{"id":"https://openalex.org/W3004302995","doi":"https://doi.org/10.1089/cmb.2019.0469","title":"DTD: An R Package for Digital Tissue Deconvolution","display_name":"DTD: An R Package for Digital Tissue Deconvolution","publication_year":2020,"publication_date":"2020-01-29","ids":{"openalex":"https://openalex.org/W3004302995","doi":"https://doi.org/10.1089/cmb.2019.0469","mag":"3004302995","pmid":"https://pubmed.ncbi.nlm.nih.gov/31995409"},"language":"en","primary_location":{"id":"doi:10.1089/cmb.2019.0469","is_oa":true,"landing_page_url":"https://doi.org/10.1089/cmb.2019.0469","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1089/cmb.2019.0469","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043556428","display_name":"Marian Sch\u00f6n","orcid":"https://orcid.org/0000-0003-0882-5392"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Marian Sch\u00f6n","raw_affiliation_strings":["Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083781067","display_name":"Jakob Simeth","orcid":"https://orcid.org/0000-0002-7832-2582"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jakob Simeth","raw_affiliation_strings":["Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085031735","display_name":"Paul V. Heinrich","orcid":"https://orcid.org/0000-0003-4899-8343"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Paul Heinrich","raw_affiliation_strings":["Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064922206","display_name":"Franziska G\u00f6rtler","orcid":"https://orcid.org/0000-0003-2015-5766"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Franziska G\u00f6rtler","raw_affiliation_strings":["Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079231325","display_name":"Stefan Solbrig","orcid":"https://orcid.org/0009-0002-0338-3142"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stefan Solbrig","raw_affiliation_strings":["Department of Physics, University of Regensburg, Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Physics, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017848833","display_name":"Tilo Wettig","orcid":"https://orcid.org/0000-0001-6732-9204"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tilo Wettig","raw_affiliation_strings":["Department of Physics, University of Regensburg, Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Physics, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081742830","display_name":"Peter J. Oefner","orcid":"https://orcid.org/0000-0002-1499-3977"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Peter J. Oefner","raw_affiliation_strings":["Institute of Functional Genomics, University of Regensburg, Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Functional Genomics, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041687654","display_name":"Michael Altenbuchinger","orcid":"https://orcid.org/0000-0003-1102-6532"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michael Altenbuchinger","raw_affiliation_strings":["Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003217898","display_name":"Rainer Spang","orcid":"https://orcid.org/0000-0002-1326-4297"},"institutions":[{"id":"https://openalex.org/I60668342","display_name":"University of Regensburg","ror":"https://ror.org/01eezs655","country_code":"DE","type":"education","lineage":["https://openalex.org/I60668342"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rainer Spang","raw_affiliation_strings":["Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Bioinformatics, Institute of Functional Genomics, University of Regensburg, Regensburg, Germany","institution_ids":["https://openalex.org/I60668342"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5043556428"],"corresponding_institution_ids":["https://openalex.org/I60668342"],"apc_list":null,"apc_paid":null,"fwci":0.4173,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.5893414,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"27","issue":"3","first_page":"386","last_page":"389"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9987000226974487,"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":0.9987000226974487,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9926000237464905,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.987500011920929,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.9136043787002563},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6272921562194824},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6108760833740234},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.47438719868659973},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4309028089046478},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.41220569610595703},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3783346116542816},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2228066325187683},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1788935363292694},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.1617172658443451}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.9136043787002563},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6272921562194824},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6108760833740234},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.47438719868659973},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4309028089046478},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.41220569610595703},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3783346116542816},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2228066325187683},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1788935363292694},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.1617172658443451},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1089/cmb.2019.0469","is_oa":true,"landing_page_url":"https://doi.org/10.1089/cmb.2019.0469","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:31995409","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31995409","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7074920","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7074920","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1089/cmb.2019.0469","is_oa":true,"landing_page_url":"https://doi.org/10.1089/cmb.2019.0469","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W2035252444","https://openalex.org/W2056833048","https://openalex.org/W2171501288","https://openalex.org/W2274866051","https://openalex.org/W2788357641","https://openalex.org/W3004333698","https://openalex.org/W3100442728","https://openalex.org/W4254644117"],"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/W1966302070"],"abstract_inverted_index":{"<b>Digital":[0],"tissue":[1,10,58,67],"deconvolution":[2,53,72],"(DTD)":[3],"estimates":[4],"the":[5,20,52,71,96],"cellular":[6,33],"composition":[7],"of":[8,25,73,79],"a":[9,23,56,65,76],"from":[11,50],"its":[12,89],"bulk":[13,21],"gene-expression":[14],"profile.":[15],"For":[16],"this,":[17],"DTD":[18,47,63,97],"approximates":[19],"as":[22,70],"mixture":[24],"cell-specific":[26],"expression":[27],"profiles.":[28],"Different":[29],"tissues":[30],"have":[31],"different":[32,38,44],"compositions,":[34],"with":[35],"cells":[36],"in":[37,43],"activation":[39],"states,":[40],"and":[41,91,93],"embedded":[42],"environments.":[45],"Consequently,":[46],"can":[48],"profit":[49],"tailoring":[51],"model":[54],"to":[55,64,99],"specific":[57,66,77],"context.</b>":[59],"<b>Loss-function":[60],"learning":[61],"adapts":[62],"context,":[68],"such":[69],"blood,":[74],"or":[75],"type":[78],"tumor":[80],"tissue.":[81],"We":[82],"provide":[83],"software":[84],"for":[85,88,94],"loss-function":[86],"learning,":[87],"validation":[90],"visualization,":[92],"applying":[95],"models":[98],"new":[100],"data.</b>":[101]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
