{"id":"https://openalex.org/W2108160018","doi":"https://doi.org/10.1093/bioinformatics/btk003","title":"HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana","display_name":"HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana","publication_year":2005,"publication_date":"2005-12-15","ids":{"openalex":"https://openalex.org/W2108160018","doi":"https://doi.org/10.1093/bioinformatics/btk003","mag":"2108160018","pmid":"https://pubmed.ncbi.nlm.nih.gov/16357035"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btk003","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk003","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/523/48840298/bioinformatics_22_5_523.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/22/5/523/48840298/bioinformatics_22_5_523.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042971895","display_name":"Guojun Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guojun Yang","raw_affiliation_strings":["Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University \u00a0 College Station, TX 77843, USA","Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University College Station, TX 77843, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University \u00a0 College Station, TX 77843, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University College Station, TX 77843, USA#TAB#","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112197764","display_name":"Timothy C. Hall","orcid":null},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Timothy C. Hall","raw_affiliation_strings":["Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University \u00a0 College Station, TX 77843, USA","Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University College Station, TX 77843, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University \u00a0 College Station, TX 77843, USA","institution_ids":["https://openalex.org/I91045830"]},{"raw_affiliation_string":"Institute of Developmental and Molecular Biology and Department of Biology, Texas A&M University College Station, TX 77843, USA#TAB#","institution_ids":["https://openalex.org/I91045830"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5112197764"],"corresponding_institution_ids":["https://openalex.org/I91045830"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.237,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.54157282,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"5","first_page":"523","last_page":"526"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10240","display_name":"Plant tissue culture and regeneration","score":0.18199999630451202,"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"}},"topics":[{"id":"https://openalex.org/T10240","display_name":"Plant tissue culture and regeneration","score":0.18199999630451202,"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/T12929","display_name":"Animal Genetics and Reproduction","score":0.17880000174045563,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.08640000224113464,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/transgene","display_name":"Transgene","score":0.8859652280807495},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6201627254486084},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5685065984725952},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5598362684249878},{"id":"https://openalex.org/keywords/insert","display_name":"Insert (composites)","score":0.5440040230751038},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5135088562965393},{"id":"https://openalex.org/keywords/restriction-enzyme","display_name":"Restriction enzyme","score":0.46447813510894775},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.4376761019229889},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4201357960700989},{"id":"https://openalex.org/keywords/restriction-site","display_name":"Restriction site","score":0.41505491733551025},{"id":"https://openalex.org/keywords/restriction-digest","display_name":"Restriction digest","score":0.41002780199050903},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.39639878273010254},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3543667495250702}],"concepts":[{"id":"https://openalex.org/C102230213","wikidata":"https://www.wikidata.org/wiki/Q430117","display_name":"Transgene","level":3,"score":0.8859652280807495},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6201627254486084},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5685065984725952},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5598362684249878},{"id":"https://openalex.org/C2780098074","wikidata":"https://www.wikidata.org/wiki/Q6037362","display_name":"Insert (composites)","level":2,"score":0.5440040230751038},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5135088562965393},{"id":"https://openalex.org/C128319531","wikidata":"https://www.wikidata.org/wiki/Q219715","display_name":"Restriction enzyme","level":3,"score":0.46447813510894775},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.4376761019229889},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4201357960700989},{"id":"https://openalex.org/C58301748","wikidata":"https://www.wikidata.org/wiki/Q1074969","display_name":"Restriction site","level":4,"score":0.41505491733551025},{"id":"https://openalex.org/C2889275","wikidata":"https://www.wikidata.org/wiki/Q7316313","display_name":"Restriction digest","level":4,"score":0.41002780199050903},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.39639878273010254},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3543667495250702},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015183","descriptor_name":"Restriction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018745","descriptor_name":"Genome, Plant","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019076","descriptor_name":"Transgenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019076","descriptor_name":"Transgenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019076","descriptor_name":"Transgenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btk003","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk003","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/523/48840298/bioinformatics_22_5_523.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:16357035","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16357035","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":"Evaluation Study"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btk003","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk003","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/523/48840298/bioinformatics_22_5_523.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":[{"id":"https://openalex.org/F4320310164","display_name":"Texas A and M University","ror":"https://ror.org/01f5ytq51"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108160018.pdf"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W85339462","https://openalex.org/W1499400826","https://openalex.org/W1582301784","https://openalex.org/W1966148673","https://openalex.org/W1967397130","https://openalex.org/W2008282869","https://openalex.org/W2046971422","https://openalex.org/W2063450941","https://openalex.org/W2084445314","https://openalex.org/W2086794780","https://openalex.org/W2106540431","https://openalex.org/W2135599428","https://openalex.org/W2149857208","https://openalex.org/W2150934173","https://openalex.org/W2159686532","https://openalex.org/W2340606561","https://openalex.org/W6603379590","https://openalex.org/W6634806186","https://openalex.org/W6704216060"],"related_works":["https://openalex.org/W2163480816","https://openalex.org/W3199198580","https://openalex.org/W2155139595","https://openalex.org/W787269129","https://openalex.org/W2077097444","https://openalex.org/W2000439691","https://openalex.org/W2008487588","https://openalex.org/W2751503389","https://openalex.org/W30564900","https://openalex.org/W1998301160"],"abstract_inverted_index":{"SUMMARY:":[0],"Determination":[1],"of":[2,11,20,33,59,84,123],"transgene":[3,14,34,44,60,86,93],"location":[4,35,122],"is":[5,45,51,71,77,89,118,170],"essential":[6],"for":[7,31],"investigating":[8],"the":[9,21,43,74,81,85,134],"effects":[10],"position":[12],"on":[13,80,131],"expression":[15],"levels":[16],"and":[17,39,103,140,145,160,165],"facilitates":[18],"cloning":[19],"resident":[22],"gene":[23],"affected":[24],"by":[25,104],"insertion.":[26],"Currently":[27],"used":[28],"PCR-based":[29],"approaches":[30],"determination":[32],"are":[36,150],"relatively":[37],"complicated":[38],"often":[40],"fail":[41],"when":[42],"duplicated,":[46],"rearranged":[47],"or":[48,96],"fragmented.":[49],"HideNseek":[50,98,138],"a":[52,64],"new":[53,75],"bioinformatics":[54],"tool":[55],"that":[56,63,114],"allows":[57],"computation":[58],"locations,":[61],"provided":[62,111,151],"suitable":[65],"genomic":[66],"restriction":[67],"enzyme":[68],"digestion":[69],"profile":[70],"available.":[72],"Since":[73],"approach":[76,117],"not":[78],"based":[79],"terminal":[82],"sequences":[83],"insert,":[87],"it":[88],"less":[90],"sensitive":[91],"to":[92],"duplication,":[94],"rearrangement":[95],"fragmentation.":[97],"has":[99],"been":[100],"tested":[101],"experimentally":[102],"in":[105],"silico":[106],"simulation.":[107],"The":[108],"experimental":[109,143,148],"example":[110],"here":[112],"shows":[113],"this":[115],"simple":[116],"feasible,":[119],"permitting":[120],"rapid":[121],"transgenes":[124],"with":[125],"little":[126],"bench":[127],"work.":[128],"AVAILABILITY:":[129],"available":[130,171],"request":[132],"from":[133],"authors.":[135],"SUPPLEMENTARY":[136],"DATA:":[137],"input":[139],"output":[141],"examples,":[142],"procedures":[144],"figures":[146,162],"showing":[147],"results":[149],"as":[152],"supplementary":[153],"files:":[154],"Supplementary":[155,161,168],"material":[156],"1,":[157],"2,":[158],"3":[159],"(Figs":[163],"1":[164],"2),":[166],"respectively.":[167],"data":[169],"at":[172],"Bioinformatics":[173],"online.":[174]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2016-06-24T00:00:00"}