{"id":"https://openalex.org/W3089037602","doi":"https://doi.org/10.1093/bioinformatics/btaa830","title":"Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed\u00a0data","display_name":"Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed\u00a0data","publication_year":2020,"publication_date":"2020-09-09","ids":{"openalex":"https://openalex.org/W3089037602","doi":"https://doi.org/10.1093/bioinformatics/btaa830","mag":"3089037602","pmid":"https://pubmed.ncbi.nlm.nih.gov/32966546"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa830","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa830","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/4/439/37757571/btaa830.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","license_id":"https://openalex.org/licenses/cc-by","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/37/4/439/37757571/btaa830.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081318122","display_name":"Jacob Schreiber","orcid":"https://orcid.org/0000-0003-4230-6625"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Jacob Schreiber","raw_affiliation_strings":["Paul G. Allen School of Computer Science and Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School of Computer Science and Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091674429","display_name":"Jeffrey A. Bilmes","orcid":"https://orcid.org/0000-0002-7372-8778"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jeffrey Bilmes","raw_affiliation_strings":["Department of Electrical and Computer Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057375933","display_name":"William Stafford Noble","orcid":"https://orcid.org/0000-0001-7283-4715"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"William Stafford Noble","raw_affiliation_strings":["University of Washington Department of Genome Sciences, , Seattle, WA 98195, USA"],"raw_orcid":"https://orcid.org/0000-0001-7283-4715","affiliations":[{"raw_affiliation_string":"University of Washington Department of Genome Sciences, , Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5057375933","https://openalex.org/A5081318122"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2502,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.54635128,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"37","issue":"4","first_page":"439","last_page":"447"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.4571000039577484,"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":0.4571000039577484,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0868000015616417,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.08349999785423279,"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/epigenomics","display_name":"Epigenomics","score":0.7869881987571716},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.749451756477356},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4895397126674652},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4275514483451843},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3993021249771118},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.32179751992225647},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1438167691230774},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12455213069915771},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07167929410934448}],"concepts":[{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.7869881987571716},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.749451756477356},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4895397126674652},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4275514483451843},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3993021249771118},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.32179751992225647},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1438167691230774},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12455213069915771},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07167929410934448},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"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},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa830","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa830","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/4/439/37757571/btaa830.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32966546","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32966546","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:8088321","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8088321","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa830","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa830","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/4/439/37757571/btaa830.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.41999998688697815,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G1018597006","display_name":null,"funder_award_id":"U01 HG009395","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8737913810","display_name":null,"funder_award_id":"U01 HG009395","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3089037602.pdf","grobid_xml":"https://content.openalex.org/works/W3089037602.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1498671329","https://openalex.org/W1576820654","https://openalex.org/W1680189815","https://openalex.org/W1898824936","https://openalex.org/W2019251848","https://openalex.org/W2076154138","https://openalex.org/W2102304447","https://openalex.org/W2259938310","https://openalex.org/W2482182218","https://openalex.org/W2790597304","https://openalex.org/W2822674993","https://openalex.org/W2906884244","https://openalex.org/W2950489610","https://openalex.org/W2951810596","https://openalex.org/W3013674494","https://openalex.org/W3013690547"],"related_works":["https://openalex.org/W2795212387","https://openalex.org/W2030573967","https://openalex.org/W2988805143","https://openalex.org/W4285490847","https://openalex.org/W2101726782","https://openalex.org/W3201524181","https://openalex.org/W3131932045","https://openalex.org/W1931295451","https://openalex.org/W2347051579","https://openalex.org/W4239393031"],"abstract_inverted_index":{"MOTIVATION:":[0],"Successful":[1],"science":[2],"often":[3],"involves":[4],"not":[5],"only":[6],"performing":[7],"experiments":[8,124,151,192],"well,":[9],"but":[10],"also":[11],"choosing":[12,23,28],"well":[13,26],"among":[14],"many":[15],"possible":[16,91,102],"experiments.":[17],"In":[18,37],"a":[19,61,88,99,138,148,189,195,211,235],"hypothesis":[20],"generation":[21],"setting,":[22],"an":[24,29],"experiment":[25,30,110],"means":[27],"whose":[31,73],"results":[32],"are":[33,268],"interesting":[34],"or":[35,94,221],"novel.":[36],"this":[38,42,135],"work,":[39],"we":[40,55,121,166,201],"formalize":[41],"selection":[43],"procedure":[44],"in":[45,83,114],"the":[46,57,66,80,84,143,154,177,206,224,245,256],"context":[47],"of":[48,69,79,90,101,150,161,191,197,205,218],"genomics":[49],"and":[50,98,117,240,255],"epigenomics":[51],"data":[52,267],"generation.":[53],"Specifically,":[54],"consider":[56],"task":[58,136],"faced":[59],"by":[60],"scientific":[62],"consortium":[63],"such":[64],"as":[65,137,234],"National":[67],"Institutes":[68],"Health":[70],"ENCODE":[71,126],"Consortium,":[72],"goal":[74,144],"is":[75,145,164,232],"to":[76,133,146,174],"characterize":[77],"all":[78],"functional":[81],"elements":[82],"human":[85],"genome.":[86],"Given":[87],"list":[89,100],"cell":[92],"types":[93,96],"tissue":[95],"('biosamples')":[97],"high-throughput":[103],"sequencing":[104],"assays,":[105],"where":[106,142],"at":[107,238,262,270],"least":[108],"one":[109],"has":[111],"been":[112],"performed":[113],"each":[115,119],"biosample":[116],"for":[118],"assay,":[120],"ask":[122],"'Which":[123],"should":[125],"perform":[127],"next?'":[128],"RESULTS:":[129],"We":[130,180],"demonstrate":[131],"how":[132],"represent":[134],"submodular":[139],"optimization":[140,225],"problem,":[141],"choose":[147],"panel":[149,190],"that":[152,165,193,215],"maximize":[153],"facility":[155,207],"location":[156,208],"function.":[157],"A":[158],"key":[159],"aspect":[160],"our":[162,186],"approach":[163],"use":[167],"imputed":[168],"data,":[169,173],"rather":[170],"than":[171],"experimental":[172],"directly":[175],"answer":[176],"posed":[178],"question.":[179],"find":[181],"that,":[182],"across":[183],"several":[184],"evaluations,":[185],"method":[187,231],"chooses":[188],"span":[194],"diversity":[196],"biochemical":[198],"activity.":[199],"Finally,":[200],"propose":[202],"two":[203],"modifications":[204],"function,":[209,214],"including":[210],"novel":[212],"submodular-supermodular":[213],"allow":[216],"incorporation":[217],"domain":[219],"knowledge":[220],"constraints":[222],"into":[223],"procedure.":[226],"AVAILABILITY":[227],"AND":[228],"IMPLEMENTATION:":[229],"Our":[230],"available":[233,269],"Python":[236],"package":[237],"https://github.com/jmschrei/kiwano":[239],"can":[241,259],"be":[242,260],"installed":[243],"using":[244],"command":[246],"pip":[247],"install":[248],"kiwano.":[249],"The":[250],"source":[251],"code":[252],"used":[253],"here":[254],"similarity":[257],"matrix":[258],"found":[261],"http://doi.org/10.5281/zenodo.3708538.":[263],"SUPPLEMENTARY":[264],"INFORMATION:":[265],"Supplementary":[266],"Bioinformatics":[271],"online.":[272]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}