{"id":"https://openalex.org/W2921304627","doi":"https://doi.org/10.1186/s12859-019-2641-8","title":"Shambhala: a platform-agnostic data harmonizer for gene expression data","display_name":"Shambhala: a platform-agnostic data harmonizer for gene expression data","publication_year":2019,"publication_date":"2019-02-06","ids":{"openalex":"https://openalex.org/W2921304627","doi":"https://doi.org/10.1186/s12859-019-2641-8","mag":"2921304627","pmid":"https://pubmed.ncbi.nlm.nih.gov/30727942"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2641-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2641-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2641-8","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/track/pdf/10.1186/s12859-019-2641-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113454268","display_name":"Nicolas Borisov","orcid":null},"institutions":[{"id":"https://openalex.org/I17877952","display_name":"Sechenov University","ror":"https://ror.org/02yqqv993","country_code":"RU","type":"education","lineage":["https://openalex.org/I17877952"]},{"id":"https://openalex.org/I4210143161","display_name":"IDEX Corporation (United States)","ror":"https://ror.org/03jqyh750","country_code":"US","type":"company","lineage":["https://openalex.org/I4210143161"]}],"countries":["RU","US"],"is_corresponding":true,"raw_author_name":"Nicolas Borisov","raw_affiliation_strings":["Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA. borisov@oncobox.com","I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia. borisov@oncobox.com","I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia"],"raw_orcid":"https://orcid.org/0000-0002-1671-5524","affiliations":[{"raw_affiliation_string":"Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA. borisov@oncobox.com","institution_ids":["https://openalex.org/I4210143161"]},{"raw_affiliation_string":"I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia. borisov@oncobox.com","institution_ids":["https://openalex.org/I17877952"]},{"raw_affiliation_string":"I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia","institution_ids":["https://openalex.org/I17877952"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011848694","display_name":"Irina Shabalina","orcid":null},"institutions":[{"id":"https://openalex.org/I197524780","display_name":"Petrozavodsk State University","ror":"https://ror.org/0176aa147","country_code":"RU","type":"education","lineage":["https://openalex.org/I197524780"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Irina Shabalina","raw_affiliation_strings":["Faculty of Mathematics and Information Technologies, Petrozavodsk State University, Anokhina str., 20, Petrozavodsk, 185910, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Mathematics and Information Technologies, Petrozavodsk State University, Anokhina str., 20, Petrozavodsk, 185910, Russia","institution_ids":["https://openalex.org/I197524780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030144117","display_name":"Victor Tkachev","orcid":"https://orcid.org/0000-0002-8733-2205"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Victor Tkachev","raw_affiliation_strings":["Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073346552","display_name":"Maxim Sorokin","orcid":"https://orcid.org/0000-0001-7685-3446"},"institutions":[{"id":"https://openalex.org/I17877952","display_name":"Sechenov University","ror":"https://ror.org/02yqqv993","country_code":"RU","type":"education","lineage":["https://openalex.org/I17877952"]},{"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":"Maxim Sorokin","raw_affiliation_strings":["Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA","Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia","I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA","institution_ids":[]},{"raw_affiliation_string":"Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia","institution_ids":["https://openalex.org/I4210105571"]},{"raw_affiliation_string":"I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia","institution_ids":["https://openalex.org/I17877952"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077749610","display_name":"Andrew Garazha","orcid":"https://orcid.org/0000-0001-9679-149X"},"institutions":[{"id":"https://openalex.org/I4210127411","display_name":"Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology","ror":"https://ror.org/02h8dsx08","country_code":"RU","type":"facility","lineage":["https://openalex.org/I4210127411"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Andrew Garazha","raw_affiliation_strings":["Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA","Laboratory of Bioinformatics, Oncology and Immunology, D. Rogachyov Federal Research Center of Pediatric Hematology, Moscow, 117198, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA","institution_ids":[]},{"raw_affiliation_string":"Laboratory of Bioinformatics, Oncology and Immunology, D. Rogachyov Federal Research Center of Pediatric Hematology, Moscow, 117198, Russia","institution_ids":["https://openalex.org/I4210127411"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012501903","display_name":"\u0410. \u0410 \u041f\u0443\u043b\u0438\u043d","orcid":"https://orcid.org/0000-0002-9499-4979"},"institutions":[{"id":"https://openalex.org/I4210131054","display_name":"Research Institute of General Pathology and Pathophysiology, the Russian Academy of Medical Sciences","ror":"https://ror.org/03jmc9t23","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210110862","https://openalex.org/I4210131054"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Andrey Pulin","raw_affiliation_strings":["Laboratory for Cell Biology and Developmental Pathology, Federal State Institution \"Institute of General Pathology and Pathophysiology\", FSBSI \"IGPP\", Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Cell Biology and Developmental Pathology, Federal State Institution \"Institute of General Pathology and Pathophysiology\", FSBSI \"IGPP\", Moscow, Russia","institution_ids":["https://openalex.org/I4210131054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054556936","display_name":"I. I Eremin","orcid":"https://orcid.org/0000-0002-4336-8986"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ilya I. Eremin","raw_affiliation_strings":["Department for Regenerative Medicine, JSC Generium, Moscow, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department for Regenerative Medicine, JSC Generium, Moscow, Russia","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008472454","display_name":"Anton Buzdin","orcid":"https://orcid.org/0000-0001-9866-3424"},"institutions":[{"id":"https://openalex.org/I17877952","display_name":"Sechenov University","ror":"https://ror.org/02yqqv993","country_code":"RU","type":"education","lineage":["https://openalex.org/I17877952"]},{"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":"Anton Buzdin","raw_affiliation_strings":["Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA","Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia","I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of bioinformatics and molecular networks, OmicsWay Corporation, Walnut, CA, USA","institution_ids":[]},{"raw_affiliation_string":"Group for Genomic Regulation of Cell Signaling Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia","institution_ids":["https://openalex.org/I4210105571"]},{"raw_affiliation_string":"I.M. Sechenov First Moscow State Medical University, Sechenov University, Moscow, 119991, Russia","institution_ids":["https://openalex.org/I17877952"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5113454268"],"corresponding_institution_ids":["https://openalex.org/I17877952","https://openalex.org/I4210143161"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.6457,"has_fulltext":true,"cited_by_count":48,"citation_normalized_percentile":{"value":0.94078091,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"66","last_page":"66"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9573000073432922,"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"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9573000073432922,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.004800000227987766,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.004399999976158142,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/dna-microarray","display_name":"DNA microarray","score":0.6377330422401428},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.544866681098938},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5310792326927185},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4731284976005554},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4713950455188751},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4487426280975342},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.40857815742492676},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3724138140678406},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3579159379005432},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33489230275154114},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2681563198566437},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11306837201118469}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6377330422401428},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.544866681098938},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5310792326927185},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4731284976005554},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4713950455188751},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4487426280975342},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40857815742492676},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3724138140678406},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3579159379005432},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33489230275154114},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2681563198566437},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11306837201118469}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-2641-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2641-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2641-8","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:30727942","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30727942","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:pubmedcentral.nih.gov:6366102","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6366102","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:5eecde675783479d9739b2c4756b0a22","is_oa":true,"landing_page_url":"https://doaj.org/article/5eecde675783479d9739b2c4756b0a22","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 20, Iss 1, Pp 1-10 (2019)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2641-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2641-8","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2641-8","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":[],"awards":[{"id":"https://openalex.org/G4458894619","display_name":null,"funder_award_id":"17-75-","funder_id":"https://openalex.org/F4320324099","funder_display_name":"Russian Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1523843467","https://openalex.org/W1800724332","https://openalex.org/W1952999593","https://openalex.org/W1968295800","https://openalex.org/W2006138378","https://openalex.org/W2010637767","https://openalex.org/W2011480812","https://openalex.org/W2015042232","https://openalex.org/W2018838463","https://openalex.org/W2020541351","https://openalex.org/W2025183726","https://openalex.org/W2046872827","https://openalex.org/W2054789404","https://openalex.org/W2064397275","https://openalex.org/W2076394567","https://openalex.org/W2098574180","https://openalex.org/W2100471807","https://openalex.org/W2103868202","https://openalex.org/W2113878188","https://openalex.org/W2120865735","https://openalex.org/W2134459098","https://openalex.org/W2134787419","https://openalex.org/W2139345901","https://openalex.org/W2143290174","https://openalex.org/W2149107469","https://openalex.org/W2150376021","https://openalex.org/W2152239989","https://openalex.org/W2168113705","https://openalex.org/W2179438025","https://openalex.org/W2238410310","https://openalex.org/W2300980227","https://openalex.org/W2514382336","https://openalex.org/W2746728221","https://openalex.org/W2750132486","https://openalex.org/W2796220975","https://openalex.org/W2950788368","https://openalex.org/W4253759977"],"related_works":["https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W106077234","https://openalex.org/W2084813257","https://openalex.org/W2043690326","https://openalex.org/W2052655934","https://openalex.org/W2041374557","https://openalex.org/W2045929470","https://openalex.org/W2081929287","https://openalex.org/W2144348650"],"abstract_inverted_index":{"BACKGROUND:":[0],"Harmonization":[1],"techniques":[2],"make":[3,95],"different":[4,35,154],"gene":[5,30,82,120],"expression":[6,31,83,121],"profiles":[7,84,122],"and":[8,12,38,43,152,160,177,188],"their":[9],"sets":[10],"compatible":[11],"ready":[13],"for":[14,25,56,71,193],"comparisons.":[15,73],"Here":[16],"we":[17],"present":[18],"a":[19],"new":[20],"bioinformatic":[21],"tool":[22],"termed":[23],"Shambhala":[24,60,74,129,180],"harmonization":[26,55,75,181],"of":[27,40,63,81,101,118],"multiple":[28,64,145,198],"human":[29,119],"datasets":[32,65],"obtained":[33,196],"using":[34,85,150],"experimental":[36,155,199],"methods":[37,50],"platforms":[39],"microarray":[41,102],"hybridization":[42,103],"RNA":[44],"sequencing.":[45],"RESULTS:":[46],"Unlike":[47],"previously":[48],"published":[49],"enabling":[51],"good":[52],"quality":[53],"data":[54,195],"only":[57,184],"two":[58],"datasets,":[59],"allows":[61],"conversion":[62],"into":[66],"the":[67,79,86,99,115,183,194],"universal":[68],"form":[69],"suitable":[70],"further":[72],"is":[76,92],"based":[77],"on":[78],"calibration":[80],"auxiliary":[87],"standardization":[88],"dataset.":[89],"Each":[90],"profile":[91],"transformed":[93],"to":[94,98,131],"it":[96,113],"similar":[97],"output":[100],"platform":[104,109],"Affymetrix":[105],"Human":[106],"Gene.":[107],"This":[108],"was":[110,182],"chosen":[111],"because":[112],"has":[114],"biggest":[116],"number":[117],"deposited":[123],"in":[124,144],"public":[125],"databases.":[126],"We":[127],"evaluated":[128],"ability":[130],"retain":[132],"biologically":[133,190],"important":[134],"features":[135],"after":[136],"harmonization.":[137],"The":[138],"same":[139],"four":[140,153],"biological":[141],"samples":[142],"taken":[143],"replicates":[146],"were":[147],"profiled":[148],"independently":[149],"three":[151],"platforms,":[156],"respectively,":[157],"then":[158],"Shambhala-harmonized":[159],"investigated":[161],"by":[162],"hierarchical":[163],"clustering.":[164],"CONCLUSION:":[165],"Our":[166],"results":[167],"showed":[168],"that":[169],"unlike":[170],"other":[171],"frequently":[172],"used":[173],"methods:":[174],"quantile":[175],"normalization":[176],"DESeq/DESeq2":[178],"normalization,":[179],"method":[185],"supporting":[186],"sample-specific":[187],"platform-independent":[189],"meaningful":[191],"clustering":[192],"from":[197],"platforms.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":8}],"updated_date":"2026-05-19T21:40:30.786675","created_date":"2025-10-10T00:00:00"}