{"id":"https://openalex.org/W1622160096","doi":"https://doi.org/10.1186/1471-2105-7-429","title":"Design of a combinatorial DNA microarray for protein-DNA interaction studies","display_name":"Design of a combinatorial DNA microarray for protein-DNA interaction studies","publication_year":2006,"publication_date":"2006-10-01","ids":{"openalex":"https://openalex.org/W1622160096","doi":"https://doi.org/10.1186/1471-2105-7-429","mag":"1622160096"},"language":"en","primary_location":{"id":"pmh:oai:doaj.org/article:dcb947bcd066475eacb60fe7995414b1","is_oa":false,"landing_page_url":"https://doaj.org/article/dcb947bcd066475eacb60fe7995414b1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 7, Iss 1, p 429 (2006)","raw_type":"article"},"type":"article","indexed_in":["doaj"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Eisen Michael B","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eisen Michael B","raw_affiliation_strings":["Bioinformatics program, Boston University, Boston, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics program, Boston University, Boston, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","author":{"id":null,"display_name":"Mintseris Julian","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mintseris Julian","raw_affiliation_strings":["Department of Genome Sciences, Lawrence Berkeley National Lab, Berkeley, USA","Department of Molecular and Cell Biology, University of California, Berkeley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, Lawrence Berkeley National Lab, Berkeley, USA","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Department of Molecular and Cell Biology, University of California, Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.8182,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.69306023,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991000294685364,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991000294685364,"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":0.9988999962806702,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9907000064849854,"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/dna-microarray","display_name":"DNA microarray","score":0.7534873485565186},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.7168624401092529},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7146116495132446},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5959259271621704},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5305688381195068},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5112535953521729},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5049267411231995},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.43996280431747437},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.4287436902523041},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4263041019439697},{"id":"https://openalex.org/keywords/dna-binding-protein","display_name":"DNA-binding protein","score":0.4190239906311035},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4138486385345459},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.37920933961868286},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35293281078338623},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2926191985607147},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.19852295517921448},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11752748489379883}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.7534873485565186},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.7168624401092529},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7146116495132446},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5959259271621704},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5305688381195068},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5112535953521729},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5049267411231995},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.43996280431747437},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4287436902523041},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4263041019439697},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.4190239906311035},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4138486385345459},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.37920933961868286},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35293281078338623},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2926191985607147},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.19852295517921448},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11752748489379883},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:doaj.org/article:dcb947bcd066475eacb60fe7995414b1","is_oa":false,"landing_page_url":"https://doaj.org/article/dcb947bcd066475eacb60fe7995414b1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 7, Iss 1, p 429 (2006)","raw_type":"article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1975036436","https://openalex.org/W1998300401","https://openalex.org/W2032942231","https://openalex.org/W2039758198","https://openalex.org/W2073850887","https://openalex.org/W2080498142","https://openalex.org/W2083052219","https://openalex.org/W2102518893","https://openalex.org/W2118304741","https://openalex.org/W2126602684","https://openalex.org/W2157523980","https://openalex.org/W2160314966","https://openalex.org/W2161420356","https://openalex.org/W2166898290","https://openalex.org/W2168157737","https://openalex.org/W2171153226","https://openalex.org/W2171517043","https://openalex.org/W4302771278"],"related_works":["https://openalex.org/W2041540252","https://openalex.org/W2138580185","https://openalex.org/W2415545834","https://openalex.org/W3203113381","https://openalex.org/W2366558827","https://openalex.org/W170658859","https://openalex.org/W4232333928","https://openalex.org/W1594655861","https://openalex.org/W2089975163","https://openalex.org/W4233699124"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Discovery":[2],"of":[3,6,21,54,63,74,82,124,135,154],"precise":[4,122],"specificity":[5,62],"transcription":[7,39,65,169],"factors":[8],"is":[9,87,99,113],"an":[10,48],"important":[11],"step":[12],"on":[13],"the":[14,18,83,110,155],"way":[15],"to":[16,37,51,68,115],"understanding":[17],"complex":[19],"mechanisms":[20],"gene":[22],"regulation":[23],"in":[24,120],"eukaryotes.":[25],"Recently,":[26],"double-stranded":[27],"protein-binding":[28],"microarrays":[29],"were":[30],"developed":[31],"as":[32],"a":[33,55,64,75,95,133,136,163],"potentially":[34],"scalable":[35],"approach":[36,50],"tackle":[38],"factor":[40,66,92,170],"binding":[41,67,72,125,171],"site":[42,172],"identification.":[43],"Results":[44],"Here":[45],"we":[46,131],"present":[47,132],"algorithmic":[49],"experimental":[52],"design":[53,86,134,164],"microarray":[56,140],"that":[57,93,106,147],"allows":[58,150],"for":[59,90,141,157,168],"testing":[60],"full":[61],"all":[69],"possible":[70],"DNA":[71,139],"sites":[73],"given":[76],"length,":[77],"with":[78,109],"optimally":[79,151],"efficient":[80,152],"use":[81,153],"array.":[84],"This":[85],"universal,":[88],"works":[89],"any":[91],"binds":[94],"sequence":[96],"motif":[97],"and":[98,117,145,174],"not":[100],"species-specific.":[101],"Furthermore,":[102],"simulation":[103],"results":[104],"show":[105,146],"data":[107],"produced":[108],"designed":[111],"arrays":[112,156],"easier":[114],"analyze":[116],"would":[118],"result":[119],"more":[121],"identification":[123,173],"sites.":[126],"Conclusion":[127],"In":[128],"this":[129,158],"study,":[130],"double":[137],"stranded":[138],"protein-DNA":[142],"interaction":[143],"studies":[144],"our":[148],"algorithm":[149],"purpose.":[159],"We":[160],"believe":[161],"such":[162],"will":[165],"prove":[166],"useful":[167],"other":[175],"biological":[176],"problems.":[177]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":6}],"updated_date":"2026-06-19T17:40:00.097472","created_date":"2025-10-10T00:00:00"}
