{"id":"https://openalex.org/W2157069656","doi":"https://doi.org/10.1093/bioinformatics/btq457","title":"NoiseMaker: simulated screens for statistical assessment","display_name":"NoiseMaker: simulated screens for statistical assessment","publication_year":2010,"publication_date":"2010-08-11","ids":{"openalex":"https://openalex.org/W2157069656","doi":"https://doi.org/10.1093/bioinformatics/btq457","mag":"2157069656","pmid":"https://pubmed.ncbi.nlm.nih.gov/20702398"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq457","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq457","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/19/2484/16896477/btq457.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/19/2484/16896477/btq457.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5078855944","display_name":"Phoenix Kwan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210142480","display_name":"Thermo Fisher Scientific (United States)","ror":"https://ror.org/03x1ewr52","country_code":"US","type":"company","lineage":["https://openalex.org/I4210142480"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Phoenix Kwan","raw_affiliation_strings":["Thermo Fisher Scientific, 2650 Crescent Drive, Lafayette, CO 80026, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Thermo Fisher Scientific, 2650 Crescent Drive, Lafayette, CO 80026, USA","institution_ids":["https://openalex.org/I4210142480"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061546513","display_name":"Amanda Birmingham","orcid":"https://orcid.org/0000-0002-4117-3317"},"institutions":[{"id":"https://openalex.org/I4210142480","display_name":"Thermo Fisher Scientific (United States)","ror":"https://ror.org/03x1ewr52","country_code":"US","type":"company","lineage":["https://openalex.org/I4210142480"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Amanda Birmingham","raw_affiliation_strings":["Thermo Fisher Scientific, 2650 Crescent Drive, Lafayette, CO 80026, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Thermo Fisher Scientific, 2650 Crescent Drive, Lafayette, CO 80026, USA","institution_ids":["https://openalex.org/I4210142480"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5061546513"],"corresponding_institution_ids":["https://openalex.org/I4210142480"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3179,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.64228942,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"26","issue":"19","first_page":"2484","last_page":"2485"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6948000192642212,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6948000192642212,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.05119999870657921,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.04569999873638153,"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/computer-science","display_name":"Computer science","score":0.6372594237327576},{"id":"https://openalex.org/keywords/statistical-analysis","display_name":"Statistical analysis","score":0.43519487977027893},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2866760492324829},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15082478523254395}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6372594237327576},{"id":"https://openalex.org/C2986587452","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical analysis","level":2,"score":0.43519487977027893},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2866760492324829},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15082478523254395}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"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":"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":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034622","descriptor_name":"RNA Interference","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq457","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq457","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/19/2484/16896477/btq457.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20702398","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20702398","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},{"id":"pmh:oai:pubmedcentral.nih.gov:2944205","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2944205","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq457","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq457","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/19/2484/16896477/btq457.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.6000000238418579,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W2150091347","https://openalex.org/W2162424885","https://openalex.org/W2166393666"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"UNLABELLED:":[0],"High-throughput":[1],"screening":[2],"(HTS)":[3],"is":[4,39,168],"a":[5,29,123,186],"common":[6],"technique":[7],"for":[8,63,180],"both":[9],"drug":[10],"discovery":[11],"and":[12,44,79,174,189,199,208,210],"basic":[13],"research,":[14],"but":[15],"researchers":[16],"often":[17],"struggle":[18],"with":[19,178],"how":[20,81,93],"best":[21],"to":[22,49,76,122,149],"derive":[23],"hits":[24,87],"from":[25],"HTS":[26],"data.":[27],"While":[28],"wide":[30],"range":[31,124],"of":[32,65,83,109,125,157],"hit":[33,73,161],"identification":[34,74,162],"techniques":[35,111],"exist,":[36],"little":[37],"information":[38],"available":[40,194],"about":[41,105,154],"their":[42],"sensitivity":[43],"specificity,":[45],"especially":[46],"in":[47,170],"comparison":[48],"each":[50],"other.":[51],"To":[52],"address":[53],"this,":[54],"we":[55,142],"have":[56],"developed":[57],"the":[58,84,106,155,158,211],"open-source":[59],"NoiseMaker":[60,167],"software":[61],"tool":[62],"generation":[64],"realistically":[66],"noisy":[67],"virtual":[68],"screens.":[69],"By":[70],"applying":[71],"potential":[72],"methods":[75],"NoiseMaker-simulated":[77],"data":[78,114],"determining":[80],"many":[82,94],"pre-defined":[85],"true":[86,117],"are":[88,97,193,201],"recovered":[89],"(as":[90],"well":[91],"as":[92,99,128],"known":[95],"non-hits":[96],"misidentified":[98],"hits),":[100],"one":[101],"can":[102],"draw":[103],"conclusions":[104],"likely":[107],"performance":[108,156],"these":[110],"on":[112],"real":[113],"containing":[115],"unknown":[116],"hits.":[118],"Such":[119],"simulations":[120],"apply":[121],"screens,":[126],"such":[127],"those":[129],"using":[130,147],"small":[131],"molecules,":[132],"siRNAs,":[133],"shRNAs,":[134],"miRNA":[135],"mimics":[136],"or":[137,139],"inhibitors,":[138],"gene":[140],"over-expression;":[141],"demonstrate":[143],"this":[144],"utility":[145],"by":[146],"it":[148],"explain":[150],"apparently":[151],"conflicting":[152],"reports":[153],"B":[159],"score":[160],"method.":[163],"AVAILABILITY":[164],"AND":[165],"IMPLEMENTATION:":[166],"written":[169],"C#,":[171],"an":[172,204],"ECMA":[173],"ISO":[175],"standard":[176],"language":[177],"compilers":[179],"multiple":[181],"operating":[182],"systems.":[183],"Source":[184],"code,":[185],"Windows":[187],"installer":[188],"complete":[190],"unit":[191],"tests":[192],"at":[195],"http://sourceforge.net/projects/noisemaker.":[196],"Full":[197],"documentation":[198],"support":[200],"provided":[202],"via":[203],"extensive":[205],"help":[206],"file":[207],"tool-tips,":[209],"developers":[212],"welcome":[213],"user":[214],"suggestions.":[215]},"counts_by_year":[{"year":2015,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
