{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T07:25:00Z","timestamp":1775373900122,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2017,3,11]],"date-time":"2017-03-11T00:00:00Z","timestamp":1489190400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["5P50CA127003"],"award-info":[{"award-number":["5P50CA127003"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["1R35CA197449"],"award-info":[{"award-number":["1R35CA197449"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["1U01CA190234"],"award-info":[{"award-number":["1U01CA190234"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["5P30CA006516"],"award-info":[{"award-number":["5P30CA006516"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that begins with a model of transcription factor\u2013target gene interactions and uses message passing to update the network model given available transcriptomic and protein\u2013protein interaction data. PANDA is used to estimate networks for each experimental group and the network models are then compared between groups to explore transcriptional processes that distinguish the groups. We present pandaR (bioconductor.org\/packages\/pandaR), a Bioconductor package that implements PANDA and provides a framework for exploratory data analysis on gene regulatory networks.<\/jats:p>\n               <jats:p>Availability and Implementation: PandaR is provided as a Bioconductor R Package and is available at bioconductor.org\/packages\/pandaR.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btx139","type":"journal-article","created":{"date-parts":[[2017,3,9]],"date-time":"2017-03-09T20:24:58Z","timestamp":1489091098000},"page":"2232-2234","source":"Crossref","is-referenced-by-count":20,"title":["Estimating gene regulatory networks with pandaR"],"prefix":"10.1093","volume":"33","author":[{"given":"Daniel","family":"Schlauch","sequence":"first","affiliation":[{"name":"Department of Computational Biology and Biostatistics, Dana-Farber Cancer Institute, Brigham and Women\u2019s Hospital, Boston, MA, USA"},{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health, Brigham and Women\u2019s Hospital, Boston, MA, USA"}]},{"given":"Joseph N","family":"Paulson","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Biostatistics, Dana-Farber Cancer Institute, Brigham and Women\u2019s Hospital, Boston, MA, USA"},{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health, Brigham and Women\u2019s Hospital, Boston, MA, USA"}]},{"given":"Albert","family":"Young","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Biostatistics, Dana-Farber Cancer Institute, Brigham and Women\u2019s Hospital, Boston, MA, USA"},{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health, Brigham and Women\u2019s Hospital, Boston, MA, USA"}]},{"given":"Kimberly","family":"Glass","sequence":"additional","affiliation":[{"name":"Channing Division of Network Medicine, Brigham and Women\u2019s Hospital, Boston, MA, USA"}]},{"given":"John","family":"Quackenbush","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Biostatistics, Dana-Farber Cancer Institute, Brigham and Women\u2019s Hospital, Boston, MA, USA"},{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health, Brigham and Women\u2019s Hospital, Boston, MA, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,3,11]]},"reference":[{"key":"2023051506470682100_btx139-B2","doi-asserted-by":"crossref","first-page":"e64832","DOI":"10.1371\/journal.pone.0064832","article-title":"Passing messages between biological networks to refine predicted interactions","volume":"8","author":"Glass","year":"2013","journal-title":"PLoS ONE"},{"key":"2023051506470682100_btx139-B3","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1186\/s12918-014-0118-y","article-title":"Sexually-dimorphic targeting of functionally-related genes in COPD","volume":"8","author":"Glass","year":"2014","journal-title":"BMC Syst. 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