{"id":"https://openalex.org/W2807497370","doi":"https://doi.org/10.1186/s12859-018-2144-z","title":"IRProfiler \u2013 a software toolbox for high throughput immune receptor profiling","display_name":"IRProfiler \u2013 a software toolbox for high throughput immune receptor profiling","publication_year":2018,"publication_date":"2018-04-18","ids":{"openalex":"https://openalex.org/W2807497370","doi":"https://doi.org/10.1186/s12859-018-2144-z","mag":"2807497370","pmid":"https://pubmed.ncbi.nlm.nih.gov/29669518"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2144-z","is_oa":true,"landing_page_url":"10.1186/s12859-018-2144-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2144-z","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/s12859-018-2144-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Christos Maramis","orcid":null},"institutions":[{"id":"https://openalex.org/I21370196","display_name":"Aristotle University of Thessaloniki","ror":"https://ror.org/02j61yw88","country_code":"GR","type":"education","lineage":["https://openalex.org/I21370196"]},{"id":"https://openalex.org/I4210134249","display_name":"Centre for Research and Technology Hellas","ror":"https://ror.org/03bndpq63","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210134249"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Christos Maramis","raw_affiliation_strings":["Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece. chmaramis@med.auth.gr","Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece. chmaramis@med.auth.gr","Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece. chmaramis@med.auth.gr","institution_ids":["https://openalex.org/I4210134249"]},{"raw_affiliation_string":"Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece. chmaramis@med.auth.gr","institution_ids":["https://openalex.org/I21370196"]},{"raw_affiliation_string":"Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece","institution_ids":["https://openalex.org/I21370196"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053965730","display_name":"Athanasios Gkoufas","orcid":null},"institutions":[{"id":"https://openalex.org/I21370196","display_name":"Aristotle University of Thessaloniki","ror":"https://ror.org/02j61yw88","country_code":"GR","type":"education","lineage":["https://openalex.org/I21370196"]},{"id":"https://openalex.org/I4210134249","display_name":"Centre for Research and Technology Hellas","ror":"https://ror.org/03bndpq63","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210134249"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Athanasios Gkoufas","raw_affiliation_strings":["Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","institution_ids":["https://openalex.org/I4210134249"]},{"raw_affiliation_string":"Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece","institution_ids":["https://openalex.org/I21370196"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083412701","display_name":"Anna Vardi","orcid":"https://orcid.org/0000-0002-1927-4242"},"institutions":[{"id":"https://openalex.org/I4210134249","display_name":"Centre for Research and Technology Hellas","ror":"https://ror.org/03bndpq63","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210134249"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Anna Vardi","raw_affiliation_strings":["Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","institution_ids":["https://openalex.org/I4210134249"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023652883","display_name":"Evangelia Stalika","orcid":"https://orcid.org/0000-0001-7856-5480"},"institutions":[{"id":"https://openalex.org/I4210134249","display_name":"Centre for Research and Technology Hellas","ror":"https://ror.org/03bndpq63","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210134249"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Evangelia Stalika","raw_affiliation_strings":["Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","institution_ids":["https://openalex.org/I4210134249"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044130307","display_name":"\u039a\u03ce\u03c3\u03c4\u03b1\u03c2 \u03a3\u03c4\u03b1\u03bc\u03b1\u03c4\u03cc\u03c0\u03bf\u03c5\u03bb\u03bf\u03c2","orcid":"https://orcid.org/0000-0001-8529-640X"},"institutions":[{"id":"https://openalex.org/I4210134249","display_name":"Centre for Research and Technology Hellas","ror":"https://ror.org/03bndpq63","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210134249"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Kostas Stamatopoulos","raw_affiliation_strings":["Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","institution_ids":["https://openalex.org/I4210134249"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089558959","display_name":"Anastasia Hatzidimitriou","orcid":null},"institutions":[{"id":"https://openalex.org/I4210134249","display_name":"Centre for Research and Technology Hellas","ror":"https://ror.org/03bndpq63","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210134249"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Anastasia Hatzidimitriou","raw_affiliation_strings":["Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","institution_ids":["https://openalex.org/I4210134249"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082929636","display_name":"Nicos Maglaveras","orcid":"https://orcid.org/0000-0002-4919-0664"},"institutions":[{"id":"https://openalex.org/I21370196","display_name":"Aristotle University of Thessaloniki","ror":"https://ror.org/02j61yw88","country_code":"GR","type":"education","lineage":["https://openalex.org/I21370196"]},{"id":"https://openalex.org/I4210134249","display_name":"Centre for Research and Technology Hellas","ror":"https://ror.org/03bndpq63","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210134249"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Nicos Maglaveras","raw_affiliation_strings":["Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","institution_ids":["https://openalex.org/I4210134249"]},{"raw_affiliation_string":"Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece","institution_ids":["https://openalex.org/I21370196"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078023454","display_name":"Ioanna Chouvarda","orcid":"https://orcid.org/0000-0001-8915-6658"},"institutions":[{"id":"https://openalex.org/I21370196","display_name":"Aristotle University of Thessaloniki","ror":"https://ror.org/02j61yw88","country_code":"GR","type":"education","lineage":["https://openalex.org/I21370196"]},{"id":"https://openalex.org/I4210134249","display_name":"Centre for Research and Technology Hellas","ror":"https://ror.org/03bndpq63","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210134249"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Ioanna Chouvarda","raw_affiliation_strings":["Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece","institution_ids":["https://openalex.org/I4210134249"]},{"raw_affiliation_string":"Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece","institution_ids":["https://openalex.org/I21370196"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I21370196","https://openalex.org/I4210134249"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.476,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.61495382,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"19","issue":"1","first_page":"144","last_page":"144"},"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":0.2660999894142151,"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":0.2660999894142151,"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/T11725","display_name":"Immunodeficiency and Autoimmune Disorders","score":0.16509999334812164,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.14350000023841858,"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/profiling","display_name":"Profiling (computer programming)","score":0.6382900476455688},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5871767401695251},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.5805631279945374},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5603123307228088},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5589233040809631},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5309960842132568},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4441821575164795},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.36385083198547363},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3291707932949066},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16713687777519226},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12738913297653198},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11390116810798645},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11043253540992737},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09871545433998108}],"concepts":[{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.6382900476455688},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5871767401695251},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.5805631279945374},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5603123307228088},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5589233040809631},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5309960842132568},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4441821575164795},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.36385083198547363},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3291707932949066},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16713687777519226},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12738913297653198},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11390116810798645},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11043253540992737},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09871545433998108},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006402","descriptor_name":"Hematologic Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D006402","descriptor_name":"Hematologic Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D006402","descriptor_name":"Hematologic Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D006402","descriptor_name":"Hematologic Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006402","descriptor_name":"Hematologic Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006402","descriptor_name":"Hematologic Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011947","descriptor_name":"Receptors, Antigen, B-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","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":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","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":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-018-2144-z","is_oa":true,"landing_page_url":"10.1186/s12859-018-2144-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2144-z","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:29669518","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29669518","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:f7464bdc06da41c19eb11255091589b9","is_oa":true,"landing_page_url":"https://doaj.org/article/f7464bdc06da41c19eb11255091589b9","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 19, Iss 1, Pp 1-11 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4848042","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5907363","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5907363","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5907363","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"},{"id":"pmh:oai:zenodo.org:1409396","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2144-z","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2144-z","is_oa":true,"landing_page_url":"10.1186/s12859-018-2144-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-018-2144-z","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":[{"score":0.5299999713897705,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G3146086885","display_name":null,"funder_award_id":"644906","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2807497370.pdf","grobid_xml":"https://content.openalex.org/works/W2807497370.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W135571511","https://openalex.org/W655534426","https://openalex.org/W1506890399","https://openalex.org/W1890359263","https://openalex.org/W1965235372","https://openalex.org/W2009125186","https://openalex.org/W2029525307","https://openalex.org/W2089041106","https://openalex.org/W2091670726","https://openalex.org/W2105195133","https://openalex.org/W2105273832","https://openalex.org/W2115206258","https://openalex.org/W2136169373","https://openalex.org/W2136476597","https://openalex.org/W2136482257","https://openalex.org/W2138968719","https://openalex.org/W2144420540","https://openalex.org/W2155499644","https://openalex.org/W2161645441","https://openalex.org/W2172403535","https://openalex.org/W2396171593","https://openalex.org/W2546585365","https://openalex.org/W2556824914","https://openalex.org/W2559115935","https://openalex.org/W4297944090"],"related_works":["https://openalex.org/W4205140848","https://openalex.org/W2068663075","https://openalex.org/W2978678743","https://openalex.org/W2797837731","https://openalex.org/W2150344375","https://openalex.org/W829257147","https://openalex.org/W3081389670","https://openalex.org/W4390832911","https://openalex.org/W4385302116","https://openalex.org/W1925744677"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"study":[2],"of":[3,7,25,31,37,48,59,91,115,123,130,141,152,170,187,199,209,240,262,273],"the":[4,29,35,45,57,60,134,171,185,197,227,274],"huge":[5],"diversity":[6,125],"immune":[8,14,70,241],"receptors,":[9],"often":[10],"referred":[11],"to":[12,62,191,196],"as":[13,167],"repertoire":[15,71,94,242],"profiling,":[16],"is":[17,218],"a":[18,83,89,113,168,207,233,237,260],"prerequisite":[19],"for":[20,44,66,117,133,155,253],"diagnosis,":[21],"prognostication":[22],"and":[23,52,68,96,102,126,136,143,149,157,179,277],"monitoring":[24],"hematological":[26,214],"disorders.":[27,215],"In":[28],"era":[30],"high-throughput":[32,100],"sequencing":[33,104],"(HTS),":[34],"abundance":[36],"immunogenetic":[38],"data":[39,61,119],"has":[40,164,182,203],"revealed":[41],"unprecedented":[42],"opportunities":[43],"thorough":[46],"profiling":[47,72,243],"T-cell":[49],"receptors":[50,54],"(TR)":[51],"B-cell":[53],"(BcR).":[55],"However,":[56],"volume":[58],"be":[63],"analyzed":[64],"mandates":[65],"efficient":[67],"ease-to-use":[69],"software":[73,85],"applications.":[74],"RESULTS:":[75],"This":[76],"work":[77],"introduces":[78],"Immune":[79],"Repertoire":[80],"Profiler":[81],"(IRProfiler),":[82],"novel":[84],"pipeline":[86],"that":[87,184],"delivers":[88],"number":[90,208],"core":[92],"receptor":[93],"quantification":[95],"comparison":[97,151],"functionalities":[98],"on":[99,250],"TR":[101],"BcR":[103],"data.":[105],"Adopting":[106],"5":[107],"alternative":[108,254],"clonotype":[109,124,255],"definitions,":[110],"IRProfiler":[111,163,188,202,217,245],"implements":[112],"series":[114],"algorithms":[116],"1)":[118],"filtering,":[120],"2)":[121],"calculation":[122,129],"expression,":[127],"3)":[128],"gene":[131,153],"usage":[132,154],"V":[135,156],"J":[137,158],"subgroups,":[138],"4)":[139],"detection":[140],"shared":[142],"exclusive":[144],"clonotypes":[145],"among":[146,160],"multiple":[147,161],"repertoires,":[148],"5)":[150],"subgroups":[159],"repertoires.":[162],"been":[165,204],"implemented":[166],"toolbox":[169],"Galaxy":[172,228],"bioinformatics":[173],"platform,":[174],"comprising":[175],"6":[176],"tools.":[177],"Theoretical":[178],"experimental":[180],"evaluation":[181],"shown":[183],"tools":[186],"are":[189],"able":[190],"scale":[192],"well":[193],"with":[194,259],"respect":[195],"size":[198],"input":[200],"dataset(s).":[201],"utilized":[205],"by":[206],"recently":[210],"published":[211],"studies":[212],"concerning":[213],"CONCLUSION:":[216],"made":[219],"freely":[220],"available":[221],"via":[222],"3":[223],"distribution":[224],"channels,":[225],"including":[226],"Tool":[229],"Shed.":[230],"Despite":[231],"being":[232],"new":[234],"entry":[235],"in":[236,257],"crowded":[238],"ecosystem":[239],"software,":[244],"founds":[246],"its":[247,251,266],"added":[248],"value":[249],"support":[252],"definitions":[256],"conjunction":[258],"combination":[261],"properties":[263],"stemming":[264],"from":[265],"user-centric":[267],"design,":[268],"namely":[269],"ease-of-use,":[270],"ease-of-access,":[271],"exploitability":[272],"output":[275],"data,":[276],"analysis":[278],"flexibility.":[279]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
