{"id":"https://openalex.org/W4388822209","doi":"https://doi.org/10.1371/journal.pcbi.1011491","title":"Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation","display_name":"Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation","publication_year":2023,"publication_date":"2023-11-20","ids":{"openalex":"https://openalex.org/W4388822209","doi":"https://doi.org/10.1371/journal.pcbi.1011491","pmid":"https://pubmed.ncbi.nlm.nih.gov/37983292"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011491","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011491","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011491","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048574347","display_name":"Sarvesh Nikumbh","orcid":"https://orcid.org/0000-0003-3163-4447"},"institutions":[{"id":"https://openalex.org/I2801748203","display_name":"Hammersmith Hospital","ror":"https://ror.org/05jg8yp15","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I153355300","https://openalex.org/I2801748203"]},{"id":"https://openalex.org/I4210151791","display_name":"Genomics (United Kingdom)","ror":"https://ror.org/053a6xa29","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151791"]},{"id":"https://openalex.org/I4210161592","display_name":"MRC London Institute of Medical Sciences","ror":"https://ror.org/05p1n6x86","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210161592","https://openalex.org/I47508984"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Sarvesh Nikumbh","raw_affiliation_strings":["Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom","Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-3163-4447","affiliations":[{"raw_affiliation_string":"Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom","institution_ids":["https://openalex.org/I4210161592","https://openalex.org/I4210151791"]},{"raw_affiliation_string":"Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom","institution_ids":["https://openalex.org/I2801748203","https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052661284","display_name":"Boris Lenhard","orcid":"https://orcid.org/0000-0002-1114-1509"},"institutions":[{"id":"https://openalex.org/I2801748203","display_name":"Hammersmith Hospital","ror":"https://ror.org/05jg8yp15","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I153355300","https://openalex.org/I2801748203"]},{"id":"https://openalex.org/I4210151791","display_name":"Genomics (United Kingdom)","ror":"https://ror.org/053a6xa29","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151791"]},{"id":"https://openalex.org/I4210161592","display_name":"MRC London Institute of Medical Sciences","ror":"https://ror.org/05p1n6x86","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210161592","https://openalex.org/I47508984"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Boris Lenhard","raw_affiliation_strings":["Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom","Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-1114-1509","affiliations":[{"raw_affiliation_string":"Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom","institution_ids":["https://openalex.org/I4210161592","https://openalex.org/I4210151791"]},{"raw_affiliation_string":"Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom","institution_ids":["https://openalex.org/I2801748203","https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5048574347","https://openalex.org/A5052661284"],"corresponding_institution_ids":["https://openalex.org/I2801748203","https://openalex.org/I4210151791","https://openalex.org/I4210161592","https://openalex.org/I47508984"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.7287,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.7305044,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"19","issue":"11","first_page":"e1011491","last_page":"e1011491"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9954000115394592,"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":0.992900013923645,"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/promoter","display_name":"Promoter","score":0.8003025650978088},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5813411474227905},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.466564804315567},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.45903444290161133},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4490096867084503},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.4389888346195221},{"id":"https://openalex.org/keywords/nucleosome","display_name":"Nucleosome","score":0.4383251965045929},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.42944854497909546},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41080939769744873},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38716524839401245},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.3144441246986389},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18742838501930237}],"concepts":[{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.8003025650978088},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5813411474227905},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.466564804315567},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.45903444290161133},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4490096867084503},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.4389888346195221},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.4383251965045929},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.42944854497909546},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41080939769744873},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38716524839401245},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.3144441246986389},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18742838501930237}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024363","descriptor_name":"Transcription Initiation Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011491","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011491","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37983292","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37983292","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10695386","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10695386","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10695386/pdf/pcbi.1011491.pdf","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1011491","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011491","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:34b9f53529054f9b899bfcfef82cf886","is_oa":true,"landing_page_url":"https://doaj.org/article/34b9f53529054f9b899bfcfef82cf886","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 11, p e1011491 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011491","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011491","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1397540217","display_name":null,"funder_award_id":"106955/Z/15/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G5473497568","display_name":null,"funder_award_id":"MC_UP_1102/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G6868616705","display_name":null,"funder_award_id":"/Z/15/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G8541333319","display_name":"The core promoter: an unexplored regulatory level of transcription during vertebrate development.","funder_award_id":"106955","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W1811589942","https://openalex.org/W1902027874","https://openalex.org/W1963740134","https://openalex.org/W1979028385","https://openalex.org/W1985567287","https://openalex.org/W2012114217","https://openalex.org/W2015583498","https://openalex.org/W2015845481","https://openalex.org/W2016597274","https://openalex.org/W2019344358","https://openalex.org/W2026034143","https://openalex.org/W2026570758","https://openalex.org/W2029201460","https://openalex.org/W2037809333","https://openalex.org/W2040891939","https://openalex.org/W2041877620","https://openalex.org/W2049868101","https://openalex.org/W2057692691","https://openalex.org/W2077173342","https://openalex.org/W2078757082","https://openalex.org/W2091230759","https://openalex.org/W2097140065","https://openalex.org/W2097353028","https://openalex.org/W2113174377","https://openalex.org/W2115358825","https://openalex.org/W2119297694","https://openalex.org/W2121116352","https://openalex.org/W2126939295","https://openalex.org/W2129656350","https://openalex.org/W2130925862","https://openalex.org/W2133464819","https://openalex.org/W2136787567","https://openalex.org/W2149305968","https://openalex.org/W2151658462","https://openalex.org/W2154854793","https://openalex.org/W2155472755","https://openalex.org/W2158094337","https://openalex.org/W2158609592","https://openalex.org/W2160972778","https://openalex.org/W2173100207","https://openalex.org/W2259938310","https://openalex.org/W2274378441","https://openalex.org/W2315452447","https://openalex.org/W2487810004","https://openalex.org/W2527951543","https://openalex.org/W2588635522","https://openalex.org/W2767826728","https://openalex.org/W2787894218","https://openalex.org/W2898981235","https://openalex.org/W2916872998","https://openalex.org/W2949152404","https://openalex.org/W2950245999","https://openalex.org/W2951020107","https://openalex.org/W2982414522","https://openalex.org/W2999555406","https://openalex.org/W3104577407","https://openalex.org/W3133140988","https://openalex.org/W4283789731","https://openalex.org/W4318027109","https://openalex.org/W6756220963","https://openalex.org/W6950175630"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W2354198838","https://openalex.org/W1989130879","https://openalex.org/W2103419012","https://openalex.org/W2988126442","https://openalex.org/W1974414866","https://openalex.org/W1969771092","https://openalex.org/W2795723184","https://openalex.org/W3124098632","https://openalex.org/W2027133237"],"abstract_inverted_index":{"Core":[0],"promoters":[1,29,63],"are":[2,199,221],"stretches":[3],"of":[4,9,18,25,37,43,74,156,173,194,228],"DNA":[5],"at":[6,114,211],"the":[7,16,41,70,101,154],"beginning":[8],"genes":[10,26,157],"that":[11,14,82,106],"contain":[12],"information":[13],"facilitates":[15],"binding":[17],"transcription":[19,44],"initiation":[20],"complexes.":[21],"Different":[22],"functional":[23,66,192],"subsets":[24],"have":[27],"core":[28],"with":[30,51,126,159,179],"distinct":[31],"architectures":[32,175],"and":[33,72,100,143,153,191],"characteristic":[34],"motifs.":[35],"Some":[36],"these":[38],"motifs":[39,50,113,152,210],"inform":[40],"selection":[42],"start":[45],"sites":[46],"(TSS).":[47],"By":[48,161],"discovering":[49],"fixed":[52],"distances":[53,116,213],"from":[54,117,129,214],"known":[55,138],"TSS":[56],"positions,":[57],"we":[58,89,168],"could":[59],"in":[60,223],"principle":[61],"classify":[62],"into":[64],"different":[65],"groups.":[67],"Due":[68],"to":[69,207],"variability":[71],"overlap":[73],"architectures,":[75],"promoter":[76,108,174],"classification":[77,190],"is":[78,183],"a":[79,91,118,184,215,225],"difficult":[80],"task":[81],"requires":[83],"new":[84,92],"approaches.":[85],"In":[86],"this":[87],"study,":[88],"present":[90,222],"method":[93],"based":[94,110],"on":[95,111,164],"non-negative":[96],"matrix":[97],"factorisation":[98],"(NMF)":[99],"associated":[102,158],"software":[103],"called":[104],"seqArchR":[105,131,163,182],"clusters":[107],"sequences":[109],"their":[112],"near-fixed":[115,212],"reference":[119,216],"point,":[120,217],"such":[121],"as":[122,147,149],"TSS.":[123],"When":[124],"combined":[125],"experimental":[127],"data":[128],"CAGE,":[130],"can":[132,203],"efficiently":[133],"identify":[134],"TSS-directing":[135],"motifs,":[136],"including":[137],"ones":[139],"like":[140],"TATA,":[141],"DPE,":[142],"nucleosome":[144],"positioning":[145],"signal,":[146],"well":[148],"novel":[150],"lineage-specific":[151],"function":[155],"them.":[160],"using":[162],"developmental":[165],"time":[166,178],"courses,":[167],"reveal":[169],"how":[170],"relative":[171],"use":[172,197],"changes":[176],"over":[177],"stage-specific":[180],"expression.":[181],"powerful":[185],"tool":[186],"for":[187],"initial":[188],"genome-wide":[189],"characterisation":[193],"promoters.":[195],"Its":[196],"cases":[198],"more":[200],"general:":[201],"it":[202],"also":[204],"be":[205],"used":[206],"discover":[208],"any":[209],"even":[218],"if":[219],"they":[220],"only":[224],"small":[226],"subset":[227],"sequences.":[229]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2025-10-10T00:00:00"}
