{"id":"https://openalex.org/W2098039811","doi":"https://doi.org/10.1186/1471-2105-13-32","title":"CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences","display_name":"CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences","publication_year":2012,"publication_date":"2012-02-14","ids":{"openalex":"https://openalex.org/W2098039811","doi":"https://doi.org/10.1186/1471-2105-13-32","mag":"2098039811","pmid":"https://pubmed.ncbi.nlm.nih.gov/22333114"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-32","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-32","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-32","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-32","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055926977","display_name":"Yang Ding","orcid":"https://orcid.org/0000-0001-8530-7981"},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Ding","raw_affiliation_strings":["Department of Biology, Boston College, Chestnut Hill, MA 02467, USA","Department of Biology, University of Pennsylvania, Philadelphia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Boston College, Chestnut Hill, MA 02467, USA","institution_ids":["https://openalex.org/I103531236"]},{"raw_affiliation_string":"Department of Biology, University of Pennsylvania, Philadelphia, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085162142","display_name":"William Andrew Lorenz","orcid":null},"institutions":[{"id":"https://openalex.org/I20577493","display_name":"Denison University","ror":"https://ror.org/05pqx1c24","country_code":"US","type":"education","lineage":["https://openalex.org/I20577493"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William A Lorenz","raw_affiliation_strings":["Department of Mathematics and Computer Science, Denison University, Granville, OH, 43023, USA","Department of Mathematics and Computer Science, Denison University, Granville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, Denison University, Granville, OH, 43023, USA","institution_ids":["https://openalex.org/I20577493"]},{"raw_affiliation_string":"Department of Mathematics and Computer Science, Denison University, Granville, USA","institution_ids":["https://openalex.org/I20577493"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078627287","display_name":"Jeffrey H. Chuang","orcid":"https://orcid.org/0000-0002-3298-2358"},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey H Chuang","raw_affiliation_strings":["Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA","Department of Biology, Boston College,Chestnut Hill,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA","institution_ids":["https://openalex.org/I103531236"]},{"raw_affiliation_string":"Department of Biology, Boston College,Chestnut Hill,USA","institution_ids":["https://openalex.org/I103531236"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1344,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.53271696,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"13","issue":"1","first_page":"32","last_page":"32"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.613099992275238,"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":0.613099992275238,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.1307000070810318,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.08330000191926956,"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/encode","display_name":"ENCODE","score":0.6141042709350586},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.6054539680480957},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5212217569351196},{"id":"https://openalex.org/keywords/coding-region","display_name":"Coding region","score":0.49140894412994385},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43917790055274963},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4094742238521576},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4042338728904724},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34039825201034546},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1898220181465149}],"concepts":[{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6141042709350586},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.6054539680480957},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5212217569351196},{"id":"https://openalex.org/C91779695","wikidata":"https://www.wikidata.org/wiki/Q3780824","display_name":"Coding region","level":3,"score":0.49140894412994385},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43917790055274963},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4094742238521576},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4042338728904724},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34039825201034546},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1898220181465149}],"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":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016366","descriptor_name":"Open Reading Frames","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020506","descriptor_name":"Untranslated Regions","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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":5,"locations":[{"id":"doi:10.1186/1471-2105-13-32","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-32","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-32","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22333114","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22333114","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:cd62e389706f4a72820c2a3f3e110255","is_oa":true,"landing_page_url":"https://doaj.org/article/cd62e389706f4a72820c2a3f3e110255","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":"BMC Bioinformatics, Vol 13, Iss 1, p 32 (2012)","raw_type":"article"},{"id":"pmh:oai:mouseion.jax.org:stfb2012-1227","is_oa":false,"landing_page_url":"https://mouseion.jax.org/stfb2012/229","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Research 2012","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3298695","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3298695","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-32","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-32","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-32","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G285112738","display_name":"Computational and Experimental Approaches to Characterizing  Noncoding Selection in Coding Sequences","funder_award_id":"0850155","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2098039811.pdf","grobid_xml":"https://content.openalex.org/works/W2098039811.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1592870802","https://openalex.org/W1815093033","https://openalex.org/W1988692621","https://openalex.org/W1994527936","https://openalex.org/W1996454973","https://openalex.org/W2018590530","https://openalex.org/W2019136439","https://openalex.org/W2023648355","https://openalex.org/W2042392223","https://openalex.org/W2049595315","https://openalex.org/W2058323291","https://openalex.org/W2067382504","https://openalex.org/W2077055994","https://openalex.org/W2087439897","https://openalex.org/W2097220641","https://openalex.org/W2102046311","https://openalex.org/W2102304447","https://openalex.org/W2104806799","https://openalex.org/W2113498255","https://openalex.org/W2117041283","https://openalex.org/W2124202878","https://openalex.org/W2128742161","https://openalex.org/W2136482257","https://openalex.org/W2140882426","https://openalex.org/W2142961247","https://openalex.org/W2147879818","https://openalex.org/W2149393094","https://openalex.org/W2149480306","https://openalex.org/W2154688988","https://openalex.org/W2158391627","https://openalex.org/W2161435986","https://openalex.org/W2162674813","https://openalex.org/W2163670532","https://openalex.org/W2166187656","https://openalex.org/W2510854709","https://openalex.org/W2752573522","https://openalex.org/W3145128584","https://openalex.org/W7029321148"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W2354198838","https://openalex.org/W1989130879","https://openalex.org/W2443522885","https://openalex.org/W2385813177","https://openalex.org/W2148862069","https://openalex.org/W2152128819","https://openalex.org/W2605190264","https://openalex.org/W1980429866","https://openalex.org/W2039465881"],"abstract_inverted_index":{"BACKGROUND:":[0],"It":[1],"has":[2,42],"been":[3,43,64],"increasingly":[4],"appreciated":[5],"that":[6,130,193],"coding":[7,128,211,241,266],"sequences":[8,29,129],"harbor":[9],"regulatory":[10],"sequence":[11,20,74],"motifs":[12,21,41,95,199,238,251],"in":[13,27,100,207,240,252],"addition":[14],"to":[15,24,56,66,92,112,175,246],"encoding":[16],"for":[17,141,219,234,249],"protein.":[18],"These":[19],"are":[22,110],"expected":[23],"be":[25,247],"overrepresented":[26,40,239],"nucleotide":[28],"bound":[30],"by":[31,48,77],"a":[32,86,104,123,138,157,183,208,229],"common":[33],"protein":[34,52],"or":[35,188,262],"small":[36],"RNA.":[37],"However,":[38],"detecting":[39],"difficult":[44],"because":[45],"of":[46,72,80,96,117,120,122,151,154,170,181,210,213,237],"interference":[47],"constraints":[49],"at":[50,273],"the":[51,73,115,118,132,152,165,171,177,220,235],"level.":[53],"Sampling-based":[54],"approaches":[55,206],"solve":[57],"this":[58],"problem":[59],"based":[60],"on":[61],"codon-shuffling":[62],"have":[63],"limited":[65],"exploring":[67],"only":[68],"an":[69],"infinitesimal":[70],"fraction":[71],"space":[75],"and":[76,144,204,224,231],"their":[78],"use":[79],"parametric":[81],"approximations.":[82],"RESULTS:":[83],"We":[84,191,243],"present":[85],"novel":[87],"O(N(log":[88],"N)2)-time":[89],"algorithm,":[90],"CodingMotif,":[91],"identify":[93],"nucleotide-level":[94],"unusual":[97],"copy":[98],"number":[99,119],"protein-coding":[101],"regions.":[102,267],"Using":[103],"new":[105],"dynamic":[106],"programming":[107],"algorithm":[108],"we":[109],"able":[111],"exhaustively":[113],"calculate":[114],"distribution":[116,172],"occurrences":[121],"motif":[124,159,185],"over":[125],"all":[126],"possible":[127],"encode":[131],"same":[133],"amino":[134],"acid":[135],"sequence,":[136],"given":[137,158,184],"background":[139],"model":[140],"codon":[142],"usage":[143],"dinucleotide":[145],"biases.":[146],"Our":[147],"method":[148,195],"takes":[149],"advantage":[150],"sparseness":[153],"loci":[155],"where":[156],"can":[160],"occur,":[161],"greatly":[162],"speeding":[163],"up":[164],"required":[166],"convolution":[167],"calculations.":[168],"Knowledge":[169],"allows":[173],"one":[174],"assess":[176],"exact":[178],"non-parametric":[179],"p-value":[180],"whether":[182],"is":[186,271],"over-":[187],"under-":[189],"represented.":[190],"demonstrate":[192],"our":[194],"identifies":[196],"known":[197],"functional":[198,253],"more":[200],"accurately":[201],"than":[202],"sampling":[203],"parametric-based":[205],"variety":[209],"datasets":[212,255],"various":[214],"size,":[215],"including":[216],"ChIP-seq":[217],"data":[218],"transcription":[221],"factors":[222],"NRSF":[223],"GABP.":[225],"CONCLUSIONS:":[226],"CodingMotif":[227,245],"provides":[228],"theoretically":[230],"empirically-demonstrated":[232],"advance":[233],"detection":[236],"sequences.":[242],"expect":[244],"useful":[248],"identifying":[250],"genomic":[254],"such":[256],"as":[257],"DNA-protein":[258],"binding,":[259,261],"RNA-protein":[260],"microRNA-RNA":[263],"binding":[264],"within":[265],"A":[268],"software":[269],"implementation":[270],"available":[272],"http://bioinformatics.bc.edu/chuanglab/codingmotif.tar.":[274]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
