{"id":"https://openalex.org/W2611802561","doi":"https://doi.org/10.1371/journal.pcbi.1005480","title":"MAGERI: Computational pipeline for molecular-barcoded targeted resequencing","display_name":"MAGERI: Computational pipeline for molecular-barcoded targeted resequencing","publication_year":2017,"publication_date":"2017-05-05","ids":{"openalex":"https://openalex.org/W2611802561","doi":"https://doi.org/10.1371/journal.pcbi.1005480","mag":"2611802561","pmid":"https://pubmed.ncbi.nlm.nih.gov/28475621"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005480","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005480","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005480&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":"article","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.1005480&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079193050","display_name":"Mikhail Shugay","orcid":"https://orcid.org/0000-0001-7826-7942"},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["CZ","RU"],"is_corresponding":false,"raw_author_name":"Mikhail Shugay","raw_affiliation_strings":["Central European Institute of Technology, Masaryk University, Brno, Czech republic","Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia"],"raw_orcid":"https://orcid.org/0000-0001-7826-7942","affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Masaryk University, Brno, Czech republic","institution_ids":["https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000678885","display_name":"Andrew R. Zaretsky","orcid":"https://orcid.org/0000-0002-7778-6617"},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Andrew R. Zaretsky","raw_affiliation_strings":["Evrogen JSC, Miklukho-Maklaya 16/10, Moscow, Russia","Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia"],"raw_orcid":"https://orcid.org/0000-0002-7778-6617","affiliations":[{"raw_affiliation_string":"Evrogen JSC, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":[]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060135405","display_name":"Dmitry A. Shagin","orcid":"https://orcid.org/0000-0003-1995-9871"},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Dmitriy A. Shagin","raw_affiliation_strings":["Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072589899","display_name":"Irina A. Shagina","orcid":"https://orcid.org/0000-0003-3954-9108"},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Irina A. Shagina","raw_affiliation_strings":["Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000249308","display_name":"Ivan A. Volchenkov","orcid":null},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ivan A. Volchenkov","raw_affiliation_strings":["Evrogen JSC, Miklukho-Maklaya 16/10, Moscow, Russia","Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Evrogen JSC, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":[]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042917299","display_name":"Andrey Shelenkov","orcid":null},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Andrew A. Shelenkov","raw_affiliation_strings":["Evrogen JSC, Miklukho-Maklaya 16/10, Moscow, Russia","Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia"],"raw_orcid":"https://orcid.org/0000-0002-7409-077X","affiliations":[{"raw_affiliation_string":"Evrogen JSC, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":[]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061571823","display_name":"Mikhail Lebedin","orcid":null},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["CZ","RU"],"is_corresponding":false,"raw_author_name":"Mikhail Y. Lebedin","raw_affiliation_strings":["Central European Institute of Technology, Masaryk University, Brno, Czech republic","Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia"],"raw_orcid":"https://orcid.org/0000-0002-3877-7195","affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Masaryk University, Brno, Czech republic","institution_ids":["https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089140534","display_name":"Dmitriy V. Bagaev","orcid":null},"institutions":[{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Dmitriy V. Bagaev","raw_affiliation_strings":["Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101719293","display_name":"Sergey Lukyanov","orcid":"https://orcid.org/0000-0001-7734-2402"},"institutions":[{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Sergey Lukyanov","raw_affiliation_strings":["Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060028352","display_name":"Dmitriy M. Chudakov","orcid":"https://orcid.org/0000-0003-0430-790X"},"institutions":[{"id":"https://openalex.org/I125989756","display_name":"Skolkovo Institute of Science and Technology","ror":"https://ror.org/03f9nc143","country_code":"RU","type":"education","lineage":["https://openalex.org/I125989756"]},{"id":"https://openalex.org/I337778094","display_name":"Pirogov Russian National Research Medical University","ror":"https://ror.org/018159086","country_code":"RU","type":"education","lineage":["https://openalex.org/I337778094","https://openalex.org/I4210117042"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]},{"id":"https://openalex.org/I4210105571","display_name":"Institute of Bioorganic Chemistry","ror":"https://ror.org/01dg04253","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210105571","https://openalex.org/I4210129690"]}],"countries":["CZ","RU"],"is_corresponding":true,"raw_author_name":"Dmitriy M. Chudakov","raw_affiliation_strings":["Central European Institute of Technology, Masaryk University, Brno, Czech republic","Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia","Skolkovo Institute of Science and Technology, Nobel 3, Moscow, Russia"],"raw_orcid":"https://orcid.org/0000-0003-0430-790X","affiliations":[{"raw_affiliation_string":"Central European Institute of Technology, Masaryk University, Brno, Czech republic","institution_ids":["https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Pirogov Russian National Research Medical University, Ostrovityanova 1, Moscow, Russia","institution_ids":["https://openalex.org/I337778094"]},{"raw_affiliation_string":"Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Miklukho-Maklaya 16/10, Moscow, Russia","institution_ids":["https://openalex.org/I4210105571"]},{"raw_affiliation_string":"Skolkovo Institute of Science and Technology, Nobel 3, Moscow, Russia","institution_ids":["https://openalex.org/I125989756"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5060028352"],"corresponding_institution_ids":["https://openalex.org/I125989756","https://openalex.org/I337778094","https://openalex.org/I4210090417","https://openalex.org/I4210105571"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.3785,"has_fulltext":true,"cited_by_count":72,"citation_normalized_percentile":{"value":0.97049256,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"13","issue":"5","first_page":"e1005480","last_page":"e1005480"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9961000084877014,"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/pipeline","display_name":"Pipeline (software)","score":0.6729092001914978},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6500710248947144},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6020359992980957},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5482809543609619},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.529689371585846},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.49427294731140137},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.43615221977233887},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28674548864364624}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6729092001914978},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6500710248947144},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6020359992980957},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5482809543609619},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.529689371585846},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.49427294731140137},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.43615221977233887},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28674548864364624},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"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":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1005480","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005480","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005480&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:28475621","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28475621","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:0b51a4001a6245a080de45dd1c585258","is_oa":true,"landing_page_url":"https://doaj.org/article/0b51a4001a6245a080de45dd1c585258","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":"PLoS Computational Biology, Vol 13, Iss 5, p e1005480 (2017)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/4978343","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/MAGERI_Computational_pipeline_for_molecular-barcoded_targeted_resequencing/4978343","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:5419444","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5419444","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.1005480","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005480","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005480&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":[],"awards":[{"id":"https://openalex.org/G2825885002","display_name":null,"funder_award_id":"14-35-00105","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"},{"id":"https://openalex.org/G3114638291","display_name":null,"funder_award_id":"633592","funder_id":"https://openalex.org/F4320335254","funder_display_name":"Horizon 2020"},{"id":"https://openalex.org/G3496015395","display_name":null,"funder_award_id":"LQ1601","funder_id":"https://openalex.org/F4320323870","funder_display_name":"Central European Institute of Technology"},{"id":"https://openalex.org/G5066036532","display_name":null,"funder_award_id":"LQ1601","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G5108073634","display_name":null,"funder_award_id":"CEITEC 2020","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G5771046484","display_name":"APERIM: Advanced bioinformatics platform for PERsonalised cancer IMmunotherapy","funder_award_id":"633592","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6956621353","display_name":null,"funder_award_id":"15-34-21052","funder_id":"https://openalex.org/F4320321079","funder_display_name":"Russian Foundation for Basic Research"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"},{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"},{"id":"https://openalex.org/F4320323870","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986"},{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"},{"id":"https://openalex.org/F4320335254","display_name":"Horizon 2020","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2611802561.pdf","grobid_xml":"https://content.openalex.org/works/W2611802561.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W978228178","https://openalex.org/W1211915768","https://openalex.org/W1240977584","https://openalex.org/W1563668677","https://openalex.org/W1939559871","https://openalex.org/W1964023306","https://openalex.org/W1968217876","https://openalex.org/W1981641790","https://openalex.org/W1983466841","https://openalex.org/W1985805774","https://openalex.org/W1992125357","https://openalex.org/W1996536755","https://openalex.org/W1997478924","https://openalex.org/W2009518556","https://openalex.org/W2009694933","https://openalex.org/W2015438948","https://openalex.org/W2039512961","https://openalex.org/W2040539483","https://openalex.org/W2040928840","https://openalex.org/W2041677964","https://openalex.org/W2042202252","https://openalex.org/W2051241958","https://openalex.org/W2076155303","https://openalex.org/W2077353422","https://openalex.org/W2085283923","https://openalex.org/W2099797874","https://openalex.org/W2106578986","https://openalex.org/W2108447672","https://openalex.org/W2110684718","https://openalex.org/W2113187853","https://openalex.org/W2121377606","https://openalex.org/W2123370218","https://openalex.org/W2133385595","https://openalex.org/W2137195441","https://openalex.org/W2137890831","https://openalex.org/W2138601221","https://openalex.org/W2140412193","https://openalex.org/W2141420424","https://openalex.org/W2143197030","https://openalex.org/W2152241467","https://openalex.org/W2154018281","https://openalex.org/W2155943701","https://openalex.org/W2161969272","https://openalex.org/W2171237493","https://openalex.org/W2198945881","https://openalex.org/W2238713843","https://openalex.org/W2295828257","https://openalex.org/W2464329385"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553","https://openalex.org/W4230315250","https://openalex.org/W2394308601","https://openalex.org/W1869907491"],"abstract_inverted_index":{"Unique":[0],"molecular":[1],"identifiers":[2],"(UMIs)":[3],"show":[4],"outstanding":[5],"performance":[6],"in":[7,23,31,104,127],"targeted":[8],"high-throughput":[9],"resequencing,":[10],"being":[11],"the":[12,17],"most":[13],"promising":[14],"approach":[15,28],"for":[16,119],"accurate":[18,116],"identification":[19],"of":[20,55,71,110],"rare":[21,106],"variants":[22],"complex":[24],"DNA":[25,83,122],"samples.":[26],"This":[27],"has":[29],"application":[30],"multiple":[32],"areas,":[33],"including":[34,74],"cancer":[35],"diagnostics,":[36],"thus":[37],"demanding":[38],"dedicated":[39],"software":[40,112],"and":[41,63,89,102,123],"algorithms.":[42],"Here":[43],"we":[44,94],"introduce":[45],"MAGERI,":[46],"a":[47],"computational":[48],"pipeline":[49],"that":[50,96],"efficiently":[51],"handles":[52],"all":[53],"caveats":[54],"UMI-based":[56,133],"analysis":[57],"to":[58],"obtain":[59],"high-fidelity":[60],"mutation":[61],"profiles":[62],"call":[64],"ultra-rare":[65],"variants.":[66,107],"Using":[67],"an":[68],"extensive":[69],"set":[70],"benchmark":[72],"datasets":[73,93,128],"gold-standard":[75],"biological":[76],"samples":[77,88,126],"with":[78],"known":[79],"variant":[80],"frequencies,":[81],"cell-free":[82],"from":[84],"tumor":[85,121],"patient":[86],"blood":[87],"publicly":[90],"available":[91],"UMI-encoded":[92],"demonstrate":[95],"our":[97,111],"method":[98],"is":[99,113],"both":[100,120],"robust":[101],"efficient":[103],"calling":[105],"The":[108],"versatility":[109],"supported":[114],"by":[115],"results":[117],"obtained":[118],"viral":[124],"RNA":[125],"prepared":[129],"using":[130],"three":[131],"different":[132],"protocols.":[134]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":27},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":2}],"updated_date":"2026-05-08T15:41:06.802602","created_date":"2025-10-10T00:00:00"}