{"id":"https://openalex.org/W1966447099","doi":"https://doi.org/10.1186/1471-2105-10-304","title":"MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs","display_name":"MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs","publication_year":2009,"publication_date":"2009-09-22","ids":{"openalex":"https://openalex.org/W1966447099","doi":"https://doi.org/10.1186/1471-2105-10-304","mag":"1966447099","pmid":"https://pubmed.ncbi.nlm.nih.gov/19772626"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-304","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-304","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-304","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/10.1186/1471-2105-10-304","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016398897","display_name":"Ahmet Sa\u00e7an","orcid":"https://orcid.org/0000-0002-3570-3270"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["TR","US"],"is_corresponding":true,"raw_author_name":"Ahmet Sacan","raw_affiliation_strings":["Computer Engineering Department, Middle East Technical University, Ankara, Turkey. ahmet@ceng.metu.edu.tr","Computer Engineering Department, Middle East Technical University, Ankara, Turkey","Department of Computer Science and Engineering, The Ohio State University, Columbus, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Engineering Department, Middle East Technical University, Ankara, Turkey. ahmet@ceng.metu.edu.tr","institution_ids":["https://openalex.org/I201799495"]},{"raw_affiliation_string":"Computer Engineering Department, Middle East Technical University, Ankara, Turkey","institution_ids":["https://openalex.org/I201799495"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, The Ohio State University, Columbus, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054889730","display_name":"Nilg\u00fcn Ferhatosmano\u011flu","orcid":null},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nilgun Ferhatosmanoglu","raw_affiliation_strings":["Department of Industrial and Systems Engineering, The Ohio State University, Columbus, OH, USA","Department of Industrial and Systems Engineering, The Ohio State University, Columbus, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Industrial and Systems Engineering, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Department of Industrial and Systems Engineering, The Ohio State University, Columbus, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078571347","display_name":"Hakan Ferhatosmano\u011flu","orcid":"https://orcid.org/0000-0002-5181-4712"},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hakan Ferhatosmanoglu","raw_affiliation_strings":["Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, USA","[Department of Computer Science & Engineering, The Ohio State University, Columbus, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"[Department of Computer Science & Engineering, The Ohio State University, Columbus, USA]","institution_ids":["https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5016398897"],"corresponding_institution_ids":["https://openalex.org/I201799495","https://openalex.org/I52357470"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.1283,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.50858299,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"10","issue":"1","first_page":"304","last_page":"304"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6133000254631042,"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/T10885","display_name":"Gene expression and cancer classification","score":0.6133000254631042,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.22390000522136688,"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/T11798","display_name":"Optimal Experimental Design Methods","score":0.017799999564886093,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7412718534469604},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6510468125343323},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5395187139511108},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5083350539207458},{"id":"https://openalex.org/keywords/optimal-design","display_name":"Optimal design","score":0.4866255223751068},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4360942840576172},{"id":"https://openalex.org/keywords/channel","display_name":"Channel (broadcasting)","score":0.424723744392395},{"id":"https://openalex.org/keywords/binary-search-algorithm","display_name":"Binary search algorithm","score":0.42401015758514404},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.3548021614551544},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2447950541973114},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.23629072308540344},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18546077609062195},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1808919608592987}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7412718534469604},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6510468125343323},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5395187139511108},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5083350539207458},{"id":"https://openalex.org/C186394612","wikidata":"https://www.wikidata.org/wiki/Q7098942","display_name":"Optimal design","level":2,"score":0.4866255223751068},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4360942840576172},{"id":"https://openalex.org/C127162648","wikidata":"https://www.wikidata.org/wiki/Q16858953","display_name":"Channel (broadcasting)","level":2,"score":0.424723744392395},{"id":"https://openalex.org/C121610932","wikidata":"https://www.wikidata.org/wiki/Q243754","display_name":"Binary search algorithm","level":3,"score":0.42401015758514404},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.3548021614551544},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2447950541973114},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23629072308540344},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18546077609062195},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1808919608592987},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-10-304","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-304","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-304","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:19772626","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19772626","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2761410","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2761410","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"},{"id":"pmh:oai:doaj.org/article:b2556a61fbd04d4d8ad69ffcb15d07eb","is_oa":false,"landing_page_url":"https://doaj.org/article/b2556a61fbd04d4d8ad69ffcb15d07eb","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 10, Iss 1, p 304 (2009)","raw_type":"article"},{"id":"pmh:oai:open.metu.edu.tr:11511/50940","is_oa":true,"landing_page_url":"https://hdl.handle.net/11511/50940","pdf_url":null,"source":{"id":"https://openalex.org/S4306402495","display_name":"OpenMETU (Middle East Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201799495","host_organization_name":"Middle East Technical University","host_organization_lineage":["https://openalex.org/I201799495"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-304","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-304","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-304","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":[],"awards":[{"id":"https://openalex.org/G4832972255","display_name":"Similarity-Based Indexing and Integration of Protein Sequence and Structure Databases","funder_award_id":"0750891","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6473113437","display_name":"CAREER: Exploration of Dynamic Sequences in Scientific Databases","funder_award_id":"0546713","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/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1966447099.pdf","grobid_xml":"https://content.openalex.org/works/W1966447099.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1549647993","https://openalex.org/W1556472699","https://openalex.org/W1914896851","https://openalex.org/W1977511407","https://openalex.org/W2074515414","https://openalex.org/W2077146895","https://openalex.org/W2105598099","https://openalex.org/W2133094193","https://openalex.org/W2162169788","https://openalex.org/W2188356987"],"related_works":["https://openalex.org/W2461970972","https://openalex.org/W2364921833","https://openalex.org/W2388030554","https://openalex.org/W3136652852","https://openalex.org/W156991389","https://openalex.org/W2151632297","https://openalex.org/W1914095056","https://openalex.org/W4212818355","https://openalex.org/W2136662899","https://openalex.org/W4285268299"],"abstract_inverted_index":{"BACKGROUND:":[0],"Dual-channel":[1],"microarray":[2,23,68,145],"experiments":[3,24],"are":[4,156,170],"commonly":[5],"employed":[6],"for":[7,64,143,172],"inference":[8],"of":[9,21,51,112,131],"differential":[10],"gene":[11],"expressions":[12],"across":[13],"varying":[14],"organisms":[15],"and":[16,43,47,60,89,141,153,167],"experimental":[17],"conditions.":[18],"The":[19,150],"design":[20,99],"dual-channel":[22,67],"that":[25,84],"can":[26,87],"help":[27],"minimize":[28],"the":[29,32,120,154,159],"errors":[30],"in":[31,116],"resulting":[33],"inferences":[34],"has":[35,77,102],"recently":[36],"received":[37],"increasing":[38],"attention.":[39],"However,":[40],"a":[41,48,72,127],"general":[42,110],"scalable":[44,61],"search":[45,62,139,151],"tool":[46,152],"corresponding":[49],"database":[50,142,155],"optimal":[52],"designs":[53,133,146],"were":[54],"still":[55],"missing.":[56],"DESCRIPTION:":[57],"An":[58],"efficient":[59],"method":[63,86],"finding":[65],"near-optimal":[66,92,113,132,144],"designs,":[69],"based":[70],"on":[71],"greedy":[73],"hill-climbing":[74],"optimization":[75],"strategy,":[76],"been":[78,103,148],"developed.":[79,149],"It":[80],"is":[81,134],"empirically":[82],"shown":[83],"this":[85],"successfully":[88],"efficiently":[90],"find":[91],"designs.":[93,114],"Additionally,":[94],"an":[95,107],"improved":[96],"interwoven":[97],"loop":[98],"construction":[100],"algorithm":[101,140],"developed":[104],"to":[105,118,125],"provide":[106],"easily":[108],"computable":[109],"class":[111],"Finally,":[115],"order":[117],"make":[119],"best":[121],"results":[122],"readily":[123],"available":[124,171],"biologists,":[126],"continuously":[128],"evolving":[129],"catalog":[130],"provided.":[135],"CONCLUSION:":[136],"A":[137],"new":[138],"have":[147],"accessible":[157],"via":[158],"World":[160],"Wide":[161],"Web":[162],"at":[163],"http://db.cse.ohio-state.edu/MicroarrayDesigner.":[164],"Source":[165],"code":[166],"binary":[168],"distributions":[169],"academic":[173],"use":[174],"upon":[175],"request.":[176]},"counts_by_year":[{"year":2015,"cited_by_count":3}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
