{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:50Z","timestamp":1772138090802,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2018,7,13]],"date-time":"2018-07-13T00:00:00Z","timestamp":1531440000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Lynn and Edward Streim"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Neuronal analyses such as transcriptomics, epigenetics and genome-wide association studies must be assessed in the context of the human brain to generate biologically meaningful inferences. It is often difficult to access primary human brain tissue; therefore, approximations are made using alternative sources such as peripheral tissues or in\u00a0vitro-derived neurons. Gene sets from these studies are then assessed for their association with the post-mortem human brain. However, most analyses of post-mortem datasets are achieved by building new computational tools each time in-house, which can cause discrepancies from study to study. The field is in need of a user-friendly tool to examine spatiotemporal expression with respect to the postmortem brain. Such a tool will be of use in the molecular interrogation of neurological and psychiatric disorders, with direct advantages for the disease-modeling and human genetics communities.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed brainImageR, an R package that calculates both the spatial and temporal association of a dataset with post-mortem human brain. BrainImageR identifies anatomical regions enriched for candidate gene set expression. It further predicts the developmental time point of the sample, a task that has become increasingly important in the field of in\u00a0vitro neuronal modeling. These functionalities of brainImageR enable a quick and efficient characterization of a given dataset across normal human brain development.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>BrainImageR is released under the Creative Commons CC BY-SA 4.0 license and can be accessed directly at brainimager.salk.edu or the R code can be downloaded through github at https:\/\/github.com\/saralinker\/brainImageR.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty618","type":"journal-article","created":{"date-parts":[[2018,7,13]],"date-time":"2018-07-13T07:21:52Z","timestamp":1531466512000},"page":"343-345","source":"Crossref","is-referenced-by-count":7,"title":["BrainImageR: spatiotemporal gene set analysis referencing the human brain"],"prefix":"10.1093","volume":"35","author":[{"given":"Sara B","family":"Linker","sequence":"first","affiliation":[{"name":"Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan Y","family":"Hsu","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adela","family":"Pfaff","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Debha","family":"Amatya","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shu-Meng","family":"Ko","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Voter","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Quinn","family":"Wong","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fred H","family":"Gage","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,7,13]]},"reference":[{"key":"2023013107224720100_bty618-B1","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1093\/bioinformatics\/btw726","article-title":"cerebroViz: an R package for anatomical visualization of spatiotemporal brain data","volume":"33","author":"Bahl","year":"2017","journal-title":"Bioinformatics"},{"key":"2023013107224720100_bty618-B2","doi-asserted-by":"crossref","first-page":"15672","DOI":"10.1073\/pnas.1520760112","article-title":"Human cerebral organoids recapitulate gene expression programs of fetal neocortex development","volume":"112","author":"Camp","year":"2015","journal-title":"Proc. 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