{"id":"https://openalex.org/W4220997534","doi":"https://doi.org/10.1093/bioinformatics/btac151","title":"AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design","display_name":"AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design","publication_year":2022,"publication_date":"2022-03-10","ids":{"openalex":"https://openalex.org/W4220997534","doi":"https://doi.org/10.1093/bioinformatics/btac151","pmid":"https://pubmed.ncbi.nlm.nih.gov/35274671"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac151","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac151","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/9/2628/43481024/btac151.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/38/9/2628/43481024/btac151.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061609722","display_name":"Jakub M\u0142okosiewicz","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jakub M\u0142okosiewicz","raw_affiliation_strings":["NaturalAntibody , 71-064 Szczecin, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NaturalAntibody , 71-064 Szczecin, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050415813","display_name":"Piotr Deszy\u0144ski","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Piotr Deszy\u0144ski","raw_affiliation_strings":["NaturalAntibody , 71-064 Szczecin, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NaturalAntibody , 71-064 Szczecin, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084691972","display_name":"Wiktoria Wilman","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wiktoria Wilman","raw_affiliation_strings":["NaturalAntibody , 71-064 Szczecin, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NaturalAntibody , 71-064 Szczecin, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002328749","display_name":"Igor Jaszczyszyn","orcid":"https://orcid.org/0009-0003-3405-0372"},"institutions":[{"id":"https://openalex.org/I268303160","display_name":"Medical University of Warsaw","ror":"https://ror.org/04p2y4s44","country_code":"PL","type":"education","lineage":["https://openalex.org/I268303160"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Igor Jaszczyszyn","raw_affiliation_strings":["Medical University of Warsaw , 02-091 Warsaw, Poland","NaturalAntibody , 71-064 Szczecin, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical University of Warsaw , 02-091 Warsaw, Poland","institution_ids":["https://openalex.org/I268303160"]},{"raw_affiliation_string":"NaturalAntibody , 71-064 Szczecin, Poland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026844160","display_name":"Rajkumar Ganesan","orcid":"https://orcid.org/0000-0002-3431-9664"},"institutions":[{"id":"https://openalex.org/I4210152456","display_name":"Alector (United States)","ror":"https://ror.org/03vagve85","country_code":"US","type":"company","lineage":["https://openalex.org/I4210152456"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rajkumar Ganesan","raw_affiliation_strings":["Alector , South San Francisco, CA 94080, USA"],"raw_orcid":"https://orcid.org/0000-0002-3431-9664","affiliations":[{"raw_affiliation_string":"Alector , South San Francisco, CA 94080, USA","institution_ids":["https://openalex.org/I4210152456"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077087059","display_name":"Aleksandr Kovaltsuk","orcid":"https://orcid.org/0000-0003-3806-8302"},"institutions":[{"id":"https://openalex.org/I4210111310","display_name":"LabGenius (United Kingdom)","ror":"https://ror.org/01y659x67","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210111310"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Aleksandr Kovaltsuk","raw_affiliation_strings":["LabGenius , SE16 4DG London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LabGenius , SE16 4DG London, UK","institution_ids":["https://openalex.org/I4210111310"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054519833","display_name":"Jinwoo Leem","orcid":"https://orcid.org/0000-0002-7817-3644"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jinwoo Leem","raw_affiliation_strings":["Alchemab Therapeutics Ltd,\u00a0N1C 4AX London , UK"],"raw_orcid":"https://orcid.org/0000-0002-7817-3644","affiliations":[{"raw_affiliation_string":"Alchemab Therapeutics Ltd,\u00a0N1C 4AX London , UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083246179","display_name":"Jacob D. Galson","orcid":"https://orcid.org/0000-0003-4916-800X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jacob D Galson","raw_affiliation_strings":["Alchemab Therapeutics Ltd,\u00a0N1C 4AX London , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Alchemab Therapeutics Ltd,\u00a0N1C 4AX London , UK","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015244397","display_name":"Konrad Krawczyk","orcid":"https://orcid.org/0000-0003-0697-5522"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Konrad Krawczyk","raw_affiliation_strings":["NaturalAntibody , 71-064 Szczecin, Poland"],"raw_orcid":"https://orcid.org/0000-0003-0697-5522","affiliations":[{"raw_affiliation_string":"NaturalAntibody , 71-064 Szczecin, Poland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5015244397"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.8744,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.90772784,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"38","issue":"9","first_page":"2628","last_page":"2630"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9459999799728394,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9459999799728394,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.02070000022649765,"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/T12255","display_name":"Biosimilars and Bioanalytical Methods","score":0.017100000753998756,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6582057476043701},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.6140710711479187},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5163887143135071},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5030586123466492},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4592978060245514},{"id":"https://openalex.org/keywords/antibody-repertoire","display_name":"Antibody Repertoire","score":0.433014452457428},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19152507185935974},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.11302581429481506},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08873948454856873}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6582057476043701},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.6140710711479187},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5163887143135071},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5030586123466492},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4592978060245514},{"id":"https://openalex.org/C2910693471","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody Repertoire","level":3,"score":0.433014452457428},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19152507185935974},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.11302581429481506},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08873948454856873},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"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":"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac151","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac151","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/9/2628/43481024/btac151.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:35274671","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35274671","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:pubmedcentral.nih.gov:9048670","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9048670","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/btac151","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac151","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/9/2628/43481024/btac151.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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2134334697","https://openalex.org/W2950118240","https://openalex.org/W2950135969","https://openalex.org/W2965921152","https://openalex.org/W2997321681","https://openalex.org/W3029868869","https://openalex.org/W3034417883","https://openalex.org/W3113000905","https://openalex.org/W3121914564","https://openalex.org/W3139404958","https://openalex.org/W3156522942","https://openalex.org/W3169434891","https://openalex.org/W3202479628"],"related_works":["https://openalex.org/W3126287804","https://openalex.org/W15021325","https://openalex.org/W2108895381","https://openalex.org/W2112284452","https://openalex.org/W2317855795","https://openalex.org/W2152844235","https://openalex.org/W2376454312","https://openalex.org/W4200126082","https://openalex.org/W2997749769","https://openalex.org/W1228353120"],"abstract_inverted_index":{"MOTIVATION:":[0],"Rational":[1],"design":[2],"of":[3,15,20,23,33,35,37,73,77,165,187,195],"therapeutic":[4,49,167,197],"antibodies":[5,24],"can":[6,62,176],"be":[7],"improved":[8],"by":[9],"harnessing":[10,92],"the":[11,21,31,74,78,114,185,193],"natural":[12,115],"sequence":[13,51,141],"diversity":[14,22,55],"these":[16],"molecules.":[17],"Our":[18],"understanding":[19],"has":[25],"recently":[26],"been":[27],"greatly":[28],"facilitated":[29],"through":[30],"deposition":[32],"hundreds":[34],"millions":[36],"human":[38],"antibody":[39,50,58,68,79,93,126,146,189,198],"sequences":[40,59,109],"in":[41,56,113],"next-generation":[42],"sequencing":[43],"(NGS)":[44],"repositories.":[45],"Contrasting":[46],"a":[47,64,100,124,144,155,163],"query":[48,108,125,145,156],"to":[52,105,110,127,143,154,162],"naturally":[53],"observed":[54,112],"similar":[57],"from":[60,132],"NGS":[61,80,94],"provide":[63],"mutational":[65],"roadmap":[66],"for":[67,171,180,192],"engineers":[69],"designing":[70],"biotherapeutics.":[71],"Because":[72],"sheer":[75],"scale":[76],"datasets,":[81],"performing":[82],"queries":[83],"across":[84],"them":[85],"is":[86,204],"computationally":[87],"challenging.":[88],"RESULTS:":[89],"To":[90],"facilitate":[91],"data,":[95],"we":[96],"developed":[97],"AbDiver":[98,117,183,203],"(http://naturalantibody.com/abdiver),":[99],"free":[101],"portal":[102],"allowing":[103],"users":[104],"compare":[106,123],"their":[107],"those":[111],"repertoires.":[116],"offers":[118],"three":[119],"antibody-specific":[120],"use-cases:":[121],"(i)":[122],"positional":[128],"variability":[129],"statistics":[130],"precomputed":[131],"multiple":[133],"independent":[134],"studies,":[135],"(ii)":[136],"retrieve":[137,149,177],"close":[138],"full":[139],"variable":[140],"matches":[142,153],"and":[147],"(iii)":[148],"CDR3":[150],"or":[151],"clonotype":[152],"antibody.":[157],"We":[158],"applied":[159],"our":[160,174],"system":[161,175],"set":[164],"742":[166],"antibodies,":[168],"demonstrating":[169],"that":[170],"each":[172],"use-case":[173],"relevant":[178],"results":[179],"most":[181],"sequences.":[182],"facilitates":[184],"navigation":[186],"vast":[188],"mutation":[190],"space":[191],"purpose":[194],"rational":[196],"design.":[199],"AVAILABILITY":[200],"AND":[201],"IMPLEMENTATION:":[202],"freely":[205],"accessible":[206],"at":[207,215],"http://naturalantibody.com/abdiver.":[208],"SUPPLEMENTARY":[209],"INFORMATION:":[210],"Supplementary":[211],"data":[212],"are":[213],"available":[214],"Bioinformatics":[216],"online.":[217]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}