{"id":"https://openalex.org/W1568929544","doi":"https://doi.org/10.1186/s12859-015-0553-9","title":"Deep convolutional neural networks for annotating gene expression patterns in the mouse brain","display_name":"Deep convolutional neural networks for annotating gene expression patterns in the mouse brain","publication_year":2015,"publication_date":"2015-05-06","ids":{"openalex":"https://openalex.org/W1568929544","doi":"https://doi.org/10.1186/s12859-015-0553-9","mag":"1568929544","pmid":"https://pubmed.ncbi.nlm.nih.gov/25948335"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-015-0553-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0553-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0553-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0553-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063558254","display_name":"Tao Zeng","orcid":"https://orcid.org/0000-0001-8006-3287"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tao Zeng","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA. tzeng@cs.odu.edu","Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA. tzeng@cs.odu.edu","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007355292","display_name":"Rongjian Li","orcid":"https://orcid.org/0000-0003-2739-5893"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rongjian Li","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA. rli@cs.odu.edu","Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA. rli@cs.odu.edu","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035065105","display_name":"Ravi Mukkamala","orcid":"https://orcid.org/0000-0001-6323-9789"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ravi Mukkamala","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA. mukka@cs.odu.edu","Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA. mukka@cs.odu.edu","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA","institution_ids":["https://openalex.org/I81365321"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010419481","display_name":"Jieping Ye","orcid":"https://orcid.org/0000-0001-8662-5818"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jieping Ye","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA. jpye@umich.edu","Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, MI, USA. jpye@umich.edu","Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA. jpye@umich.edu","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, 48109, MI, USA. jpye@umich.edu","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052278550","display_name":"Shuiwang Ji","orcid":"https://orcid.org/0000-0002-4205-4563"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shuiwang Ji","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA. sji@cs.odu.edu","Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA. sji@cs.odu.edu","institution_ids":["https://openalex.org/I81365321"]},{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, 23529, VA, USA","institution_ids":["https://openalex.org/I81365321"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052278550"],"corresponding_institution_ids":["https://openalex.org/I81365321"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":8.9803,"has_fulltext":true,"cited_by_count":65,"citation_normalized_percentile":{"value":0.97405789,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"16","issue":"1","first_page":"147","last_page":"147"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.4779999852180481,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.4779999852180481,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.29170000553131104,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.0786999985575676,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.818579375743866},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.6529976725578308},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.648020327091217},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6274843215942383},{"id":"https://openalex.org/keywords/brain-atlas","display_name":"Brain atlas","score":0.5299906134605408},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.5069808959960938},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5016486644744873},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.48132550716400146},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.44699183106422424},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3995082378387451},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.33821141719818115},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29488539695739746},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10118043422698975}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.818579375743866},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.6529976725578308},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.648020327091217},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6274843215942383},{"id":"https://openalex.org/C2780972224","wikidata":"https://www.wikidata.org/wiki/Q17047956","display_name":"Brain atlas","level":2,"score":0.5299906134605408},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.5069808959960938},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5016486644744873},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.48132550716400146},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.44699183106422424},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3995082378387451},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33821141719818115},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29488539695739746},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10118043422698975},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017403","descriptor_name":"In Situ Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017403","descriptor_name":"In Situ Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017403","descriptor_name":"In Situ Hybridization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018507","descriptor_name":"Gene Expression Regulation, Developmental","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-015-0553-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0553-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0553-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25948335","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25948335","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:digitalcommons.odu.edu:computerscience_fac_pubs-1047","is_oa":true,"landing_page_url":"https://digitalcommons.odu.edu/computerscience_fac_pubs/48","pdf_url":"https://digitalcommons.odu.edu/cgi/viewcontent.cgi?article=1047&context=computerscience_fac_pubs","source":{"id":"https://openalex.org/S4377196314","display_name":"ODU Digital Commons (Old Dominion University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I81365321","host_organization_name":"Old Dominion University","host_organization_lineage":["https://openalex.org/I81365321"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Science Faculty Publications","raw_type":"article"},{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/111637","is_oa":false,"landing_page_url":"https://hdl.handle.net/2027.42/111637","pdf_url":null,"source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:deepblue.lib.umich.edu:2027.42/134736","is_oa":false,"landing_page_url":"https://hdl.handle.net/2027.42/134736","pdf_url":null,"source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4432953","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4432953","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-015-0553-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-015-0553-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-015-0553-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.6800000071525574}],"awards":[{"id":"https://openalex.org/G179877238","display_name":null,"funder_award_id":"R01 LM010730","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3082190310","display_name":"Collaborative Research:  ABI Innovation: Integrative Analysis of the Anatomic and Genetic Landscapes in the Mouse Brain","funder_award_id":"1147134","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3182301627","display_name":null,"funder_award_id":"DBI-1147134","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4316741816","display_name":null,"funder_award_id":"DBI-1350258","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5445306524","display_name":null,"funder_award_id":"IIS-0953662","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5905345011","display_name":null,"funder_award_id":"LM010730","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6172928226","display_name":null,"funder_award_id":"R01 LM010730","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6848218983","display_name":"CAREER:  Dimensionality Reduction for Multi-Label Classification","funder_award_id":"0953662","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7696884232","display_name":null,"funder_award_id":"R01 LM010730","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G808065841","display_name":"CAREER: Towards the Next Generation of Data-Driven Computational Brain Analytics","funder_award_id":"1350258","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1568929544.pdf","grobid_xml":"https://content.openalex.org/works/W1568929544.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1508686244","https://openalex.org/W1583837637","https://openalex.org/W1849277567","https://openalex.org/W1965626594","https://openalex.org/W1985176850","https://openalex.org/W1990089119","https://openalex.org/W2046799970","https://openalex.org/W2062118960","https://openalex.org/W2066941820","https://openalex.org/W2095352482","https://openalex.org/W2098027279","https://openalex.org/W2098120923","https://openalex.org/W2112796928","https://openalex.org/W2124986204","https://openalex.org/W2143977080","https://openalex.org/W2148519517","https://openalex.org/W2151103935","https://openalex.org/W2155541015","https://openalex.org/W2158778629","https://openalex.org/W2161381512","https://openalex.org/W2163605009","https://openalex.org/W2171896402","https://openalex.org/W2913668833","https://openalex.org/W2963542991","https://openalex.org/W4254181784"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2590348769"],"abstract_inverted_index":{"BACKGROUND:":[0],"Profiling":[1],"gene":[2,38,69,160,170,194,241],"expression":[3,39,70,161,171,195,242],"in":[4,34,41,73,173,192],"brain":[5,23,76,152,175,201],"structures":[6,202],"at":[7,77,197],"various":[8,78],"spatial":[9],"and":[10,131,238],"temporal":[11],"scales":[12],"is":[13,254],"essential":[14],"to":[15,67,103,124,136,156,240,256],"understanding":[16],"how":[17],"genes":[18],"regulate":[19],"the":[20,46,50,74,82,107,133,150,224],"development":[21],"of":[22,45,84,100,110,142,149,182,200,212],"structures.":[24,176],"The":[25],"Allen":[26],"Developing":[27],"Mouse":[28],"Brain":[29],"Atlas":[30],"provides":[31],"high-resolution":[32],"3-D":[33],"situ":[35],"hybridization":[36],"(ISH)":[37],"patterns":[40,172,196],"multiple":[42,145,198],"developing":[43,111,205],"stages":[44],"mouse":[47,75,112],"brain.":[48,113],"Currently,":[49],"ISH":[51,108,129,146],"images":[52,72,102,109,130],"are":[53],"annotated":[54],"with":[55,218],"anatomical":[56],"terms":[57],"manually.":[58],"In":[59],"this":[60],"paper,":[61],"we":[62,118,208],"propose":[63],"a":[64,97,115],"computational":[65],"approach":[66,135,181],"annotate":[68],"pattern":[71,243],"structural":[79],"levels":[80,199],"over":[81],"course":[83],"development.":[85],"RESULTS:":[86],"We":[87,163],"applied":[88,119,239],"deep":[89],"convolutional":[90,184,229],"neural":[91,230],"network":[92,231],"that":[93,179],"was":[94],"trained":[95,233],"on":[96,234],"large":[98],"set":[99],"natural":[101,235],"extract":[104],"features":[105,143],"from":[106,128,144],"As":[114],"baseline":[116],"representation,":[117],"invariant":[120],"image":[121,147,236,259],"feature":[122,187],"descriptors":[123],"capture":[125],"local":[126],"statistics":[127],"used":[132],"bag-of-words":[134,225],"build":[137,157],"image-level":[138],"representations.":[139,162],"Both":[140],"types":[141],"sections":[148],"entire":[151],"were":[153],"then":[154],"combined":[155],"3-D,":[158],"brain-wide":[159],"employed":[164],"regularized":[165],"learning":[166,252],"methods":[167],"for":[168],"discriminating":[169],"different":[174],"Results":[177],"show":[178],"our":[180],"using":[183],"model":[185,232],"as":[186,216],"extractors":[188],"achieved":[189,209],"superior":[190,247],"performance":[191],"annotating":[193],"throughout":[203],"four":[204],"ages.":[206],"Overall,":[207],"average":[210],"AUC":[211],"0.894":[213],"\u00b1":[214,220],"0.014,":[215],"compared":[217],"0.820":[219],"0.046":[221],"yielded":[222,246],"by":[223],"approach.":[226],"CONCLUSIONS:":[227],"Deep":[228],"sets":[237],"annotation":[244],"tasks":[245],"performance,":[248],"demonstrating":[249],"its":[250],"transfer":[251],"property":[253],"applicable":[255],"such":[257],"biological":[258],"sets.":[260]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":12},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":11},{"year":2013,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}