{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T16:10:51Z","timestamp":1784304651774,"version":"3.55.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,6,3]],"date-time":"2022-06-03T00:00:00Z","timestamp":1654214400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Tobacco Settlement","award":["21\u20135734-0010"],"award-info":[{"award-number":["21\u20135734-0010"]}]},{"name":"Burroughs Wellcome"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>RNA structures play critical roles in regulating gene expression across all domains of life and\u00a0viruses. Chemical probing methods coupled with massively parallel sequencing have revolutionized the RNA structure field by enabling the assessment of many structures in their native, physiological context. Previously, we developed Dimethyl-Sulfate-based Mutational Profiling and Sequencing (DMS-MaPseq), which uses DMS to label the Watson-Crick face of open and accessible adenine and cytosine bases in the RNA. We used this approach to determine the genome-wide structures of HIV-1 and SARS-CoV-2 in infected cells, which permitted uncovering new biology and identifying therapeutic targets. Due to the simplicity and ease of the experimental procedure, DMS-MaPseq has been adopted by labs worldwide. However, bioinformatic\u00a0analysis remains a substantial hurdle for labs that often lack the necessary infrastructure and computational expertise. Here we present a modern web-based interface that automates the analysis of chemical probing profiles from raw sequencing files (http:\/\/rnadreem.org). The availability of a simple web-based platform for DMS-MaPseq analysis will dramatically expand studies of RNA structure and aid in the design of structure-based therapeutics.<\/jats:p>","DOI":"10.1093\/nar\/gkac435","type":"journal-article","created":{"date-parts":[[2022,6,3]],"date-time":"2022-06-03T12:22:43Z","timestamp":1654258963000},"page":"W266-W271","source":"Crossref","is-referenced-by-count":8,"title":["Web-based platform for analysis of RNA folding from high throughput chemical probing data"],"prefix":"10.1093","volume":"50","author":[{"given":"Christopher P","family":"Jurich","sequence":"first","affiliation":[{"name":"Department of Chemistry, University of Nebraska-Lincoln , Lincoln, NE 68588, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amir","family":"Brivanlou","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvi","family":"Rouskin","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Harvard Medical School , Boston, MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8878-8119","authenticated-orcid":false,"given":"Joseph D","family":"Yesselman","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Nebraska-Lincoln , Lincoln, NE 68588, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,6,3]]},"reference":[{"key":"2022070423574674900_B1","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.cell.2009.02.007","article-title":"The centrality of RNA","volume":"136","author":"Sharp","year":"2009","journal-title":"Cell"},{"key":"2022070423574674900_B2","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1038\/s41580-019-0136-0","article-title":"The roles of structural dynamics in the cellular functions of RNAs","volume":"20","author":"Ganser","year":"2019","journal-title":"Nat. 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