{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T09:27:58Z","timestamp":1775986078740,"version":"3.50.1"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2018,3,21]],"date-time":"2018-03-21T00:00:00Z","timestamp":1521590400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"United States National Institutes of Health","award":["R01HL128234"],"award-info":[{"award-number":["R01HL128234"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genetic reporter assays are a convenient, relatively inexpensive method for studying the regulation of gene expression. Massively Parallel Reporter Assays (MPRA) are high-throughput functionalization assays that interrogate the transcriptional activity of many genetic variants at once using a library of synthetic barcoded constructs. Despite growing interest in this area, there are few computational tools to design and execute MPRA studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We designed an online web-tool and R package that allows for interactive MPRA experimental design encompassing both power analysis and design of constructs. Our tool is tuned using data from real MPRA studies. Users can adjust experimental parameters to examine the predicted effect on assay power as well as upload VCFs for automated construct sequence generation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The MPRA Design Tools web application is available here: https:\/\/andrewghazi.shinyapps.io\/designmpra\/, https:\/\/github.com\/andrewGhazi\/designMPRA and https:\/\/github.com\/andrewGhazi\/mpradesigntools.<\/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\/bty150","type":"journal-article","created":{"date-parts":[[2018,3,20]],"date-time":"2018-03-20T20:24:48Z","timestamp":1521577488000},"page":"2682-2683","source":"Crossref","is-referenced-by-count":10,"title":["Design tools for MPRA experiments"],"prefix":"10.1093","volume":"34","author":[{"given":"Andrew R","family":"Ghazi","sequence":"first","affiliation":[{"name":"Department of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA"}]},{"given":"Edward S","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA"}]},{"given":"David M","family":"Henke","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA"}]},{"given":"Namrata","family":"Madan","sequence":"additional","affiliation":[{"name":"Cardeza Foundation for Hematologic Research and Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA"}]},{"given":"Leonard C","family":"Edelstein","sequence":"additional","affiliation":[{"name":"Cardeza Foundation for Hematologic Research and Department of Medicine, Thomas Jefferson University, Philadelphia, PA, USA"}]},{"given":"Chad A","family":"Shaw","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,3,21]]},"reference":[{"key":"2023012713082856000_bty150-B1","first-page":"1","article-title":"MPRAnator: a web-based tool for the design of Massively Parallel Reporter Assay experiments","volume":"33","author":"Georgakopoulos-Soares","year":"2016","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012713082856000_bty150-B2","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/nbt.2137","article-title":"Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay","volume":"30","author":"Melnikov","year":"2012","journal-title":"Nat. Biotechnol"},{"key":"2023012713082856000_bty150-B3","doi-asserted-by":"crossref","first-page":"1519","DOI":"10.1016\/j.cell.2016.04.027","article-title":"Direct identification of hundreds of expression-modulating variants using a multiplexed reporter assay","volume":"165","author":"Tewhey","year":"2016","journal-title":"Cell"},{"key":"2023012713082856000_bty150-B4","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1016\/j.cell.2016.04.048","article-title":"Systematic functional dissection of common genetic variation affecting red blood cell traits","volume":"165","author":"Ulirsch","year":"2016","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/15\/2682\/48935381\/bioinformatics_34_15_2682.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/15\/2682\/48935381\/bioinformatics_34_15_2682.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T14:13:32Z","timestamp":1674828812000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/15\/2682\/4948615"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,3,21]]},"references-count":4,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2018,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty150","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,8,1]]},"published":{"date-parts":[[2018,3,21]]}}}