{"id":"https://openalex.org/W2937564939","doi":"https://doi.org/10.1089/cmb.2018.0144","title":"DNA Motif Match Statistics Without Poisson Approximation","display_name":"DNA Motif Match Statistics Without Poisson Approximation","publication_year":2019,"publication_date":"2019-04-18","ids":{"openalex":"https://openalex.org/W2937564939","doi":"https://doi.org/10.1089/cmb.2018.0144","mag":"2937564939","pmid":"https://pubmed.ncbi.nlm.nih.gov/30998077"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2018.0144","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2018.0144","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/21.11116/0000-0005-9201-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084108745","display_name":"Wolfgang Kopp","orcid":"https://orcid.org/0000-0003-0376-0032"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Wolfgang Kopp","raw_affiliation_strings":["Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009628707","display_name":"Martin Vingron","orcid":"https://orcid.org/0000-0002-1765-4241"},"institutions":[{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Vingron","raw_affiliation_strings":["Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5084108745"],"corresponding_institution_ids":["https://openalex.org/I4210142260"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.0262592,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"26","issue":"8","first_page":"846","last_page":"865"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9941999912261963,"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/poisson-distribution","display_name":"Poisson distribution","score":0.7755790948867798},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.6891783475875854},{"id":"https://openalex.org/keywords/cutoff","display_name":"Cutoff","score":0.6675505638122559},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.5890816450119019},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.4990856647491455},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.46265703439712524},{"id":"https://openalex.org/keywords/negative-binomial-distribution","display_name":"Negative binomial distribution","score":0.4429042637348175},{"id":"https://openalex.org/keywords/binomial-approximation","display_name":"Binomial approximation","score":0.4273565709590912},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.40155673027038574},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35554367303848267},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3382461667060852},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3293188512325287},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32728394865989685},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31756412982940674},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2194887399673462},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12975722551345825}],"concepts":[{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.7755790948867798},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.6891783475875854},{"id":"https://openalex.org/C2778217198","wikidata":"https://www.wikidata.org/wiki/Q556977","display_name":"Cutoff","level":2,"score":0.6675505638122559},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.5890816450119019},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.4990856647491455},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.46265703439712524},{"id":"https://openalex.org/C199335787","wikidata":"https://www.wikidata.org/wiki/Q743364","display_name":"Negative binomial distribution","level":3,"score":0.4429042637348175},{"id":"https://openalex.org/C9209722","wikidata":"https://www.wikidata.org/wiki/Q4914487","display_name":"Binomial approximation","level":4,"score":0.4273565709590912},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.40155673027038574},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35554367303848267},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3382461667060852},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3293188512325287},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32728394865989685},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31756412982940674},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2194887399673462},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12975722551345825},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059372","descriptor_name":"Nucleotide Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1089/cmb.2018.0144","is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2018.0144","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:30998077","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30998077","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null},{"id":"pmh:oai:pure.mpg.de:item_3187273","is_oa":true,"landing_page_url":"http://hdl.handle.net/21.11116/0000-0005-9201-4","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Computational Biology","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:pure.mpg.de:item_3187273","is_oa":true,"landing_page_url":"http://hdl.handle.net/21.11116/0000-0005-9201-4","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Computational Biology","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"display_name":"Life below water","id":"https://metadata.un.org/sdg/14","score":0.6299999952316284}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1506806321","https://openalex.org/W1591710988","https://openalex.org/W1964963969","https://openalex.org/W1971793436","https://openalex.org/W1988393300","https://openalex.org/W2026731344","https://openalex.org/W2031200646","https://openalex.org/W2041877620","https://openalex.org/W2053392780","https://openalex.org/W2084620487","https://openalex.org/W2118215072","https://openalex.org/W2123490534","https://openalex.org/W2133045519","https://openalex.org/W2136292095","https://openalex.org/W2148315211","https://openalex.org/W2149769193","https://openalex.org/W2153550523","https://openalex.org/W2157009395","https://openalex.org/W2160446587","https://openalex.org/W2165102934","https://openalex.org/W2748123750"],"related_works":["https://openalex.org/W2052110748","https://openalex.org/W2073661767","https://openalex.org/W4244236455","https://openalex.org/W2380185347","https://openalex.org/W1993035125","https://openalex.org/W2370034659","https://openalex.org/W2039508579","https://openalex.org/W4249289744","https://openalex.org/W2159636084","https://openalex.org/W2117168988"],"abstract_inverted_index":{"<b>Transcription":[0],"factors":[1],"(TFs)":[2],"play":[3],"a":[4,21,37,46,75,112],"crucial":[5],"role":[6],"in":[7,26,117],"gene":[8],"regulation":[9],"by":[10,20,44],"binding":[11],"to":[12],"specific":[13],"regulatory":[14],"sequences.":[15],"The":[16],"sequence":[17,85],"motifs":[18],"recognized":[19],"TF":[22],"can":[23],"be":[24],"described":[25],"terms":[27],"of":[28,55,67,70],"position":[29,39],"frequency":[30,40],"matrices.":[31],"Searching":[32],"for":[33,82,91,119],"motif":[34,71,96],"matches":[35,56,72,97],"with":[36,104],"given":[38],"matrix":[41],"is":[42,89],"achieved":[43],"employing":[45],"predefined":[47],"score":[48,121],"cutoff":[49],"and":[50,94,111],"subsequently":[51],"counting":[52],"the":[53,65,68,123],"number":[54,69],"above":[57],"this":[58,61],"cutoff.":[59],"In":[60],"article,":[62],"we":[63],"approximate":[64],"distribution":[66],"based":[73],"on":[74,98],"novel":[76],"dynamic":[77,124],"programming":[78,125],"approach,":[79],"which":[80],"accounts":[81],"higher":[83],"order":[84],"background":[86],"(e.g.,":[87],"as":[88],"characteristic":[90],"CpG":[92],"islands)":[93],"overlapping":[95],"both":[99],"DNA":[100],"strands.":[101],"A":[102],"comparison":[103],"our":[105],"previously":[106],"published":[107],"compound":[108],"Poisson":[109],"approximation":[110,114],"binomial":[113],"demonstrates":[115],"that":[116],"particular":[118],"relaxed":[120],"thresholds,":[122],"approach":[126],"yields":[127],"more":[128],"accurate":[129],"results.</b>":[130]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}