{"id":"https://openalex.org/W4392744971","doi":"https://doi.org/10.1093/bioinformatics/btae144","title":"Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies","display_name":"Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies","publication_year":2024,"publication_date":"2024-03-01","ids":{"openalex":"https://openalex.org/W4392744971","doi":"https://doi.org/10.1093/bioinformatics/btae144","pmid":"https://pubmed.ncbi.nlm.nih.gov/38478393"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae144","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae144/56964391/btae144.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae144/56964391/btae144.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001972889","display_name":"William Lees","orcid":"https://orcid.org/0000-0001-9834-6840"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"William D Lees","raw_affiliation_strings":["Bioengineering Program, Faculty of Engineering, Bar-Ilan University , Ramat Gan, 5290002, Israel"],"raw_orcid":"https://orcid.org/0000-0001-9834-6840","affiliations":[{"raw_affiliation_string":"Bioengineering Program, Faculty of Engineering, Bar-Ilan University , Ramat Gan, 5290002, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028315481","display_name":"Swati Saha","orcid":"https://orcid.org/0000-0002-3424-3663"},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Swati Saha","raw_affiliation_strings":["Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville , Louisville, Kentucky 40292, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville , Louisville, Kentucky 40292, United States","institution_ids":["https://openalex.org/I142740786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084475280","display_name":"Gur Yaari","orcid":"https://orcid.org/0000-0001-9311-9884"},"institutions":[{"id":"https://openalex.org/I13955877","display_name":"Bar-Ilan University","ror":"https://ror.org/03kgsv495","country_code":"IL","type":"education","lineage":["https://openalex.org/I13955877"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Gur Yaari","raw_affiliation_strings":["Bioengineering Program, Faculty of Engineering, Bar-Ilan University , Ramat Gan, 5290002, Israel"],"raw_orcid":"https://orcid.org/0000-0001-9311-9884","affiliations":[{"raw_affiliation_string":"Bioengineering Program, Faculty of Engineering, Bar-Ilan University , Ramat Gan, 5290002, Israel","institution_ids":["https://openalex.org/I13955877"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058637612","display_name":"Corey T. Watson","orcid":"https://orcid.org/0000-0001-7248-8787"},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Corey T Watson","raw_affiliation_strings":["Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville , Louisville, Kentucky 40292, United States"],"raw_orcid":"https://orcid.org/0000-0001-7248-8787","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville , Louisville, Kentucky 40292, United States","institution_ids":["https://openalex.org/I142740786"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5001972889"],"corresponding_institution_ids":["https://openalex.org/I13955877"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.8758,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.93944431,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"40","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9988999962806702,"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"}},"topics":[{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9988999962806702,"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/T11020","display_name":"Immune Cell Function and Interaction","score":0.9962999820709229,"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/T11660","display_name":"Blood groups and transfusion","score":0.9954000115394592,"subfield":{"id":"https://openalex.org/subfields/2720","display_name":"Hematology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7436189651489258},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6203373074531555},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.55157870054245},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5130876302719116},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.44597673416137695},{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.4290730655193329},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39682304859161377},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.32203298807144165},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.2868693470954895},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.06852811574935913}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7436189651489258},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6203373074531555},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.55157870054245},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5130876302719116},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.44597673416137695},{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.4290730655193329},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39682304859161377},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32203298807144165},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.2868693470954895},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.06852811574935913}],"mesh":[{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007136","descriptor_name":"Immunoglobulins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btae144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae144","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae144/56964391/btae144.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:38478393","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38478393","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae144","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae144","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae144/56964391/btae144.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G3049837784","display_name":null,"funder_award_id":"U24 AI177622","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3915319315","display_name":null,"funder_award_id":"U24AI177622","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4257016615","display_name":null,"funder_award_id":"R24AI162317","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6246980869","display_name":null,"funder_award_id":"R24 AI162317","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392744971.pdf"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1984387553","https://openalex.org/W2040071567","https://openalex.org/W2055043387","https://openalex.org/W2125748493","https://openalex.org/W2580314844","https://openalex.org/W3022219237","https://openalex.org/W3112069035","https://openalex.org/W3125723159","https://openalex.org/W3202755776","https://openalex.org/W4214838045","https://openalex.org/W4240231372","https://openalex.org/W4280621809","https://openalex.org/W4296138401","https://openalex.org/W4312101299","https://openalex.org/W4386035017","https://openalex.org/W4387219045","https://openalex.org/W4391689453"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2251519152"],"abstract_inverted_index":{"SUMMARY:":[0],"Knowledge":[1],"of":[2,22,43],"immunoglobulin":[3],"and":[4,24,40,69,76],"T":[5],"cell":[6],"receptor":[7],"encoding":[8],"genes":[9],"is":[10,18,33,61,70],"derived":[11],"from":[12],"high-quality":[13],"genomic":[14],"sequencing.":[15],"High-throughput":[16],"sequencing":[17],"delivering":[19],"large":[20],"volumes":[21],"data,":[23],"precise,":[25],"high-throughput":[26],"approaches":[27],"to":[28,49],"annotation":[29],"are":[30],"needed.":[31],"Digger":[32,60],"an":[34],"automated":[35],"tool":[36],"that":[37],"identifies":[38],"coding":[39],"regulatory":[41],"regions":[42],"these":[44],"genes,":[45],"with":[46],"results":[47],"comparable":[48],"those":[50],"obtained":[51],"by":[52],"current":[53],"expert":[54],"curational":[55],"methods.":[56],"AVAILABILITY":[57],"AND":[58],"IMPLEMENTATION:":[59],"published":[62],"under":[63],"open":[64],"source":[65],"license":[66],"at":[67],"https://github.com/williamdlees/Digger":[68],"available":[71],"as":[72],"a":[73,77],"Python":[74],"package":[75],"Docker":[78],"container.":[79]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
