{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T02:34:18Z","timestamp":1773714858099,"version":"3.50.1"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,9,16]],"date-time":"2021-09-16T00:00:00Z","timestamp":1631750400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000864","name":"Michael J. Fox Foundation","doi-asserted-by":"publisher","award":["14899"],"award-info":[{"award-number":["14899"]}],"id":[{"id":"10.13039\/100000864","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000864","name":"Michael J. Fox Foundation","doi-asserted-by":"publisher","award":["16743"],"award-info":[{"award-number":["16743"]}],"id":[{"id":"10.13039\/100000864","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"publisher","award":["R01-AG054005"],"award-info":[{"award-number":["R01-AG054005"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017510","name":"UK Dementia Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100017510","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017510","name":"UK DRI Ltd","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100017510","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"UK Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000320","name":"Alzheimer's Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000320","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002283","name":"Alzheimer's Research UK","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002283","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>echolocatoR integrates a diverse suite of statistical and functional fine-mapping tools to identify, test enrichment in, and visualize high-confidence causal consensus variants in any phenotype. It requires minimal input from users (a summary statistics file), can be run in a single R function, and provides extensive access to relevant datasets (e.g. reference linkage disequilibrium panels, quantitative trait loci, genome-wide annotations, cell-type-specific epigenomics), thereby enabling rapid, robust and scalable end-to-end fine-mapping investigations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>echolocatoR is an open-source R package available through GitHub under the GNU General Public License (Version 3) license: https:\/\/github.com\/RajLabMSSM\/echolocatoR.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab658","type":"journal-article","created":{"date-parts":[[2021,9,13]],"date-time":"2021-09-13T15:14:43Z","timestamp":1631546083000},"page":"536-539","source":"Crossref","is-referenced-by-count":29,"title":["<i>echolocatoR<\/i>\n                    : an automated end-to-end statistical and functional genomic fine-mapping pipeline"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5949-2191","authenticated-orcid":false,"given":"Brian M","family":"Schilder","sequence":"first","affiliation":[{"name":"Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Ronald M. Loeb Center for Alzheimer\u2019s Disease, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jack","family":"Humphrey","sequence":"additional","affiliation":[{"name":"Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Ronald M. Loeb Center for Alzheimer\u2019s Disease, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Towfique","family":"Raj","sequence":"additional","affiliation":[{"name":"Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Ronald M. Loeb Center for Alzheimer\u2019s Disease, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"},{"name":"Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai , New York 10029, NY, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,9,16]]},"reference":[{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1016\/j.ajhg.2019.03.012","article-title":"IMPACT: genomic annotation of cell-state-specific regulatory elements inferred from the epigenome of bound transcription factors","volume":"104","author":"Amariuta","year":"2019","journal-title":"Am. J. Hum. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1038\/s41588-019-0455-2","article-title":"High-throughput identification of human SNPs affecting regulatory element activity","volume":"51","author":"van Arensbergen","year":"2019","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1093\/bioinformatics\/btw018","article-title":"FINEMAP: efficient variable selection using summary data from genome-wide association studies","volume":"32","author":"Benner","year":"2016","journal-title":"Bioinformatics"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/j.ajhg.2017.08.012","article-title":"Prospects of fine-mapping trait-associated genomic regions by using summary statistics from genome-wide association studies","volume":"101","author":"Benner","year":"2017","journal-title":"Am. J. Hum. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1038\/nbt1010-1045","article-title":"The NIH roadmap epigenomics mapping consortium","volume":"28","author":"Bernstein","year":"2010","journal-title":"Nat. Biotechnol"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"190221","DOI":"10.1098\/rsob.190221","article-title":"A practical view of fine-mapping and gene prioritization in the post-genome-wide association era","volume":"10","author":"Broekema","year":"2020","journal-title":"Open Biol"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/ng.3211","article-title":"LD Score regression distinguishes confounding from polygenicity in genome-wide association studies","volume":"47","author":"Bulik-Sullivan","year":"2015","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/s41586-018-0579-z","article-title":"The UK Biobank resource with deep phenotyping and genomic data","volume":"562","author":"Bycroft","year":"2018","journal-title":"Nature"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"3847","DOI":"10.1093\/bioinformatics\/btv470","article-title":"motifbreakR: an R\/Bioconductor package for predicting variant effects at transcription factor binding sites","volume":"31","author":"Coetzee","year":"2015","journal-title":"Bioinformatics"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1158","DOI":"10.1038\/s41588-020-00721-x","article-title":"Single-cell epigenomic identification of inherited risk loci in Alzheimer\u2019s and Parkinson\u2019s disease","volume":"52","author":"Corces","year":"2020","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","article-title":"Atlas of genetic effects in human microglia transcriptome across brain regions, aging, and disease pathologies","author":"de Paiva Lopes","year":"2021","journal-title":"Nat. Genet."},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"4703","DOI":"10.1038\/s41467-020-18515-4","article-title":"Evaluating the informativeness of deep learning annotations for human complex diseases","volume":"11","author":"Dey","year":"2020","journal-title":"Nat. Commun"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/nprot.2009.97","article-title":"Mapping identifiers for the integration of genomic datasets with the R\/Bioconductor package biomaRt","volume":"4","author":"Durinck","year":"2009","journal-title":"Nat. Protoc"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1186\/s13073-016-0384-y","article-title":"XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits","volume":"8","author":"Fang","year":"2016","journal-title":"Genome Med"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.1038\/ng.3404","article-title":"Partitioning heritability by functional annotation using genome-wide association summary statistics","volume":"47","author":"Finucane","year":"2015","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1038\/ng.3437","article-title":"Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci","volume":"47","author":"Gaulton","year":"2015","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1038\/ng.3954","article-title":"Linkage disequilibrium-dependent architecture of human complex traits shows action of negative selection","volume":"49","author":"Gazal","year":"2017","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"e1004383","DOI":"10.1371\/journal.pgen.1004383","article-title":"Bayesian test for colocalisation between pairs of genetic association studies using summary statistics","volume":"10","author":"Giambartolomei","year":"2014","journal-title":"PLoS Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"R81","DOI":"10.1093\/hmg\/ddaa148","article-title":"Fine-mapping genetic associations","volume":"29","author":"Hutchinson","year":"2020","journal-title":"Hum. Mol. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"e89","DOI":"10.1002\/cpbi.89","article-title":"The ENCODE Portal as an Epigenomics Resource","volume":"68","author":"Jou","year":"2019","journal-title":"Curr. Protoc. Bioinf"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","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":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1093\/bioinformatics\/btw615","article-title":"Improved methods for multi-trait fine mapping of pleiotropic risk loci","volume":"33","author":"Kichaev","year":"2017","journal-title":"Bioinformatics"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.ajhg.2015.06.007","article-title":"Leveraging functional-annotation data in trans-ethnic fine-mapping studies","volume":"97","author":"Kichaev","year":"2015","journal-title":"Am. J. Hum. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1093\/bioinformatics\/btq671","article-title":"Tabix: fast retrieval of sequence features from generic TAB-delimited files","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"3555","DOI":"10.1093\/bioinformatics\/btv402","article-title":"LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants","volume":"31","author":"Machiela","year":"2015","journal-title":"Bioinformatics"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1038\/s41588-018-0241-6","article-title":"Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps","volume":"50","author":"Mahajan","year":"2018","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","DOI":"10.1038\/s43587-021-00110-x","article-title":"Dysregulation of mitochondrial and proteo-lysosomal genes in Parkinson's disease myeloid cells","author":"Navarro","year":"2021","journal-title":"Nat. Aging"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1126\/science.aay0793","article-title":"Brain cell type-specific enhancer-promoter interactome maps and disease risk association","volume":"366","author":"Nott","year":"2019","journal-title":"Science"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nrg.2016.142","article-title":"Dissecting the genetics of complex traits using summary association statistics","volume":"18","author":"Pasaniuc","year":"2017","journal-title":"Nat. Rev. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/321275","article-title":"Linkage disequilibrium in humans: models and data","volume":"69","author":"Pritchard","year":"2001","journal-title":"Am. J. Hum. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"eaaw6507","DOI":"10.1126\/sciadv.aaw6507","article-title":"The NIH common fund\/roadmap epigenomics program: successes of a comprehensive consortium","volume":"5","author":"Satterlee","year":"2019","journal-title":"Sci. Adv"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/s41576-018-0016-z","article-title":"From genome-wide associations to candidate causal variants by statistical fine-mapping","volume":"19","author":"Schaid","year":"2018","journal-title":"Nat. Rev. Genet"},{"key":"2023033004311024900_","article-title":"Fine-mapping of Parkinson\u2019s disease susceptibility loci identifies putative causal variants","author":"Schilder","year":"2021","journal-title":"Accepted at Hum. Mol. Genet."},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"R111","DOI":"10.1093\/hmg\/ddv260","article-title":"Strategies for fine-mapping complex traits","volume":"24","author":"Spain","year":"2015","journal-title":"Hum. Mol. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"e1001779","DOI":"10.1371\/journal.pmed.1001779","article-title":"UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age","volume":"12","author":"Sudlow","year":"2015","journal-title":"PLoS Med"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1016\/j.cell.2018.02.021","article-title":"Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay","volume":"172","author":"Tewhey","year":"2018","journal-title":"Cell"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/j.ajhg.2015.05.016","article-title":"Disentangling the effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex-trait loci","volume":"97","author":"Trynka","year":"2015","journal-title":"Am. J. Hum. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1086\/519024","article-title":"A Bayesian measure of the probability of false discovery in genetic epidemiology studies","volume":"81","author":"Wakefield","year":"2007","journal-title":"Am. J. Hum. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1111\/rssb.12388","article-title":"A simple new approach to variable selection in regression, with application to genetic fine mapping","author":"Wang","year":"2020","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"D930","DOI":"10.1093\/nar\/gkr917","article-title":"HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants","volume":"40","author":"Ward","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1038\/s41588-020-00735-5","article-title":"Functionally informed fine-mapping and polygenic localization of complex trait heritability","volume":"52","author":"Weissbrod","year":"2020","journal-title":"Nature Genetics"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1038\/ng.2435","article-title":"Bayesian refinement of association signals for 14 loci in 3 common diseases","volume":"44","year":"2012","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1038\/s41588-018-0216-7","article-title":"Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes","volume":"50","author":"Westra","year":"2018","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/ng.2213","article-title":"Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits","volume":"44","author":"Yang","year":"2012","journal-title":"Nat. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1038\/ejhg.2011.39","article-title":"Genomic inflation factors under polygenic inheritance","volume":"19","author":"Yang","year":"2011","journal-title":"Eur. J. Hum. Genet"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1038\/s41431-018-0168-5","article-title":"A fine-mapping study of central obesity loci incorporating functional annotation and imputation","volume":"26","author":"Zhang","year":"2018","journal-title":"Eur. J. Hum. Genet"},{"key":"2023033004311024900_","first-page":"97","article-title":"haploR: an R-package for querying web-based annotation tools","volume":"6","author":"Zhbannikov","year":"2017","journal-title":"F1000Research"},{"key":"2023033004311024900_","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1038\/nmeth.3547","article-title":"Predicting effects of noncoding variants with deep learning-based sequence model","volume":"12","author":"Zhou","year":"2015","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab658\/40453216\/btab658.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/2\/536\/49692797\/btab658.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/2\/536\/49692797\/btab658.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,8]],"date-time":"2023-11-08T14:03:56Z","timestamp":1699452236000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/2\/536\/6371178"}},"subtitle":[],"editor":[{"given":"Peter","family":"Robinson","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,9,16]]},"references-count":49,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,1,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab658","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.10.22.351221","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,15]]},"published":{"date-parts":[[2021,9,16]]}}}