{"id":"https://openalex.org/W2163396356","doi":"https://doi.org/10.1111/j.0105-2896.2004.00171.x","title":"Computational tools for understanding sequence variability in recombination signals","display_name":"Computational tools for understanding sequence variability in recombination signals","publication_year":2004,"publication_date":"2004-07-09","ids":{"openalex":"https://openalex.org/W2163396356","doi":"https://doi.org/10.1111/j.0105-2896.2004.00171.x","mag":"2163396356","pmid":"https://pubmed.ncbi.nlm.nih.gov/15242396"},"language":"en","primary_location":{"id":"doi:10.1111/j.0105-2896.2004.00171.x","doi":"https://doi.org/10.1111/j.0105-2896.2004.00171.x","is_oa":false,"landing_page_url":"https://doi.org/10.1111/j.0105-2896.2004.00171.x","pdf_url":null,"source":{"id":"https://openalex.org/S133112385","display_name":"Immunological Reviews","issn_l":"0105-2896","issn":["0105-2896","1600-065X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-2","ki-jl-1","medline","norway-1","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Immunological Reviews","raw_type":"journal-article"},"volume":null,"type":"review","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090203652","display_name":"Lindsay Grey Cowell","orcid":"https://orcid.org/0000-0003-1617-8244","observed_orcids":["https://orcid.org/0000-0003-1617-8244"]},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lindsay G. Cowell","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, Center for Bioinformatics and Computational Biology, Duke University, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, Center for Bioinformatics and Computational Biology, Duke University, Durham, NC, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040390930","display_name":"Marco L. Davila","orcid":"https://orcid.org/0000-0002-6270-3065","observed_orcids":["https://orcid.org/0000-0002-6270-3065"]},"institutions":[{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marco Davila","raw_affiliation_strings":["Department of Immunology, Duke University Medical Center, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology, Duke University Medical Center, Durham, NC, USA","institution_ids":["https://openalex.org/I4210126298"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076234244","display_name":"Dale A. Ramsden","orcid":"https://orcid.org/0000-0003-1575-4748","observed_orcids":["https://orcid.org/0000-0003-1575-4748"]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dale Ramsden","raw_affiliation_strings":["Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065001474","display_name":"Garnett H. Kelsoe","orcid":"https://orcid.org/0000-0002-8770-040X","observed_orcids":["https://orcid.org/0000-0002-8770-040X"]},"institutions":[{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Garnett Kelsoe","raw_affiliation_strings":["Department of Immunology, Duke University Medical Center, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Immunology, Duke University Medical Center, Durham, NC, USA","institution_ids":["https://openalex.org/I4210126298"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065001474"],"corresponding_institution_ids":["https://openalex.org/I4210126298"],"apc_list":{"value":5000,"currency":"USD","value_usd":5000},"apc_paid":null,"fwci":0.1522,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.1388525,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"200","issue":"1","first_page":"57","last_page":"69"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10123","display_name":"DNA Repair Mechanisms","score":0.3418000042438507,"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/T10123","display_name":"DNA Repair Mechanisms","score":0.3418000042438507,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.2808000147342682,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.21080000698566437,"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/v-d-j-recombination","display_name":"V(D)J recombination","score":0.9810000061988831},{"id":"https://openalex.org/keywords/sequence-variation","display_name":"sequence variation","score":0.7139999866485596},{"id":"https://openalex.org/keywords/heptamer","display_name":"heptamer","score":0.6389999985694885},{"id":"https://openalex.org/keywords/spacer-sequences","display_name":"spacer sequences","score":0.7289999723434448},{"id":"https://openalex.org/keywords/allelic-exclusion","display_name":"allelic exclusion","score":0.8539999723434448},{"id":"https://openalex.org/keywords/antigen-receptor-repertoire","display_name":"antigen receptor repertoire","score":0.7599999904632568},{"id":"https://openalex.org/keywords/b-cells","display_name":"B cells","score":0.6570000052452087},{"id":"https://openalex.org/keywords/computational-model","display_name":"computational model","score":0.6150000095367432},{"id":"https://openalex.org/keywords/mouse-immunoglobulin-genes","display_name":"mouse immunoglobulin genes","score":0.6179999709129333}],"concepts":[{"id":"https://openalex.org/C2385561","wikidata":"https://www.wikidata.org/wiki/Q45432","display_name":"RSS","level":2,"score":0.9637797474861145},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7079265117645264},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6370446681976318},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6076933741569519},{"id":"https://openalex.org/C178300618","wikidata":"https://www.wikidata.org/wiki/Q1898509","display_name":"Extant taxon","level":2,"score":0.5292607545852661},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4801051914691925},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.456904798746109},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4137600362300873},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3803651034832001},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3435109853744507},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.08060002326965332}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","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":false},{"descriptor_ui":"D009687","descriptor_name":"Nuclear Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012045","descriptor_name":"Regulatory Sequences, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015322","descriptor_name":"Gene Rearrangement, B-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015329","descriptor_name":"Gene Rearrangement, T-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016654","descriptor_name":"Genes, RAG-1","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017385","descriptor_name":"Sequence Homology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021901","descriptor_name":"DNA, Intergenic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1111/j.0105-2896.2004.00171.x","doi":"https://doi.org/10.1111/j.0105-2896.2004.00171.x","is_oa":false,"landing_page_url":"https://doi.org/10.1111/j.0105-2896.2004.00171.x","pdf_url":null,"source":{"id":"https://openalex.org/S133112385","display_name":"Immunological Reviews","issn_l":"0105-2896","issn":["0105-2896","1600-065X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-2","ki-jl-1","medline","norway-1","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Immunological Reviews","raw_type":"journal-article"},{"id":"pmid:15242396","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15242396","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,"listed_in":[],"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":"Immunological reviews","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2102269554","display_name":"Resolution of Complex Breaks by Nonhomologous End Joining","funder_award_id":"R01CA084442","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1498410508","https://openalex.org/W1502641732","https://openalex.org/W1513093379","https://openalex.org/W1518026427","https://openalex.org/W1525759724","https://openalex.org/W1540362944","https://openalex.org/W1595674107","https://openalex.org/W1896423162","https://openalex.org/W1974596630","https://openalex.org/W1983405741","https://openalex.org/W1983450672","https://openalex.org/W1986320226","https://openalex.org/W1986902849","https://openalex.org/W1987552589","https://openalex.org/W2003525376","https://openalex.org/W2004707654","https://openalex.org/W2013607137","https://openalex.org/W2018237947","https://openalex.org/W2022372517","https://openalex.org/W2031121939","https://openalex.org/W2032414205","https://openalex.org/W2032548898","https://openalex.org/W2036331912","https://openalex.org/W2040870580","https://openalex.org/W2041404167","https://openalex.org/W2041877620","https://openalex.org/W2056649927","https://openalex.org/W2057000344","https://openalex.org/W2064879068","https://openalex.org/W2067022774","https://openalex.org/W2074703985","https://openalex.org/W2080686406","https://openalex.org/W2083170703","https://openalex.org/W2084354924","https://openalex.org/W2087604899","https://openalex.org/W2089432059","https://openalex.org/W2090804789","https://openalex.org/W2103425962","https://openalex.org/W2106188260","https://openalex.org/W2106882534","https://openalex.org/W2110510545","https://openalex.org/W2117789925","https://openalex.org/W2118077304","https://openalex.org/W2120746509","https://openalex.org/W2122161903","https://openalex.org/W2125622789","https://openalex.org/W2135214113","https://openalex.org/W2136842312","https://openalex.org/W2140336226","https://openalex.org/W2142923239","https://openalex.org/W2149769193","https://openalex.org/W2157260959","https://openalex.org/W2160089420","https://openalex.org/W2167216803","https://openalex.org/W2170909437","https://openalex.org/W2231089260","https://openalex.org/W2397123409","https://openalex.org/W2578150941","https://openalex.org/W4245668478"],"related_works":["https://openalex.org/W2167216803","https://openalex.org/W4308834724","https://openalex.org/W7096406593","https://openalex.org/W2022372517","https://openalex.org/W4200392269","https://openalex.org/W4385687889","https://openalex.org/W7133023560","https://openalex.org/W2082272502","https://openalex.org/W4416450845","https://openalex.org/W7098765663"],"abstract_inverted_index":{"The":[0,63],"recombination":[1,111],"signals":[2],"(RSs)":[3],"that":[4,35,126,158],"guide":[5],"V(D)J":[6],"rearrangement":[7],"are":[8,85],"remarkably":[9],"diverse.":[10],"In":[11,108],"mice,":[12],"fewer":[13],"than":[14],"16%":[15],"of":[16,53,66,74,113,129,134,145,151,163],"RSs":[17,43,67,118,136,176,184],"carry":[18],"consensus":[19,28],"heptamers":[20],"and":[21,23,57,122,172,185,190,199],"nonamers":[22],"none":[24],"also":[25],"contain":[26],"a":[27,131,192],"spacer":[29],"sequence.":[30],"It":[31],"is":[32,124],"increasingly":[33],"clear":[34],"this":[36],"variability":[37,41],"regulates":[38],"recombination:":[39],"genetic":[40],"in":[42,60,105],"may":[44],"help":[45],"enforce":[46],"allelic":[47],"exclusion,":[48],"determine":[49],"the":[50,106,110,127,143,149,160],"general":[51],"nature":[52],"antigen":[54],"receptor":[55],"repertoires,":[56],"mitigate":[58],"autoreactivity":[59],"B":[61],"lymphocytes.":[62],"great":[64],"diversity":[65],"has":[68],"largely":[69],"precluded,":[70],"however,":[71],"empiric":[72,188],"determinations":[73],"how":[75,146],"RS":[76,152,170,197],"sequence":[77,147],"affects":[78],"recombination.":[79],"For":[80],"example,":[81],"4(39)":[82],"unique":[83,97],"23-RSs":[84,98],"possible":[86],"or":[87,116],"approximately":[88],"3":[89],"x":[90,95],"10(23)":[91],"sequences;":[92],"some":[93],"7":[94],"10(13)":[96],"can":[99,137],"be":[100,138],"produced":[101],"just":[102],"by":[103,154],"changes":[104],"spacer.":[107],"contrast,":[109],"activities":[112,128],"only":[114],"100":[115],"so":[117],"have":[119,141],"been":[120],"measured,":[121],"it":[123],"unlikely":[125],"even":[130],"tiny":[132],"fraction":[133],"extant":[135],"determined.":[139],"We":[140],"addressed":[142],"problem":[144],"determines":[148],"efficiency":[150],"templates":[153],"generating":[155],"computational":[156],"models":[157,167,179],"describe":[159],"correlation":[161],"structure":[162,198],"mouse":[164],"RSs.":[165],"These":[166,178],"successfully":[168],"predict":[169],"activity":[171],"identify":[173,183],"functional,":[174],"cryptic":[175],"(cRSs).":[177],"permit":[180],"studies":[181],"to":[182],"cRSs":[186],"for":[187,195],"study":[189],"constitute":[191],"tool":[193],"useful":[194],"understanding":[196],"function.":[200]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
