44","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1039\/c5ib00321k","article-title":"The appeasement of Doug: a synthetic approach to enhancer biology","volume":"8","author":"Vincent","year":"2016","journal-title":"Integr Biol (Camb)"},{"key":"2026091504194087300_B45","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1534\/g3.111.001081","article-title":"Conserved motifs and prediction of regulatory modules in Caenorhabditis elegans","volume":"2","author":"Zhao","year":"2012","journal-title":"G3 (Bethesda)"},{"key":"2026091504194087300_B46","doi-asserted-by":"publisher","first-page":"D933","DOI":"10.1093\/nar\/gkac958","article-title":"Ensembl 2023","volume":"51","author":"Martin","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B47","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1101\/gr.084228.108","article-title":"Phylogenomics of primates and their ancestral populations","volume":"19","author":"Siepel","year":"2009","journal-title":"Genome Res"},{"key":"2026091504194087300_B48","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1101\/gr.3002305","article-title":"Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages","volume":"15","author":"Bourque","year":"2005","journal-title":"Genome Res"},{"key":"2026091504194087300_B49","first-page":"D58","article-title":"EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue\/cell types across nine species","volume":"48","author":"Gao","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B50","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1038\/s41586-020-2493-4","article-title":"Expanded encyclopaedias of DNA elements in the human and mouse genomes","volume":"583","author":"Consortium","year":"2020","journal-title":"Nature"},{"key":"2026091504194087300_B51","doi-asserted-by":"publisher","first-page":"D729","DOI":"10.1093\/nar\/gky1094","article-title":"Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis","volume":"47","author":"Zheng","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B52","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1038\/s41586-021-03604-1","article-title":"An atlas of gene regulatory elements in adult mouse cerebrum","volume":"598","author":"Li","year":"2021","journal-title":"Nature"},{"key":"2026091504194087300_B53","doi-asserted-by":"publisher","first-page":"5985","DOI":"10.1016\/j.cell.2021.10.024","article-title":"A single-cell atlas of chromatin accessibility in the human genome","volume":"184","author":"Zhang","year":"2021","journal-title":"Cell"},{"key":"2026091504194087300_B54","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1126\/science.adp3957","article-title":"Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium","volume":"387","author":"Hecker","year":"2025","journal-title":"Science"},{"key":"2026091504194087300_B55","doi-asserted-by":"publisher","first-page":"782409","DOI":"10.3389\/fvets.2021.782409","article-title":"Comparative enhancer map of cattle muscle genome annotated by ATAC-seq","volume":"8","author":"Cao","year":"2021","journal-title":"Front Vet Sci"},{"key":"2026091504194087300_B56","doi-asserted-by":"publisher","article-title":"Zebrahub-Multiome: uncovering gene regulatory network dynamics during zebrafish embryogenesis","author":"Kim","DOI":"10.1101\/2024.10.18.618987"},{"key":"2026091504194087300_B57","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1146\/annurev-animal-020518-114913","article-title":"Functional Annotation of Animal genomes (FAANG): current achievements and roadmap","volume":"7","author":"Giuffra","year":"2019","journal-title":"Annu Rev Anim Biosci"},{"key":"2026091504194087300_B58","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/1471-2164-6-140","article-title":"The distribution of SNPs in human gene regulatory regions","volume":"6","author":"Guo","year":"2005","journal-title":"BMC Genomics"},{"key":"2026091504194087300_B59","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1186\/1471-2105-12-495","article-title":"MotifMap: integrative genome-wide maps of regulatory motif sites for model species","volume":"12","author":"Daily","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2026091504194087300_B60","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.tig.2024.09.007","article-title":"A bioinformatics toolbox to prioritize causal genetic variants in candidate regions","volume":"41","author":"Simon","year":"2025","journal-title":"Trends Genet"},{"key":"2026091504194087300_B61","doi-asserted-by":"publisher","first-page":"17400","DOI":"10.1073\/pnas.0505147102","article-title":"Identifying the conserved network of cis-regulatory sites of a eukaryotic genome","volume":"102","author":"Wang","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091504194087300_B62","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1093\/bioinformatics\/btg329","article-title":"Combining phylogenetic data with co-regulated genes to identify regulatory motifs","volume":"19","author":"Wang","year":"2003","journal-title":"Bioinformatics"},{"key":"2026091504194087300_B63","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1093\/nar\/gkg108","article-title":"TRANSFAC: transcriptional regulation, from patterns to profiles","volume":"31","author":"Matys","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B64","doi-asserted-by":"publisher","first-page":"1431","DOI":"10.1016\/j.cell.2014.08.009","article-title":"Determination and inference of eukaryotic transcription factor sequence specificity","volume":"158","author":"Weirauch","year":"2014","journal-title":"Cell"},{"key":"2026091504194087300_B65","doi-asserted-by":"publisher","first-page":"e46255","DOI":"10.15252\/embr.201846255","article-title":"ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data","volume":"19","author":"Oki","year":"2018","journal-title":"EMBO Rep"},{"key":"2026091504194087300_B66","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"Omics"},{"key":"2026091504194087300_B67","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","article-title":"Identifying DNA and protein patterns with statistically significant alignments of multiple sequences","volume":"15","author":"Hertz","year":"1999","journal-title":"Bioinformatics"},{"key":"2026091504194087300_B68","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2026091504194087300_B69","doi-asserted-by":"publisher","first-page":"2382","DOI":"10.1093\/bioinformatics\/btv145","article-title":"ChIPseeker: an R\/bioconductor package for ChIP peak annotation, comparison and visualization","volume":"31","author":"Yu","year":"2015","journal-title":"Bioinformatics"},{"key":"2026091504194087300_B70","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1038\/s41597-019-0071-0","article-title":"An ATAC-seq atlas of chromatin accessibility in mouse tissues","volume":"6","author":"Liu","year":"2019","journal-title":"Sci Data"},{"key":"2026091504194087300_B71","doi-asserted-by":"publisher","first-page":"3208","DOI":"10.1093\/bioinformatics\/bty311","article-title":"GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor","volume":"34","author":"Puigdevall","year":"2018","journal-title":"Bioinformatics"},{"key":"2026091504194087300_B72","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1038\/nrg2845","article-title":"Determining the specificity of protein\u2013DNA interactions","volume":"11","author":"Stormo","year":"2010","journal-title":"Nat Rev Genet"},{"key":"2026091504194087300_B73","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1093\/nar\/24.1.238","article-title":"TRANSFAC: a database on transcription factors and their DNA binding sites","volume":"24","author":"Wingender","year":"1996","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B74","doi-asserted-by":"publisher","first-page":"10294","DOI":"10.1073\/pnas.0506945103","article-title":"Nanog binds to Smad1 and blocks bone morphogenetic protein-induced differentiation of embryonic stem cells","volume":"103","author":"Suzuki","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091504194087300_B75","doi-asserted-by":"publisher","first-page":"4018","DOI":"10.1242\/dev.115709","article-title":"Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification","volume":"141","author":"Wilkinson","year":"2014","journal-title":"Development"},{"key":"2026091504194087300_B76","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1038\/ncb2709","article-title":"Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis","volume":"15","author":"Moignard","year":"2013","journal-title":"Nat Cell Biol"},{"key":"2026091504194087300_B77","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.bbagrm.2011.03.001","article-title":"Retinal expression of the X-linked juvenile retinoschisis (RS1) gene is controlled by an upstream CpG island and two opposing CRX-bound regions","volume":"1809","author":"Kraus","year":"2011","journal-title":"Biochim Biophys Acta"},{"key":"2026091504194087300_B78","doi-asserted-by":"publisher","first-page":"6339","DOI":"10.1038\/s41598-018-24544-3","article-title":"Differential contribution of cis and trans gene transcription regulatory mechanisms in amygdala and prefrontal cortex and modulation by social stress","volume":"8","author":"Reuveni","year":"2018","journal-title":"Sci Rep"},{"key":"2026091504194087300_B79","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1016\/j.gene.2008.10.014","article-title":"A functional NF-kappaB enhancer element in the first intron contributes to the control of c-fos transcription","volume":"430","author":"Charital","year":"2009","journal-title":"Gene"},{"key":"2026091504194087300_B80","doi-asserted-by":"publisher","first-page":"6808","DOI":"10.1523\/JNEUROSCI.5448-11.2012","article-title":"Egr-1 induces DARPP-32 expression in striatal medium spiny neurons via a conserved intragenic element","volume":"32","author":"Keilani","year":"2012","journal-title":"J Neurosci"},{"key":"2026091504194087300_B81","doi-asserted-by":"publisher","first-page":"19955","DOI":"10.1073\/pnas.1010708107","article-title":"Evolution of the mammalian embryonic pluripotency gene regulatory network","volume":"107","author":"Fernandez-Tresguerres","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091504194087300_B82","doi-asserted-by":"publisher","first-page":"e40828","DOI":"10.1371\/journal.pone.0040828","article-title":"Looping mediated interaction between the promoter and 3\u2032 UTR regulates type II collagen expression in chondrocytes","volume":"7","author":"Jash","year":"2012","journal-title":"PLoS One"},{"key":"2026091504194087300_B83","doi-asserted-by":"publisher","first-page":"5692","DOI":"10.1093\/nar\/gkt279","article-title":"A novel cis-acting element from the 3\u2032UTR of DNA damage-binding protein 2 mRNA links transcriptional and post-transcriptional regulation of gene expression","volume":"41","author":"Melanson","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B84","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1186\/s12864-018-5212-x","article-title":"Mapping the Pax6 3\u2032 untranslated region microRNA regulatory landscape","volume":"19","author":"Ryan","year":"2018","journal-title":"BMC Genomics"},{"key":"2026091504194087300_B85","doi-asserted-by":"publisher","first-page":"E8855","DOI":"10.1073\/pnas.1706611114","article-title":"Period2 3\u2032-UTR and microRNA-24 regulate circadian rhythms by repressing PERIOD2 protein accumulation","volume":"114","author":"Yoo","year":"2017","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091504194087300_B86","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1186\/s12864-016-2479-7","article-title":"High-throughput discovery of post-transcriptional cis-regulatory elements","volume":"17","author":"Wissink","year":"2016","journal-title":"BMC Genomics"},{"key":"2026091504194087300_B87","doi-asserted-by":"publisher","first-page":"2449","DOI":"10.1016\/j.molcel.2023.06.012","article-title":"Transcription factors interact with RNA to regulate genes","volume":"83","author":"Oksuz","year":"2023","journal-title":"Mol Cell"},{"key":"2026091504194087300_B88","doi-asserted-by":"publisher","first-page":"e0217580","DOI":"10.1371\/journal.pone.0217580","article-title":"The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages","volume":"14","author":"Repele","year":"2019","journal-title":"PLoS One"},{"key":"2026091504194087300_B89","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/s41467-020-14853-5","article-title":"Candidate silencer elements for the human and mouse genomes","volume":"11","author":"Doni\u00a0Jayavelu","year":"2020","journal-title":"Nat Commun"},{"key":"2026091504194087300_B90","doi-asserted-by":"publisher","first-page":"3820","DOI":"10.1128\/MCB.22.11.3820-3831.2002","article-title":"Conserved CTCF insulator elements flank the mouse and human beta-globin loci","volume":"22","author":"Farrell","year":"2002","journal-title":"Mol Cell Biol"},{"key":"2026091504194087300_B91","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1016\/0896-6273(92)90181-C","article-title":"A locus control region adjacent to the human red and green visual pigment genes","volume":"9","author":"Wang","year":"1992","journal-title":"Neuron"},{"key":"2026091504194087300_B92","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"Consortium","year":"2012","journal-title":"Nature"},{"key":"2026091504194087300_B93","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-025-09909-9","article-title":"An expanded registry of candidate cis-regulatory elements","author":"Moore","year":"2026","journal-title":"Nature"},{"key":"2026091504194087300_B94","volume-title":"2022 Census of Agriculture Highlights: Cattle and Cattle on Feed","author":"USDA National Agricultural Statistics Service","year":"2024"},{"key":"2026091504194087300_B95","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/s13059-021-02570-1","article-title":"The Agricultural Genome to Phenome Initiative (AG2PI): creating a shared vision across crop and livestock research communities","volume":"23","author":"Tuggle","year":"2022","journal-title":"Genome Biol"},{"key":"2026091504194087300_B96","volume-title":"2022 Census of Agriculture Highlights: Poultry and Egg Production","author":"USDA National Agricultural Statistics Service","year":"2024"},{"key":"2026091504194087300_B97","doi-asserted-by":"publisher","first-page":"eade1204","DOI":"10.1126\/sciadv.ade1204","article-title":"An atlas of regulatory elements in chicken: a resource for chicken genetics and genomics","volume":"9","author":"Pan","year":"2023","journal-title":"Sci Adv"},{"key":"2026091504194087300_B98","doi-asserted-by":"publisher","first-page":"R110","DOI":"10.1186\/gb-2005-6-13-r110","article-title":"A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks","volume":"6","author":"Reece-Hoyes","year":"2005","journal-title":"Genome Biol"},{"key":"2026091504194087300_B99","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1186\/1471-2164-9-399","article-title":"Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution","volume":"9","author":"Haerty","year":"2008","journal-title":"BMC Genomics"},{"key":"2026091504194087300_B100","doi-asserted-by":"publisher","first-page":"14086","DOI":"10.1073\/pnas.0603424103","article-title":"A conserved role for a GATA transcription factor in regulating epithelial innate immune responses","volume":"103","author":"Shapira","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091504194087300_B101","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/j.cell.2012.12.009","article-title":"DNA-binding specificities of human transcription factors","volume":"152","author":"Jolma","year":"2013","journal-title":"Cell"},{"key":"2026091504194087300_B102","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1016\/0092-8674(87)90511-3","article-title":"The DNA-binding domains of the jun oncoprotein and the yeast GCN4 transcriptional activator protein are functionally homologous","volume":"50","author":"Struhl","year":"1987","journal-title":"Cell"},{"key":"2026091504194087300_B103","doi-asserted-by":"publisher","first-page":"e04837","DOI":"10.7554\/eLife.04837","article-title":"Conservation of transcription factor binding specificities across 600 million years of bilateria evolution","volume":"4","author":"Nitta","year":"2015","journal-title":"eLife"},{"key":"2026091504194087300_B104","doi-asserted-by":"publisher","first-page":"e06967","DOI":"10.7554\/eLife.06967","article-title":"Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities","volume":"4","author":"Narasimhan","year":"2015","journal-title":"eLife"},{"key":"2026091504194087300_B105","doi-asserted-by":"publisher","first-page":"7596","DOI":"10.1038\/s41598-017-07761-0","article-title":"Modelling the evolution of transcription factor binding preferences in complex eukaryotes","volume":"7","author":"Rosanova","year":"2017","journal-title":"Sci Rep"},{"key":"2026091504194087300_B106","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1186\/s12915-019-0726-5","article-title":"Multi-species annotation of transcriptome and chromatin structure in domesticated animals","volume":"17","author":"Foissac","year":"2019","journal-title":"BMC Biol"},{"key":"2026091504194087300_B107","doi-asserted-by":"publisher","first-page":"lqab052","DOI":"10.1093\/nargab\/lqab052","article-title":"Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans","volume":"3","author":"Ni","year":"2021","journal-title":"NAR Genom Bioinform"},{"key":"2026091504194087300_B108","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1006\/bbrc.1996.5882","article-title":"Comparison of three nonviral transfection methods for foreign gene expression in early chicken embryos in ovo","volume":"230","author":"Muramatsu","year":"1997","journal-title":"Biochem Biophys Res Commun"},{"key":"2026091504194087300_B109","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/978-1-4939-9412-0_6","article-title":"In ovo electroporation of plasmid DNA and morpholinos into specific tissues during early embryogenesis","volume":"1976","author":"McLennan","year":"2019","journal-title":"Methods Mol Biol"},{"key":"2026091504194087300_B110","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511897948","volume-title":"The Neural Crest","author":"Le\u00a0Douarin","year":"1999"},{"key":"2026091504194087300_B111","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1016\/S0955-0674(99)00038-1","article-title":"Induction and differentiation of the neural crest","volume":"11","author":"Garcia-Castro","year":"1999","journal-title":"Curr Opin Cell Biol"},{"key":"2026091504194087300_B112","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1101\/gr.5592107","article-title":"Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data","volume":"17","author":"King","year":"2007","journal-title":"Genome Res"},{"key":"2026091504194087300_B113","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1093\/bib\/bbs038","article-title":"The UCSC genome browser and associated tools","volume":"14","author":"Kuhn","year":"2013","journal-title":"Briefings Bioinf"},{"key":"2026091504194087300_B114","doi-asserted-by":"publisher","first-page":"e13075","DOI":"10.1371\/journal.pone.0013075","article-title":"Expression of rod-derived cone viability factor: dual role of CRX in regulating promoter activity and cell-type specificity","volume":"5","author":"Lambard","year":"2010","journal-title":"PLoS One"},{"key":"2026091504194087300_B115","doi-asserted-by":"crossref","first-page":"100321","DOI":"10.1016\/j.crmeth.2022.100321","article-title":"Normalization benchmark of ATAC-seq datasets shows the importance of accounting for GC-content effects","volume":"2","author":"Van\u00a0den\u00a0Berge","year":"2022","journal-title":"Cell Rep Methods"},{"key":"2026091504194087300_B116","doi-asserted-by":"publisher","first-page":"6454","DOI":"10.3390\/ijms22126454","article-title":"Regulatory SNPs: altered transcription factor binding sites implicated in complex traits and diseases","volume":"22","author":"Degtyareva","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2026091504194087300_B117","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.ajhg.2011.11.029","article-title":"Five years of GWAS discovery","volume":"90","author":"Visscher","year":"2012","journal-title":"Am Hum Genet"},{"key":"2026091504194087300_B118","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1038\/s41576-019-0127-1","article-title":"Benefits and limitations of genome-wide association studies","volume":"20","author":"Tam","year":"2019","journal-title":"Nat Rev Genet"},{"key":"2026091504194087300_B119","first-page":"662","article-title":"Human-genome single nucleotide polymorphisms affecting transcription factor binding and their role in pathogenesis","volume":"27","author":"Antontseva","year":"2023","journal-title":"Vavilovskii Zhurnal Genet Selektsii"},{"key":"2026091504194087300_B120","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1126\/science.1222794","article-title":"Systematic localization of common disease-associated variation in regulatory DNA","volume":"337","author":"Maurano","year":"2012","journal-title":"Science"},{"key":"2026091504194087300_B121","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1126\/science.1262110","article-title":"Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans","volume":"348","author":"Consortium","year":"2015","journal-title":"Science"},{"key":"2026091504194087300_B122","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1038\/s41588-020-00773-z","article-title":"Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer\u2019s disease pathogenesis","volume":"53","author":"Wingo","year":"2021","journal-title":"Nat Genet"},{"key":"2026091504194087300_B123","doi-asserted-by":"publisher","first-page":"1418","DOI":"10.1038\/nn.4632","article-title":"An xQTL map integrates the genetic architecture of the human brain\u2019s transcriptome and epigenome","volume":"20","author":"Ng","year":"2017","journal-title":"Nat Neurosci"},{"key":"2026091504194087300_B124","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1038\/s41588-020-0622-5","article-title":"Exploring and visualizing large-scale genetic associations by using PheWeb","volume":"52","author":"Gagliano\u00a0Taliun","year":"2020","journal-title":"Nat Genet"},{"key":"2026091504194087300_B125","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/s41588-023-01300-6","article-title":"Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases","volume":"55","author":"de\u00a0Klein","year":"2023","journal-title":"Nat Genet"},{"key":"2026091504194087300_B126","doi-asserted-by":"publisher","first-page":"762544","DOI":"10.3389\/fnmol.2022.762544","article-title":"Blood SSR1: a possible biomarker for early prediction of Parkinson\u2019s disease","volume":"15","author":"Zhang","year":"2022","journal-title":"Front Mol Neurosci"},{"key":"2026091504194087300_B127","doi-asserted-by":"publisher","first-page":"bax028","DOI":"10.1093\/database\/bax028","article-title":"GeneHancer: genome-wide integration of enhancers and target genes in GeneCards","volume":"2017","author":"Fishilevich","year":"2017","journal-title":"Database (Oxford)"},{"key":"2026091504194087300_B128","doi-asserted-by":"publisher","first-page":"D126","DOI":"10.1093\/nar\/gkv1203","article-title":"ORegAnno 3.0: a community-driven resource for curated regulatory annotation","volume":"44","author":"Lesurf","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B129","doi-asserted-by":"crossref","first-page":"e2302720120","DOI":"10.1073\/pnas.2302720120","article-title":"Multiancestry analysis of the HLA locus in Alzheimer\u2019s and Parkinson\u2019s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes","volume":"120","author":"Le\u00a0Guen","year":"2023","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026091504194087300_B130","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/alzrt268","article-title":"Association of MAPT haplotypes with Alzheimer\u2019s disease risk and MAPT brain gene expression levels","volume":"6","author":"Allen","year":"2014","journal-title":"Alz Res Therapy"},{"key":"2026091504194087300_B131","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1186\/s12920-022-01216-w","article-title":"The landscape of GWAS validation: systematic review identifying 309 validated non-coding variants across 130 human diseases","volume":"15","author":"Alsheikh","year":"2022","journal-title":"BMC Med Genomics"},{"key":"2026091504194087300_B132","doi-asserted-by":"publisher","first-page":"2634","DOI":"10.1038\/s41380-024-02502-y","article-title":"The Alzheimer\u2019s disease risk gene BIN1 regulates activity-dependent gene expression in human-induced glutamatergic neurons","volume":"29","author":"Saha","year":"2024","journal-title":"Mol Psychiatry"},{"key":"2026091504194087300_B133","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1242\/dev.00921","article-title":"Global expression analysis of gene regulatory pathways during endocrine pancreatic development","volume":"131","author":"Gu","year":"2004","journal-title":"Development"},{"key":"2026091504194087300_B134","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1016\/j.molmed.2021.07.012","article-title":"Enhancers in disease: molecular basis and emerging treatment strategies","volume":"27","author":"Claringbould","year":"2021","journal-title":"Trends Mol Med"},{"key":"2026091504194087300_B135","doi-asserted-by":"publisher","first-page":"D316","DOI":"10.1093\/nar\/gkab996","article-title":"ReMap 2022: a database of human, mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments","volume":"50","author":"Hammal","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B136","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1186\/s13059-020-1929-3","article-title":"From reads to insight: a hitchhiker\u2019s guide to ATAC-seq data analysis","volume":"21","author":"Yan","year":"2020","journal-title":"Genome Biol"},{"key":"2026091504194087300_B137","doi-asserted-by":"publisher","first-page":"e201401002","DOI":"10.5936\/csbj.201401002","article-title":"Leveraging biological replicates to improve analysis in ChIP-seq experiments","volume":"9","author":"Yang","year":"2014","journal-title":"Comput Struct Biotechnol J"},{"key":"2026091504194087300_B138","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1186\/s12864-019-5779-x","article-title":"Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function","volume":"20","author":"Benton","year":"2019","journal-title":"BMC Genomics"},{"key":"2026091504194087300_B139","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/s41586-021-03451-0","article-title":"Towards complete and error-free genome assemblies of all vertebrate species","volume":"592","author":"Rhie","year":"2021","journal-title":"Nature"},{"key":"2026091504194087300_B140","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1146\/annurev-animal-022516-022811","article-title":"Bat biology, genomes, and the Bat1K project: to generate chromosome-level genomes for all living bat species","volume":"6","author":"Teeling","year":"2018","journal-title":"Annu Rev Anim Biosci"},{"key":"2026091504194087300_B141","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1038\/s41586-020-2876-6","article-title":"A comparative genomics multitool for scientific discovery and conservation","volume":"587","author":"Zoonomia","year":"2020","journal-title":"Nature"},{"key":"2026091504194087300_B142","first-page":"e16","article-title":"A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells","volume":"45","author":"Maricque","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B143","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1038\/s41592-020-0965-y","article-title":"A systematic evaluation of the design and context dependencies of massively parallel reporter assays","volume":"17","author":"Klein","year":"2020","journal-title":"Nat Methods"},{"key":"2026091504194087300_B144","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1093\/nar\/gkaa1137","article-title":"Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations","volume":"49","author":"Pei","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026091504194087300_B145","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1038\/s41586-020-03145-z","article-title":"Regulatory genomic circuitry of human disease loci by integrative epigenomics","volume":"590","author":"Boix","year":"2021","journal-title":"Nature"},{"key":"2026091504194087300_B146","doi-asserted-by":"publisher","first-page":"2104","DOI":"10.1038\/s41588-024-01900-w","article-title":"Systematic prioritization of functional variants and effector genes underlying colorectal cancer risk","volume":"56","author":"Law","year":"2024","journal-title":"Nat Genet"},{"key":"2026091504194087300_B147","doi-asserted-by":"publisher","first-page":"20140331","DOI":"10.1098\/rstb.2014.0331","article-title":"What\u2019s in a genome? The C-value enigma and the evolution of eukaryotic genome content","volume":"370","author":"Elliott","year":"2015","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"2026091504194087300_B148","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1016\/j.tig.2019.09.010","article-title":"Introns: good day junk is bad day treasure","volume":"35","author":"Parenteau","year":"2019","journal-title":"Trends Genet"},{"key":"2026091504194087300_B149","doi-asserted-by":"publisher","first-page":"672","DOI":"10.3389\/fgene.2018.00672","article-title":"Introns as gene regulators: a brick on the accelerator","volume":"9","author":"Rose","year":"2019","journal-title":"Front Genet"},{"key":"2026091504194087300_B150","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1038\/s41576-023-00609-6","article-title":"Transposable elements in mammalian chromatin organization","volume":"24","author":"Lawson","year":"2023","journal-title":"Nat Rev Genet"},{"key":"2026091504194087300_B151","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2004-5-4-r25","article-title":"The regulatory content of intergenic DNA shapes genome architecture","volume":"5","author":"Nelson","year":"2004","journal-title":"Genome Biol"},{"key":"2026091504194087300_B152","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1126\/science.abj6987","article-title":"The complete sequence of a human genome","volume":"376","author":"Nurk","year":"2022","journal-title":"Science"}],"container-title":["NAR Genomics and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag107\/71084233\/lqag107.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nargab\/article-pdf\/8\/3\/lqag107\/71084233\/lqag107.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T08:25:04Z","timestamp":1789460704000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nargab\/article\/doi\/10.1093\/nargab\/lqag107\/8795402"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,27]]},"references-count":152,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,6,27]]}},"URL":"https:\/\/doi.org\/10.1093\/nargab\/lqag107","relation":{},"ISSN":["2631-9268"],"issn-type":[{"value":"2631-9268","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,6,27]]},"article-number":"lqag107"}}