{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T18:09:59Z","timestamp":1761156599311,"version":"3.37.3"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,12,5]],"date-time":"2018-12-05T00:00:00Z","timestamp":1543968000000},"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\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["61702556","202041004"],"award-info":[{"award-number":["61702556","202041004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Functional gene networks, representing how likely two genes work in the same biological process, are important models for studying gene interactions in complex tissues. However, a limitation of the current network-building scheme is the lack of leveraging evidence from multiple model organisms as well as the lack of expert curation and quality control of the input genomic data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present BaiHui, a brain-specific functional gene network built by probabilistically integrating expertly-hand-curated (by reading original publications) heterogeneous and multi-species genomic data in human, mouse and rat brains. To facilitate the use of this network, we deployed a web server through which users can query their genes of interest, visualize the network, gain functional insight from enrichment analysis and download network data. We also illustrated how this network could be used to generate testable hypotheses on disease gene prioritization of brain disorders.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>BaiHui is freely available at: http:\/\/guanlab.ccmb.med.umich.edu\/BaiHui\/.<\/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\/bty1001","type":"journal-article","created":{"date-parts":[[2018,12,4]],"date-time":"2018-12-04T20:12:24Z","timestamp":1543954344000},"page":"2486-2488","source":"Crossref","is-referenced-by-count":10,"title":["BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3438-739X","authenticated-orcid":false,"given":"Hong-Dong","family":"Li","sequence":"first","affiliation":[{"name":"Center for Bioinformatics, School of Information Science and Engineering, Central South University, Changsha, People\u2019s Republic of China"},{"name":"Department of Computational Medicine and Bioinformatics"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tianjian","family":"Bai","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erin","family":"Sandford","sequence":"additional","affiliation":[{"name":"Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Margit","family":"Burmeister","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics"},{"name":"Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanfang","family":"Guan","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,12,5]]},"reference":[{"key":"2023062712313432100_bty1001-B1","doi-asserted-by":"crossref","first-page":"7.","DOI":"10.1038\/s41531-017-0008-2","article-title":"Synaptic proteins in CSF relate to Parkinson\u2019s disease stage markers","volume":"3","author":"Bereczki","year":"2017","journal-title":"Parkinson Dis"},{"key":"2023062712313432100_bty1001-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/ejn.13760","article-title":"A review of genome-wide transcriptomics studies in Parkinson\u2019s disease","volume":"47","author":"Borrageiro","year":"2018","journal-title":"Eur. J. Neurosci"},{"key":"2023062712313432100_bty1001-B3","doi-asserted-by":"crossref","first-page":"569.","DOI":"10.1038\/ng.3259","article-title":"Understanding multicellular function and disease with human tissue-specific networks","volume":"47","author":"Greene","year":"2015","journal-title":"Nat. Genet"},{"key":"2023062712313432100_bty1001-B4","doi-asserted-by":"crossref","first-page":"e1000165.","DOI":"10.1371\/journal.pcbi.1000165","article-title":"A genomewide functional network for the laboratory mouse","volume":"4","author":"Guan","year":"2008","journal-title":"PLoS Comput. Biol"},{"key":"2023062712313432100_bty1001-B5","doi-asserted-by":"crossref","first-page":"e1000991.","DOI":"10.1371\/journal.pcbi.1000991","article-title":"Functional genomics complements quantitative genetics in identifying disease-gene associations","volume":"6","author":"Guan","year":"2010","journal-title":"PLoS Comput. 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Biol"},{"key":"2023062712313432100_bty1001-B7","doi-asserted-by":"crossref","first-page":"2289","DOI":"10.1093\/bioinformatics\/btq408","article-title":"Computational analysis of tissue-specific gene networks: application to murine retinal functional studies","volume":"26","author":"Hu","year":"2010","journal-title":"Bioinformatics"},{"key":"2023062712313432100_bty1001-B8","doi-asserted-by":"crossref","first-page":"e1002270","DOI":"10.1371\/journal.pmed.1002270","article-title":"App, Psen1, and Psen2 mutations in early-onset alzheimer disease: a genetic screening study of familial and sporadic cases","volume":"14","author":"Lanoiselee","year":"2017","journal-title":"PLoS Med"},{"key":"2023062712313432100_bty1001-B9","doi-asserted-by":"crossref","first-page":"5446","DOI":"10.1158\/0008-5472.CAN-18-0740","article-title":"Network propagation predicts drug synergy in cancers","volume":"78","author":"Li","year":"2018","journal-title":"Cancer Res"},{"key":"2023062712313432100_bty1001-B10","first-page":"167","article-title":"Minreg: a scalable algorithm for learning parsimonious regulatory networks in yeast and mammals","volume":"7","author":"Pe\u2019er","year":"2006","journal-title":"J. Mach. Learn. Res"},{"key":"2023062712313432100_bty1001-B11","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1007\/s00335-014-9508-0","article-title":"Precise genetic mapping and integrative bioinformatics in diversity outbred mice reveals hydin as a novel pain gene","volume":"25","author":"Recla","year":"2014","journal-title":"Mamm. Genome"},{"key":"2023062712313432100_bty1001-B12","doi-asserted-by":"crossref","first-page":"1607","DOI":"10.1016\/j.neurobiolaging.2009.10.011","article-title":"Cathepsin D gene and the risk of Alzheimer\u2019s disease: a population-based study and meta-analysis","volume":"32","author":"Schuur","year":"2011","journal-title":"Neurobiol. Aging"},{"key":"2023062712313432100_bty1001-B13","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/nature10110","article-title":"Transcriptomic analysis of autistic brain reveals convergent molecular pathology","volume":"474","author":"Voineagu","year":"2011","journal-title":"Nature"},{"key":"2023062712313432100_bty1001-B14","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.conb.2017.08.004","article-title":"Striatal synapses, circuits, and Parkinson\u2019s disease","volume":"48","author":"Zhai","year":"2018","journal-title":"Curr. Opin. Neurobiol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/14\/2486\/50720860\/bioinformatics_35_14_2486.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/14\/2486\/50720860\/bioinformatics_35_14_2486.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T12:32:10Z","timestamp":1687869130000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/14\/2486\/5231854"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,12,5]]},"references-count":14,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2019,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty1001","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,7]]},"published":{"date-parts":[[2018,12,5]]}}}