{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T18:52:30Z","timestamp":1770749550445,"version":"3.50.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2019,3,11]],"date-time":"2019-03-11T00:00:00Z","timestamp":1552262400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Shanghai Science and Technology Innovation Plan","award":["15JC1400101"],"award-info":[{"award-number":["15JC1400101"]}]},{"name":"Shanghai Science and Technology Innovation Plan","award":["16JC1420402"],"award-info":[{"award-number":["16JC1420402"]}]},{"name":"Shanghai Municipal Science and Technology Major Project","award":["2018SHZDZX01"],"award-info":[{"award-number":["2018SHZDZX01"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["71661167002"],"award-info":[{"award-number":["71661167002"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["91630314"],"award-info":[{"award-number":["91630314"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["61573107"],"award-info":[{"award-number":["61573107"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Special Funds for Major State Basic Research Projects of China","award":["2015CB856003"],"award-info":[{"award-number":["2015CB856003"]}]},{"DOI":"10.13039\/100007219","name":"Shanghai Natural Science Foundation","doi-asserted-by":"publisher","award":["17ZR1444200"],"award-info":[{"award-number":["17ZR1444200"]}],"id":[{"id":"10.13039\/100007219","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Basic Research Program of China","doi-asserted-by":"publisher","award":["2016YFC0906402"],"award-info":[{"award-number":["2016YFC0906402"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Sciences Foundation of China","doi-asserted-by":"crossref","award":["81701773"],"award-info":[{"award-number":["81701773"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Sciences Foundation of China","doi-asserted-by":"crossref","award":["11771010"],"award-info":[{"award-number":["11771010"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Shanghai Sailing Program","award":["17YF1426200"],"award-info":[{"award-number":["17YF1426200"]}]},{"DOI":"10.13039\/100007219","name":"Natural Science Foundation of Shanghai","doi-asserted-by":"publisher","award":["18ZR1404400"],"award-info":[{"award-number":["18ZR1404400"]}],"id":[{"id":"10.13039\/100007219","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014103","name":"Key Research and Development Plan of Shandong Province","doi-asserted-by":"publisher","award":["2017CXGC1503"],"award-info":[{"award-number":["2017CXGC1503"]}],"id":[{"id":"10.13039\/100014103","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014103","name":"Key Research and Development Plan of Shandong Province","doi-asserted-by":"publisher","award":["2018GSF118228"],"award-info":[{"award-number":["2018GSF118228"]}],"id":[{"id":"10.13039\/100014103","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007219","name":"Shanghai Natural Science Foundation","doi-asserted-by":"publisher","award":["17ZR1401600"],"award-info":[{"award-number":["17ZR1401600"]}],"id":[{"id":"10.13039\/100007219","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai AI Platform for Diagnosis and Treatment of Brain Diseases"},{"name":"Projects of Zhangjiang Hi-Tech District Management Committee"},{"name":"Base for Introducing Talents of Discipline to Universities","award":["B18015"],"award-info":[{"award-number":["B18015"]}]},{"name":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence"},{"DOI":"10.13039\/501100003347","name":"Fudan University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009950","name":"Ministry of Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009950","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Advances in neuroimaging and sequencing techniques provide an unprecedented opportunity to map the function of brain regions and identify the roots of psychiatric diseases. However, the results from most neuroimaging studies, i.e. activated clusters\/regions or functional connectivities between brain regions, frequently cannot be conveniently and systematically interpreted, rendering the biological meaning unclear.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We describe a brain annotation toolbox that generates functional and genetic annotations for neuroimaging results. The voxel-level functional description from the Neurosynth database and gene expression profile from the Allen Human Brain Atlas are used to generate functional\/genetic information for region-level neuroimaging results. The validity of the approach is demonstrated by showing that the functional and genetic annotations for specific brain regions are consistent with each other; and further the region by region functional similarity network and genetic similarity network are highly correlated for major brain atlases. One application of brain annotation toolbox is to help provide functional\/genetic annotations for newly discovered regions with unknown functions, e.g. the 97 new regions identified in the Human Connectome Project. Importantly, this toolbox can help understand differences between psychiatric patients and controls, and this is demonstrated using schizophrenia and autism data, for which the functional and genetic annotations for the neuroimaging changes in patients are consistent with each other and help interpret the results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>BAT is implemented as a free and open-source MATLAB toolbox and is publicly available at http:\/\/123.56.224.61:1313\/post\/bat.<\/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\/btz128","type":"journal-article","created":{"date-parts":[[2019,2,20]],"date-time":"2019-02-20T20:35:42Z","timestamp":1550694942000},"page":"3771-3778","source":"Crossref","is-referenced-by-count":49,"title":["Brain annotation toolbox: exploring the functional and genetic associations of neuroimaging results"],"prefix":"10.1093","volume":"35","author":[{"given":"Zhaowen","family":"Liu","sequence":"first","affiliation":[{"name":"Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital , Boston, MA, USA"},{"name":"Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School , Boston, MA, USA"},{"name":"Institute of Science and Technology for Brain Inspired Intelligence, Fudan University , Shanghai, China"}]},{"given":"Edmund T","family":"Rolls","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Warwick , Coventry, UK"},{"name":"Oxford Centre for Computational Neuroscience , Oxford, UK"}]},{"given":"Zhi","family":"Liu","sequence":"additional","affiliation":[{"name":"The School of Information Science and Engineering, Shandong University , Jinan, China"}]},{"given":"Kai","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computer and Information Sciences, Temple University , Philadelphia, PA, USA"}]},{"given":"Ming","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain Inspired Intelligence, Fudan University , Shanghai, China"}]},{"given":"Jingnan","family":"Du","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain Inspired Intelligence, Fudan University , Shanghai, China"}]},{"given":"Weikang","family":"Gong","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain Inspired Intelligence, Fudan University , Shanghai, China"}]},{"given":"Wei","family":"Cheng","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain Inspired Intelligence, Fudan University , Shanghai, China"}]},{"given":"Fei","family":"Dai","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain Inspired Intelligence, Fudan University , Shanghai, China"}]},{"given":"He","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain Inspired Intelligence, Fudan University , Shanghai, China"}]},{"given":"Kamil","family":"Ugurbil","sequence":"additional","affiliation":[{"name":"Center for Magnetic Resonance Research (CMRR), University of Minnesota , Minneapolis, MN, USA"}]},{"given":"Jie","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain Inspired Intelligence, Fudan University , Shanghai, China"},{"name":"Ministry of Education, Key Laboratory of Computational Neuroscience and Brain Inspired Intelligence (Fudan University) , Shanghai, China"}]},{"given":"Jianfeng","family":"Feng","sequence":"additional","affiliation":[{"name":"Institute of Science and Technology for Brain Inspired Intelligence, Fudan University , Shanghai, China"},{"name":"Department of Computer Science, University of Warwick , Coventry, UK"},{"name":"Ministry of Education, Key Laboratory of Computational Neuroscience and Brain Inspired Intelligence (Fudan University) , Shanghai, China"},{"name":"Collaborative Innovation Center for Brain Science, Fudan University , Shanghai, China"},{"name":"Shanghai Center for Mathematical Sciences , Shanghai, China"}]}],"member":"286","published-online":{"date-parts":[[2019,3,11]]},"reference":[{"key":"2023013108124887100_btz128-B1","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1038\/nm.4190","article-title":"The search for imaging biomarkers in psychiatric disorders","volume":"22","author":"Abi-Dargham","year":"2016","journal-title":"Nat. Med"},{"key":"2023013108124887100_btz128-B2","doi-asserted-by":"crossref","first-page":"1358","DOI":"10.1176\/ajp.156.9.1358","article-title":"Memory impairment in schizophrenia: a meta-analysis","volume":"156","author":"Aleman","year":"1999","journal-title":"Am. J. Psychiatry"},{"key":"2023013108124887100_btz128-B3","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1146\/annurev.me.39.020188.002003","article-title":"Evaluation of brain imaging techniques in mental-illness","volume":"39","author":"Andreasen","year":"1988","journal-title":"Annu. Rev. Med"},{"key":"2023013108124887100_btz128-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.pneurobio.2016.07.001","article-title":"Behavior, neuropsychology and fMRI","volume":"145","author":"Bennett","year":"2016","journal-title":"Prog. Neurobiol"},{"key":"2023013108124887100_btz128-B5","first-page":"644","volume-title":"Vergleichende Lokalisationslehre der Groshirnrinde","author":"Brodmann","year":"1909"},{"key":"2023013108124887100_btz128-B6","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.schres.2010.03.019","article-title":"Attention deficits in schizophrenia - preliminary evidence of dissociable transient and sustained deficits","volume":"122","author":"Carter","year":"2010","journal-title":"Schizophr. Res"},{"key":"2023013108124887100_btz128-B7","doi-asserted-by":"crossref","first-page":"W305","DOI":"10.1093\/nar\/gkp427","article-title":"ToppGene Suite for gene list enrichment analysis and candidate gene prioritization","volume":"37","author":"Chen","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023013108124887100_btz128-B8","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1093\/brain\/awv051","article-title":"Autism: reduced connectivity between cortical areas involved in face expression, theory of mind, and the sense of self","volume":"138","author":"Cheng","year":"2015","journal-title":"Brain"},{"key":"2023013108124887100_btz128-B9","doi-asserted-by":"crossref","first-page":"939","DOI":"10.2165\/00023210-200822110-00004","article-title":"Sleep disturbances in patients with schizophrenia impact and effect of antipsychotics","volume":"22","author":"Cohrs","year":"2008","journal-title":"CNS Drugs"},{"key":"2023013108124887100_btz128-B10","doi-asserted-by":"crossref","first-page":"1914","DOI":"10.1002\/hbm.21333","article-title":"A whole brain fMRI atlas generated via spatially constrained spectral clustering","volume":"33","author":"Craddock","year":"2012","journal-title":"Hum. Brain Mapp"},{"key":"2023013108124887100_btz128-B11","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"Edgar","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2023013108124887100_btz128-B12","first-page":"012310","article-title":"Bridging psychology and genetics using large-scale spatial analysis of neuroimaging and neurogenetic data","author":"Fox","year":"2014","journal-title":"bioRxiv"},{"key":"2023013108124887100_btz128-B13","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1038\/nrn789","article-title":"Mapping context and content: the BrainMap model","volume":"3","author":"Fox","year":"2002","journal-title":"Nat. Rev. Neurosci"},{"key":"2023013108124887100_btz128-B14","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nature18933","article-title":"A multi-modal parcellation of human cerebral cortex","volume":"536","author":"Glasser","year":"2016","journal-title":"Nature"},{"key":"2023013108124887100_btz128-B15","doi-asserted-by":"crossref","first-page":"1832","DOI":"10.1038\/nn.4171","article-title":"Canonical genetic signatures of the adult human brain","volume":"18","author":"Hawrylycz","year":"2015","journal-title":"Nat. Neurosci"},{"key":"2023013108124887100_btz128-B16","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/nature11405","article-title":"An anatomically comprehensive atlas of the adult human brain transcriptome","volume":"489","author":"Hawrylycz","year":"2012","journal-title":"Nature"},{"key":"2023013108124887100_btz128-B17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Huang","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023013108124887100_btz128-B18","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc"},{"key":"2023013108124887100_btz128-B19","doi-asserted-by":"crossref","first-page":"E469","DOI":"10.1073\/pnas.1510903113","article-title":"Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain","volume":"113","author":"Krienen","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023013108124887100_btz128-B20","first-page":"436","article-title":"Brain-Wide Analysis of Functional Connectivity in First-Episode and Chronic Stages of Schizophrenia","volume":"43","author":"Li","year":"2017","journal-title":"Schizophr. Bull"},{"key":"2023013108124887100_btz128-B21","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1016\/j.neuron.2011.09.006","article-title":"Functional network organization of the human brain","volume":"72","author":"Power","year":"2011","journal-title":"Neuron"},{"key":"2023013108124887100_btz128-B22","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1126\/science.1255905","article-title":"Correlated gene expression supports synchronous activity in brain networks","volume":"348","author":"Richiardi","year":"2015","journal-title":"Science"},{"key":"2023013108124887100_btz128-B23","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1093\/bioinformatics\/btl633","article-title":"Enrichment or depletion of a GO category within a class of genes: which test?","volume":"23","author":"Rivals","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013108124887100_btz128-B24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.neuroimage.2015.07.075","article-title":"Implementation of a new parcellation of the orbitofrontal cortex in the automated anatomical labeling atlas","volume":"122","author":"Rolls","year":"2015","journal-title":"Neuroimage"},{"key":"2023013108124887100_btz128-B25","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1016\/j.tins.2012.09.005","article-title":"The Allen Human Brain Atlas: comprehensive gene expression mapping of the human brain","volume":"35","author":"Shen","year":"2012","journal-title":"Trends Neurosci"},{"key":"2023013108124887100_btz128-B26","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.1016\/S0140-6736(12)62129-1","article-title":"Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis","volume":"381","author":"Smoller","year":"2013","journal-title":"Lancet"},{"key":"2023013108124887100_btz128-B27","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1016\/j.tics.2007.06.002","article-title":"Decoding human brain activity during real-world experiences","volume":"11","author":"Spiers","year":"2007","journal-title":"Trends Cogn. Sci"},{"key":"2023013108124887100_btz128-B28","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1007\/s00401-010-0655-4","article-title":"The neuropathology of autism: defects of neurogenesis and neuronal migration, and dysplastic changes","volume":"119","author":"Wegiel","year":"2010","journal-title":"Acta Neuropathol"},{"key":"2023013108124887100_btz128-B29","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1111\/j.1745-6924.2009.01127.x","article-title":"Big Correlations in Little Studies: inflated fMRI Correlations Reflect Low Statistical Power-Commentary on Vul et al. (2009)","volume":"4","author":"Yarkoni","year":"2009","journal-title":"Perspect. Psychol. Sci"},{"key":"2023013108124887100_btz128-B30","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1038\/nmeth.1635","article-title":"Large-scale automated synthesis of human functional neuroimaging data","volume":"8","author":"Yarkoni","year":"2011","journal-title":"Nat Methods"},{"key":"2023013108124887100_btz128-B31","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1016\/j.tics.2010.08.004","article-title":"Cognitive neuroscience 2.0: building a cumulative science of human brain function","volume":"14","author":"Yarkoni","year":"2010","journal-title":"Trends Cogn. Sci"},{"key":"2023013108124887100_btz128-B32","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1152\/jn.00338.2011","article-title":"The organization of the human cerebral cortex estimated by intrinsic functional connectivity","volume":"106","author":"Yeo","year":"2011","journal-title":"J. Neurophysiol"},{"key":"2023013108124887100_btz128-B33","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1038\/nature18914","article-title":"Systems neuroscience: a modern map of the human cerebral cortex","volume":"536","author":"Yeo","year":"2016","journal-title":"Nature"},{"key":"2023013108124887100_btz128-B34","doi-asserted-by":"crossref","first-page":"a009886","DOI":"10.1101\/cshperspect.a009886","article-title":"Synaptic dysfunction in neurodevelopmental disorders associated with autism and intellectual disabilities","volume":"4","author":"Zoghbi","year":"2012","journal-title":"Cold Spring Harb. Perspect. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/19\/3771\/48975870\/bioinformatics_35_19_3771.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/19\/3771\/48975870\/bioinformatics_35_19_3771.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T14:47:44Z","timestamp":1675176464000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/19\/3771\/5373120"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,3,11]]},"references-count":34,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2019,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz128","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,10,1]]},"published":{"date-parts":[[2019,3,11]]}}}