{"id":"https://openalex.org/W2109516134","doi":"https://doi.org/10.1093/bioinformatics/btm244","title":"Automatic recognition and annotation of gene expression patterns of fly embryos","display_name":"Automatic recognition and annotation of gene expression patterns of fly embryos","publication_year":2007,"publication_date":"2007-06-15","ids":{"openalex":"https://openalex.org/W2109516134","doi":"https://doi.org/10.1093/bioinformatics/btm244","mag":"2109516134","pmid":"https://pubmed.ncbi.nlm.nih.gov/17237064"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/12/1571/49813322/bioinformatics_23_12_1571.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/23/12/1571/49813322/bioinformatics_23_12_1571.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066557235","display_name":"Jie Zhou","orcid":"https://orcid.org/0000-0002-3836-4163"},"institutions":[{"id":"https://openalex.org/I102502594","display_name":"Northern Illinois University","ror":"https://ror.org/012wxa772","country_code":"US","type":"education","lineage":["https://openalex.org/I102502594"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Zhou","raw_affiliation_strings":["Department of Computer Science, Northern Illinois University, DeKalb, IL 60115"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Northern Illinois University, DeKalb, IL 60115","institution_ids":["https://openalex.org/I102502594"]}]},{"author_position":"last","author":{"id":null,"display_name":"Hanchuan Peng","orcid":null},"institutions":[{"id":"https://openalex.org/I102502594","display_name":"Northern Illinois University","ror":"https://ror.org/012wxa772","country_code":"US","type":"education","lineage":["https://openalex.org/I102502594"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanchuan Peng","raw_affiliation_strings":["Department of Computer Science, Northern Illinois University, DeKalb, IL 60115"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Northern Illinois University, DeKalb, IL 60115","institution_ids":["https://openalex.org/I102502594"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I102502594"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":8.2277,"has_fulltext":false,"cited_by_count":54,"citation_normalized_percentile":{"value":0.97084835,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"23","issue":"12","first_page":"1571","last_page":"1572"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.5418999791145325,"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":0.5418999791145325,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.12370000034570694,"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/T12417","display_name":"Morphological variations and asymmetry","score":0.06279999762773514,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.8312000632286072},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6311032772064209},{"id":"https://openalex.org/keywords/automatic-image-annotation","display_name":"Automatic image annotation","score":0.5502226948738098},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4840494990348816},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4766867160797119},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.46121323108673096},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.4383942186832428},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43600142002105713},{"id":"https://openalex.org/keywords/image-retrieval","display_name":"Image retrieval","score":0.3533116281032562},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.3476184606552124},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3257475793361664},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3038788437843323},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2930906116962433},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2351301908493042},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17352509498596191}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8312000632286072},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6311032772064209},{"id":"https://openalex.org/C199579030","wikidata":"https://www.wikidata.org/wiki/Q2851778","display_name":"Automatic image annotation","level":4,"score":0.5502226948738098},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4840494990348816},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4766867160797119},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.46121323108673096},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.4383942186832428},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43600142002105713},{"id":"https://openalex.org/C1667742","wikidata":"https://www.wikidata.org/wiki/Q10927554","display_name":"Image retrieval","level":3,"score":0.3533116281032562},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.3476184606552124},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3257475793361664},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3038788437843323},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2930906116962433},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2351301908493042},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17352509498596191}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000196","qualifier_name":"embryology","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004330","descriptor_name":"Drosophila","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004625","descriptor_name":"Embryo, Nonmammalian","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004625","descriptor_name":"Embryo, Nonmammalian","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004625","descriptor_name":"Embryo, Nonmammalian","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","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":true},{"descriptor_ui":"D017403","descriptor_name":"In Situ Hybridization","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btm244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/12/1571/49813322/bioinformatics_23_12_1571.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17237064","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17237064","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm244","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm244","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/23/12/1571/49813322/bioinformatics_23_12_1571.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109516134.pdf","grobid_xml":"https://content.openalex.org/works/W2109516134.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1538912020","https://openalex.org/W1969259660","https://openalex.org/W2034732817","https://openalex.org/W2046799970","https://openalex.org/W2062024414","https://openalex.org/W2105490800","https://openalex.org/W2112796928","https://openalex.org/W2115755118","https://openalex.org/W2121638006","https://openalex.org/W2122539036","https://openalex.org/W2125148312","https://openalex.org/W2132549764","https://openalex.org/W2132984323","https://openalex.org/W2136573268","https://openalex.org/W2146076056","https://openalex.org/W2150455640","https://openalex.org/W2153635508","https://openalex.org/W2154053567","https://openalex.org/W2156909104","https://openalex.org/W2158092584","https://openalex.org/W3146003712"],"related_works":["https://openalex.org/W3177930984","https://openalex.org/W2052697133","https://openalex.org/W2119028572","https://openalex.org/W2376984068","https://openalex.org/W2152482390","https://openalex.org/W2365617273","https://openalex.org/W2076896210","https://openalex.org/W2093596879","https://openalex.org/W2506386910","https://openalex.org/W2117928543"],"abstract_inverted_index":{"MOTIVATION:":[0],"Gene":[1],"expression":[2],"patterns":[3],"obtained":[4],"by":[5,27,114,121],"in":[6,61,173],"situ":[7],"mRNA":[8],"hybridization":[9],"provide":[10],"important":[11],"information":[12],"about":[13],"different":[14],"genes":[15],"during":[16],"Drosophila":[17],"embryogenesis.":[18],"So":[19],"far,":[20],"annotations":[21,99],"of":[22,32,47,139],"these":[23],"images":[24],"are":[25,164],"done":[26],"manually":[28],"assigning":[29],"a":[30,52,57,63,78,137],"subset":[31],"anatomy":[33],"ontology":[34],"terms":[35],"to":[36,54,103,108,143,154,180],"an":[37,72,93,104,132],"image.":[38],"This":[39],"time-consuming":[40],"process":[41],"depends":[42],"heavily":[43],"on":[44],"the":[45,69,110,145,181],"consistency":[46],"experts.":[48],"RESULTS:":[49],"We":[50,67,106,134],"develop":[51],"system":[53,84],"automatically":[55],"annotate":[56],"fruitfly's":[58],"embryonic":[59],"tissue":[60],"which":[62,126],"gene":[64],"has":[65],"expression.":[66],"formulate":[68],"task":[70],"as":[71],"image":[73,94,151],"pattern":[74],"recognition":[75],"problem.":[76],"For":[77],"new":[79],"fly":[80],"embryo":[81,112],"image,":[82],"our":[83],"answers":[85],"two":[86],"questions:":[87],"(1)":[88],"Which":[89,98],"stage":[90],"range":[91],"does":[92],"belong":[95],"to?":[96],"(2)":[97],"should":[100],"be":[101,176],"assigned":[102],"image?":[105],"propose":[107],"identify":[109],"wavelet":[111,117],"features":[113,130],"multi-resolution":[115],"2D":[116],"discrete":[118],"transform,":[119],"followed":[120],"min-redundancy":[122],"max-relevance":[123],"feature":[124],"selection,":[125],"yields":[127],"optimal":[128],"distinguishing":[129],"for":[131],"annotation.":[133],"then":[135],"construct":[136],"series":[138],"parallel":[140],"bi-class":[141],"predictors":[142],"solve":[144],"multi-objective":[146],"annotation":[147,161],"problem":[148],"since":[149],"each":[150],"may":[152],"correspond":[153],"multiple":[155],"annotations.":[156],"SUPPLEMENTARY":[157],"INFORMATION:":[158],"The":[159,170],"complete":[160],"prediction":[162],"results":[163],"available":[165,177],"at:":[166],"http://www.cs.niu.edu/~jzhou/papers/fruitfly":[167],"and":[168],"http://research.janelia.org/peng/proj/fly_embryo_annotation/.":[169],"datasets":[171],"used":[172],"experiments":[174],"will":[175],"upon":[178],"request":[179],"correspondence":[182],"author.":[183]},"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":4}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}