{"id":"https://openalex.org/W3159271163","doi":"https://doi.org/10.1093/bioinformatics/btab244","title":"TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures","display_name":"TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures","publication_year":2021,"publication_date":"2021-04-14","ids":{"openalex":"https://openalex.org/W3159271163","doi":"https://doi.org/10.1093/bioinformatics/btab244","mag":"3159271163","pmid":"https://pubmed.ncbi.nlm.nih.gov/33901274"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab244","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab244","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11025676","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038938973","display_name":"Mengyu Xie","orcid":"https://orcid.org/0000-0002-4661-9891"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mengyu Xie","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004629166","display_name":"Kyubum Lee","orcid":"https://orcid.org/0000-0003-2015-3939"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyubum Lee","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007381921","display_name":"John H. Lockhart","orcid":"https://orcid.org/0000-0002-2727-6969"},"institutions":[{"id":"https://openalex.org/I4210150208","display_name":"Molecular Oncology (United States)","ror":"https://ror.org/04rtkc841","country_code":"US","type":"company","lineage":["https://openalex.org/I4210150208"]},{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John H Lockhart","raw_affiliation_strings":["Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854","https://openalex.org/I4210150208"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075874956","display_name":"Scott D Cukras","orcid":null},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott D Cukras","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035247776","display_name":"Rodrigo Carvajal","orcid":"https://orcid.org/0000-0002-7607-8272"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rodrigo Carvajal","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032171890","display_name":"Amer A. Beg","orcid":"https://orcid.org/0000-0003-3834-774X"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amer A Beg","raw_affiliation_strings":["Department of Immunology H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Immunology H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005857392","display_name":"Elsa R. Flores","orcid":"https://orcid.org/0000-0002-6173-2403"},"institutions":[{"id":"https://openalex.org/I4210150208","display_name":"Molecular Oncology (United States)","ror":"https://ror.org/04rtkc841","country_code":"US","type":"company","lineage":["https://openalex.org/I4210150208"]},{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elsa R Flores","raw_affiliation_strings":["Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854","https://openalex.org/I4210150208"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049382437","display_name":"Mingxiang Teng","orcid":"https://orcid.org/0000-0002-8536-8941"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mingxiang Teng","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016127308","display_name":"Christine H. Chung","orcid":"https://orcid.org/0000-0001-5199-4306"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christine H Chung","raw_affiliation_strings":["Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019556057","display_name":"Aik Choon Tan","orcid":"https://orcid.org/0000-0003-2955-8369"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aik Choon Tan","raw_affiliation_strings":["Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA","institution_ids":["https://openalex.org/I3019308854"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5019556057"],"corresponding_institution_ids":["https://openalex.org/I3019308854"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5406,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.82921031,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"20","first_page":"3681","last_page":"3683"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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/T11482","display_name":"RNA modifications and cancer","score":0.9994000196456909,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9991000294685364,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/deconvolution","display_name":"Deconvolution","score":0.7788839340209961},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.7228813171386719},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.6257677674293518},{"id":"https://openalex.org/keywords/tumor-microenvironment","display_name":"Tumor microenvironment","score":0.5415859222412109},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4893907904624939},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41463541984558105},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4116937518119812},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.4115549325942993},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3889160454273224},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18675073981285095},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.18657758831977844},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.1109054684638977},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09338471293449402},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.05668765306472778}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.7788839340209961},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7228813171386719},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.6257677674293518},{"id":"https://openalex.org/C2776107976","wikidata":"https://www.wikidata.org/wiki/Q1786433","display_name":"Tumor microenvironment","level":3,"score":0.5415859222412109},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4893907904624939},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41463541984558105},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4116937518119812},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.4115549325942993},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3889160454273224},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18675073981285095},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.18657758831977844},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.1109054684638977},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09338471293449402},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.05668765306472778}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab244","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab244","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33901274","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33901274","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11025676","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11025676","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:11025676","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11025676","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6114876718","display_name":null,"funder_award_id":"T32 CA233399","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8216816772","display_name":null,"funder_award_id":"NCI P30 CA076292","funder_id":"https://openalex.org/F4320311073","funder_display_name":"Moffitt Cancer Center"}],"funders":[{"id":"https://openalex.org/F4320311073","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1985987855","https://openalex.org/W2130430382","https://openalex.org/W2395900612","https://openalex.org/W2533508881","https://openalex.org/W2600132724","https://openalex.org/W2761575992","https://openalex.org/W2789878273","https://openalex.org/W2911922390","https://openalex.org/W2947554843","https://openalex.org/W2952001873","https://openalex.org/W2953757801","https://openalex.org/W2981545603","https://openalex.org/W3027286012","https://openalex.org/W3047725782","https://openalex.org/W3103119004","https://openalex.org/W6728802965","https://openalex.org/W6762947200"],"related_works":["https://openalex.org/W4251527294","https://openalex.org/W3090782779","https://openalex.org/W4296701479","https://openalex.org/W4231036715","https://openalex.org/W3149087629","https://openalex.org/W2032074591","https://openalex.org/W1986156575","https://openalex.org/W4242983818","https://openalex.org/W2970288912","https://openalex.org/W3155641129"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-04T09:10:02.777135","created_date":"2025-10-10T00:00:00"}
