{"id":"https://openalex.org/W1966574758","doi":"https://doi.org/10.1371/journal.pcbi.1000128","title":"Getting Started in Computational Immunology","display_name":"Getting Started in Computational Immunology","publication_year":2008,"publication_date":"2008-08-29","ids":{"openalex":"https://openalex.org/W1966574758","doi":"https://doi.org/10.1371/journal.pcbi.1000128","mag":"1966574758","pmid":"https://pubmed.ncbi.nlm.nih.gov/18769677"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000128","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000128","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000128&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000128&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5066562919","display_name":"Steven H. Kleinstein","orcid":"https://orcid.org/0000-0003-4957-1544"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Steven H. Kleinstein","raw_affiliation_strings":["Interdepartmental Program in Computational Biology and Bioinformatics, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America. steven.kleinstein@yale.edu","Interdepartmental Program in Computational Biology and Bioinformatics, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America"],"affiliations":[{"raw_affiliation_string":"Interdepartmental Program in Computational Biology and Bioinformatics, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America. steven.kleinstein@yale.edu","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Interdepartmental Program in Computational Biology and Bioinformatics, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5066562919"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.8014,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.7063192,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"4","issue":"8","first_page":"e1000128","last_page":"e1000128"},"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":0.9994999766349792,"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":0.9994999766349792,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9988999962806702,"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/T12391","display_name":"Artificial Immune Systems Applications","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5399001836776733},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40743908286094666},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3714115619659424},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33491015434265137}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5399001836776733},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40743908286094666},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3714115619659424},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33491015434265137}],"mesh":[{"descriptor_ui":"D000220","descriptor_name":"Adaptation, Biological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000220","descriptor_name":"Adaptation, Biological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000220","descriptor_name":"Adaptation, Biological","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000220","descriptor_name":"Adaptation, Biological","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000220","descriptor_name":"Adaptation, Biological","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000220","descriptor_name":"Adaptation, Biological","qualifier_ui":"Q000276","qualifier_name":"immunology","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":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000915","descriptor_name":"Antibody Affinity","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001402","descriptor_name":"B-Lymphocytes","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D016296","descriptor_name":"Mutagenesis","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018095","descriptor_name":"Germ-Line Mutation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018095","descriptor_name":"Germ-Line Mutation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018095","descriptor_name":"Germ-Line Mutation","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1000128","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000128","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000128&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:18769677","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18769677","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:9f9564966102495e9343dc8160b45528","is_oa":true,"landing_page_url":"https://doaj.org/article/9f9564966102495e9343dc8160b45528","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 4, Iss 8, p e1000128 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2518523","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2518523","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000128","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000128","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000128&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7300000190734863,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2150262284","display_name":null,"funder_award_id":"HHSN266200500021C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5903061775","display_name":null,"funder_award_id":"NIAID","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"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":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1966574758.pdf","grobid_xml":"https://content.openalex.org/works/W1966574758.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W40267425","https://openalex.org/W93508866","https://openalex.org/W1520434148","https://openalex.org/W1549990382","https://openalex.org/W1971201122","https://openalex.org/W1976759658","https://openalex.org/W1978648487","https://openalex.org/W1987039508","https://openalex.org/W1999985136","https://openalex.org/W2005566446","https://openalex.org/W2008512164","https://openalex.org/W2010843874","https://openalex.org/W2017896543","https://openalex.org/W2020905367","https://openalex.org/W2032251250","https://openalex.org/W2056538898","https://openalex.org/W2056583190","https://openalex.org/W2057239104","https://openalex.org/W2058311887","https://openalex.org/W2064059889","https://openalex.org/W2064164319","https://openalex.org/W2078387120","https://openalex.org/W2089293301","https://openalex.org/W2095627668","https://openalex.org/W2097591929","https://openalex.org/W2104205011","https://openalex.org/W2111098506","https://openalex.org/W2122800774","https://openalex.org/W2127597278","https://openalex.org/W2127605828","https://openalex.org/W2137206510","https://openalex.org/W2138067488","https://openalex.org/W2140385774","https://openalex.org/W2143213125","https://openalex.org/W2145221987","https://openalex.org/W2163396356","https://openalex.org/W2165143211","https://openalex.org/W3123992600","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":{"The":[0,247,294],"immune":[1,41,210,272,330],"system":[2,211],"acts":[3],"across":[4],"multiple":[5,33,68,353],"scales":[6,354],"involving":[7],"complex":[8],"interactions":[9],"and":[10,37,45,84,123,130,182,271,291,311],"feedback,":[11],"from":[12,32,67],"somatic":[13,121],"modifications":[14],"of":[15,35,79,120,140,148,152,176,197,229,249,261,298,306,321,329,335,349],"DNA":[16,356],"to":[17,27,50,62,126,208,241,278,282,326,345,357],"the":[18,40,102,153,165,172,194,209,215,242,264,283,347],"systemic":[19],"inflammatory":[20],"reaction.":[21],"Computational":[22,308],"modeling":[23,158,328,344],"provides":[24,237],"a":[25,73,146,238,303,318],"framework":[26],"integrate":[28],"observational":[29],"data":[30],"collected":[31],"modes":[34],"experimentation":[36],"insight":[38],"into":[39],"response":[42,266],"in":[43,143,226,258,302,317,340],"health":[44],"disease.":[46],"This":[47],"Message":[48],"attempts":[49],"illustrate":[51],"how":[52],"different":[53],"computational":[54,157,250,279,343],"methods":[55],"have":[56,254],"been":[57,255],"integrated":[58],"with":[59,113,342],"experimental":[60,336],"observations":[61],"study":[63],"an":[64],"immunological":[65],"question":[66],"perspectives":[69],"by":[70,104,234,289],"focusing":[71],"on":[72,214],"very":[74],"particular,":[75],"though":[76],"fundamental,":[77],"component":[78],"adaptive":[80],"immunity:":[81],"B":[82,89,106,199],"cells":[83,90],"affinity":[85,115,144,243,350],"maturation":[86,100,244,351],"(Figure":[87],"1).":[88],"bind":[91,111],"foreign":[92],"antigens":[93],"through":[94,118],"their":[95],"Immunoglobulin":[96],"(Ig)":[97],"receptor.":[98],"Affinity":[99],"is":[101,150,212],"process":[103,135,245,348],"which":[105],"cell":[107,200],"receptors":[108],"that":[109],"initially":[110],"antigen":[112],"low":[114],"are":[116,338],"modified":[117],"cycles":[119],"mutation":[122],"affinity-dependent":[124],"selection":[125,179],"produce":[127],"high-affinity":[128],"memory":[129,273],"plasma":[131],"cells.":[132],"How":[133],"this":[134],"can":[136,223],"reliably":[137],"generate":[138],"orders":[139],"magnitude":[141],"increases":[142],"over":[145],"period":[147],"weeks":[149],"one":[151],"many":[154],"questions":[155,185],"where":[156],"has":[159],"made":[160],"important":[161],"contributions":[162],"(for":[163],"example,":[164],"cyclic":[166],"re-entry":[167],"model":[168],"[1]).":[169],"Yet,":[170],"even":[171],"seemingly":[173],"straightforward":[174],"matter":[175],"detecting":[177],"antigen-driven":[178],"remains":[180],"controversial,":[181],"such":[183],"fundamental":[184],"as":[186],"whether":[187],"increased":[188],"proliferation":[189],"or":[190],"decreased":[191],"death":[192],"drives":[193],"preferential":[195],"expansion":[196],"higher-affinity":[198],"mutants":[201],"remain":[202],"unanswered.":[203],"A":[204,275],"good":[205],"biological":[206],"introduction":[207,240,277],"available":[213],"NIH":[216],"website":[217],"[2],":[218],"while":[219],"more":[220,284],"detailed":[221],"information":[222],"be":[224],"found":[225],"any":[227],"number":[228],"textbooks":[230],"[3].":[231],"An":[232],"animation":[233],"Julian":[235],"Kirk-Elleker":[236],"visual":[239],"(http://web.mac.com/patrickwlee/Antibody-affinity_maturation/Movie.html).":[246],"kinds":[248],"techniques":[251,337],"described":[252],"here":[253],"widely":[256],"applied":[257],"other":[259,313],"areas":[260],"immunology,":[262],"including":[263],"innate":[265],"[4],[5],":[267],"viral":[268],"dynamics":[269],"[6],":[270],"[7].":[274],"classic":[276],"immunology":[280],"geared":[281],"mathematically":[285],"inclined":[286],"was":[287,300],"written":[288],"Perelson":[290],"Weisbuch":[292],"[8].":[293],"rapidly":[295],"expanding":[296],"area":[297],"immunoinformatics":[299],"covered":[301],"recent":[304],"issue":[305],"PLoS":[307],"Biology":[309],"[9],":[310],"several":[312],"applications":[314],"were":[315],"explored":[316],"2007":[319],"volume":[320],"Immunological":[322],"Reviews":[323],"(216)":[324],"devoted":[325],"quantitative":[327],"responses.\r\n\r\n\r\n\r\nFigure":[331],"1\r\n\r\nA":[332],"wide":[333],"range":[334],"used":[339],"combination":[341],"probe":[346],"at":[352],"(from":[355],"tissue).":[358]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}