{"id":"https://openalex.org/W2234772738","doi":"https://doi.org/10.1093/bioinformatics/btv470","title":"<i>motifbreakR</i>: an R/Bioconductor package for predicting variant effects at transcription factor binding sites","display_name":"<i>motifbreakR</i>: an R/Bioconductor package for predicting variant effects at transcription factor binding sites","publication_year":2015,"publication_date":"2015-08-12","ids":{"openalex":"https://openalex.org/W2234772738","doi":"https://doi.org/10.1093/bioinformatics/btv470","mag":"2234772738","pmid":"https://pubmed.ncbi.nlm.nih.gov/26272984"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv470","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv470","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/23/3847/49036271/bioinformatics_31_23_3847.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/31/23/3847/49036271/bioinformatics_31_23_3847.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015262217","display_name":"Simon G. Coetzee","orcid":"https://orcid.org/0000-0003-4267-5930"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Simon G. Coetzee","raw_affiliation_strings":["1 Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA and","institution_ids":["https://openalex.org/I1282927834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038379283","display_name":"Gerhard A. Coetzee","orcid":"https://orcid.org/0000-0001-8820-8364"},"institutions":[{"id":"https://openalex.org/I4210117038","display_name":"USC Norris Comprehensive Cancer Center","ror":"https://ror.org/01nmyfr60","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800154431","https://openalex.org/I4210117038"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gerhard A. Coetzee","raw_affiliation_strings":["2 Department of Urology and Preventive Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Department of Urology and Preventive Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I4210117038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050826378","display_name":"Dennis J. Hazelett","orcid":"https://orcid.org/0000-0003-0749-9935"},"institutions":[{"id":"https://openalex.org/I1282927834","display_name":"Cedars-Sinai Medical Center","ror":"https://ror.org/02pammg90","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1282927834"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dennis J. Hazelett","raw_affiliation_strings":["1 Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA and","institution_ids":["https://openalex.org/I1282927834"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5050826378"],"corresponding_institution_ids":["https://openalex.org/I1282927834"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":10.0069,"has_fulltext":true,"cited_by_count":351,"citation_normalized_percentile":{"value":0.98463194,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"31","issue":"23","first_page":"3847","last_page":"3849"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.3499999940395355,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.3499999940395355,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.2687000036239624,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.14380000531673431,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/bioconductor","display_name":"Bioconductor","score":0.796423614025116},{"id":"https://openalex.org/keywords/genome-wide-association-study","display_name":"Genome-wide association study","score":0.6010727286338806},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5938913226127625},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5867450833320618},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5773999691009521},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.541205644607544},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.529875636100769},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.49889492988586426},{"id":"https://openalex.org/keywords/1000-genomes-project","display_name":"1000 Genomes Project","score":0.47280898690223694},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.45550206303596497},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.38907015323638916},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.27089571952819824},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.21461263298988342},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18543770909309387},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.0966004729270935}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.796423614025116},{"id":"https://openalex.org/C106208931","wikidata":"https://www.wikidata.org/wiki/Q1098876","display_name":"Genome-wide association study","level":5,"score":0.6010727286338806},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5938913226127625},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5867450833320618},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5773999691009521},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.541205644607544},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.529875636100769},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.49889492988586426},{"id":"https://openalex.org/C97425143","wikidata":"https://www.wikidata.org/wiki/Q164786","display_name":"1000 Genomes Project","level":5,"score":0.47280898690223694},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.45550206303596497},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.38907015323638916},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.27089571952819824},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.21461263298988342},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18543770909309387},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0966004729270935},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","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":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv470","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv470","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/23/3847/49036271/bioinformatics_31_23_3847.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:26272984","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26272984","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:open-archive.highwire.org:bioinfo:31/23/3847","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/23/3847","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4653394","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4653394","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/btv470","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv470","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/23/3847/49036271/bioinformatics_31_23_3847.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":[],"awards":[{"id":"https://openalex.org/G1009595784","display_name":null,"funder_award_id":"U01 CA184826","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1140619197","display_name":null,"funder_award_id":"U01CA184826","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2102285915","display_name":null,"funder_award_id":"R01CA190182","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4090764117","display_name":null,"funder_award_id":"R01CA190182","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4760099799","display_name":null,"funder_award_id":"R01CA136924","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7634257778","display_name":null,"funder_award_id":"R01 CA136924","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8319304910","display_name":null,"funder_award_id":"R01CA136924","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8667204246","display_name":null,"funder_award_id":"R01 CA190182","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2234772738.pdf","grobid_xml":"https://content.openalex.org/works/W2234772738.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1975839434","https://openalex.org/W1975992663","https://openalex.org/W2014677321","https://openalex.org/W2026690931","https://openalex.org/W2088544963","https://openalex.org/W2099922553","https://openalex.org/W2104474654","https://openalex.org/W2112484474","https://openalex.org/W2118608526","https://openalex.org/W2123411711","https://openalex.org/W2131786456","https://openalex.org/W2141820415","https://openalex.org/W2149769193","https://openalex.org/W2159026625","https://openalex.org/W2161849959","https://openalex.org/W2165102934","https://openalex.org/W6683533356"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W2287365612","https://openalex.org/W2333878116","https://openalex.org/W1986387103","https://openalex.org/W2029857463","https://openalex.org/W2336964974","https://openalex.org/W4206151514","https://openalex.org/W2104474654"],"abstract_inverted_index":{"UNLABELLED:":[0],"Functional":[1],"annotation":[2],"represents":[3],"a":[4,86,91,118],"key":[5],"step":[6],"toward":[7],"the":[8,62,78,83,106,112,156],"understanding":[9],"and":[10,14,24,94],"interpretation":[11],"of":[12,54,64,105,120,124,158],"germline":[13],"somatic":[15],"variation":[16],"as":[17],"revealed":[18,33],"by":[19],"genome-wide":[20],"association":[21],"studies":[22],"(GWAS)":[23],"The":[25],"Cancer":[26],"Genome":[27],"Atlas":[28],"(TCGA),":[29],"respectively.":[30],"GWAS":[31],"have":[32],"numerous":[34],"genetic":[35],"risk":[36],"variants":[37,65,146],"residing":[38],"in":[39,102,147],"non-coding":[40],"DNA":[41],"associated":[42],"with":[43,126],"complex":[44],"diseases.":[45],"For":[46],"sequences":[47],"that":[48,132],"lie":[49],"within":[50,172],"enhancers":[51],"or":[52,88,100,108,143],"promoters":[53],"transcription,":[55],"it":[56,151,163],"is":[57,90,98,115],"not":[58],"straightforward":[59],"to":[60,80,111,167],"assess":[61],"effects":[63,140],"on":[66],"likely":[67],"transcription":[68],"factor":[69],"binding":[70],"sites.":[71],"Consequently":[72],"we":[73],"introduce":[74],"motifbreakR,":[75],"which":[76],"allows":[77],"biologist":[79],"judge":[81],"whether":[82],"sequence":[84],"surrounding":[85],"polymorphism":[87,107],"mutation":[89,109],"good":[92],"match,":[93],"how":[95],"much":[96],"information":[97],"gained":[99],"lost":[101],"one":[103],"allele":[104],"relative":[110],"other.":[113],"MotifbreakR":[114,137],"flexible,":[116],"giving":[117],"choice":[119],"algorithms":[121],"for":[122,141,153],"interrogation":[123],"genomes":[125],"motifs":[127],"from":[128],"many":[129],"public":[130,148],"sources":[131],"users":[133],"can":[134,138,164],"choose":[135],"from.":[136],"predict":[139],"novel":[142],"previously":[144],"described":[145],"databases,":[149],"making":[150],"suitable":[152],"tasks":[154],"beyond":[155],"scope":[157],"its":[159],"original":[160],"design.":[161],"Lastly,":[162],"be":[165],"used":[166],"interrogate":[168],"any":[169],"genome":[170],"curated":[171],"bioconductor.":[173],"AVAILABILITY":[174],"AND":[175],"IMPLEMENTATION:":[176],"https://github.com/Simon-Coetzee/MotifBreakR,":[177],"www.bioconductor.org.":[178],"CONTACT:":[179],"dennis.hazelett@cshs.org.":[180]},"counts_by_year":[{"year":2026,"cited_by_count":29},{"year":2025,"cited_by_count":48},{"year":2024,"cited_by_count":64},{"year":2023,"cited_by_count":43},{"year":2022,"cited_by_count":39},{"year":2021,"cited_by_count":33},{"year":2020,"cited_by_count":33},{"year":2019,"cited_by_count":21},{"year":2018,"cited_by_count":19},{"year":2017,"cited_by_count":14},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2016-06-24T00:00:00"}