{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,2]],"date-time":"2025-08-02T14:19:13Z","timestamp":1754144353480,"version":"3.41.2"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T00:00:00Z","timestamp":1752537600000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004257","name":"Helse Vest","doi-asserted-by":"publisher","award":["NCT02872259"],"award-info":[{"award-number":["NCT02872259"]}],"id":[{"id":"10.13039\/501100004257","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["SFB-TRR-247","KFO-5002"],"award-info":[{"award-number":["SFB-TRR-247","KFO-5002"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"German Federal Ministry of Education and Research","award":["01ZX1912A","01ZX1912C"],"award-info":[{"award-number":["01ZX1912A","01ZX1912C"]}]},{"name":"FDLP","award":["01KD2209D"],"award-info":[{"award-number":["01KD2209D"]}]},{"name":"FDLP2","award":["01KD2415A"],"award-info":[{"award-number":["01KD2415A"]}]},{"name":"Fairpact2","award":["01KD2414A"],"award-info":[{"award-number":["01KD2414A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Cell-type deconvolution is a computational approach to infer cellular distributions from bulk transcriptomics data. Several methods have been proposed, each with its own advantages and disadvantages. Reference based approaches make use of archetypic transcriptomic profiles representing individual cell types. Those reference profiles are ideally chosen such that the observed bulks can be reconstructed as a linear combination thereof. This strategy, however, ignores the fact that cellular populations arise through the process of cellular differentiation, which entails the gradual emergence of cell groups with diverse morphological and functional characteristics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we propose Hierarchical cell-type Deconvolution (HIDE), a cell-type deconvolution approach which incorporates a cell hierarchy for improved performance and interpretability. This is achieved by a hierarchical procedure that preserves estimates of major cell populations while inferring their respective subpopulations. We show in simulation studies that this procedure produces more reliable and more consistent results than other state-of-the-art approaches. Finally, we provide an example application of HIDE to explore breast cancer specimens from TCGA.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>A python implementation of HIDE is available at zenodo (doi: 10.5281\/zenodo.14724906).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf179","type":"journal-article","created":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T13:02:13Z","timestamp":1752584533000},"page":"i207-i216","source":"Crossref","is-referenced-by-count":0,"title":["HIDE: hierarchical cell-type deconvolution"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-9550-8434","authenticated-orcid":false,"given":"Dennis","family":"V\u00f6lkl","sequence":"first","affiliation":[{"name":"Computational Biology Unit, Department of Informatics, University of Bergen , Postboks 7803 , Bergen NO-5020,","place":["Norway"]},{"name":"Institute of Theoretical Physics, University of Regensburg , Regensburg 93053,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-3026-7061","authenticated-orcid":false,"given":"Malte","family":"Mensching-Buhr","sequence":"additional","affiliation":[{"name":"Computational Biology Unit, Department of Informatics, University of Bergen , Postboks 7803 , Bergen NO-5020,","place":["Norway"]},{"name":"Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , G\u00f6ttingen 37075,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-0839-9664","authenticated-orcid":false,"given":"Thomas","family":"Sterr","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , G\u00f6ttingen 37075,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah","family":"Bolz","sequence":"additional","affiliation":[{"name":"Institute of Human Anatomy and Embryology, University of Regensburg , Regensburg 93053,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Sch\u00e4fer","sequence":"additional","affiliation":[{"name":"Institute of Theoretical Physics, University of Regensburg , Regensburg 93053,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2191-523X","authenticated-orcid":false,"given":"Nicole","family":"Seifert","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , G\u00f6ttingen 37075,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1771-9818","authenticated-orcid":false,"given":"Jana","family":"Tauschke","sequence":"additional","affiliation":[{"name":"Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Hannover Medical School , Hannover 30625,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6298-1591","authenticated-orcid":false,"given":"Austin","family":"Rayford","sequence":"additional","affiliation":[{"name":"Department of Biomedicine and Centre for Cancer Biomarkers, University of Bergen , Bergen N-5008,","place":["Norway"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8867-3645","authenticated-orcid":false,"given":"Oddbj\u00f8rn","family":"Straume","sequence":"additional","affiliation":[{"name":"Cancer Clinic, Haukeland University Hospital , Haukelandsveien 22 , Bergen N-5021,","place":["Norway"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3633-1330","authenticated-orcid":false,"given":"Helena U","family":"Zacharias","sequence":"additional","affiliation":[{"name":"Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Hannover Medical School , Hannover 30625,","place":["Germany"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6410-1749","authenticated-orcid":false,"given":"Sushma Nagaraja","family":"Grellscheid","sequence":"additional","affiliation":[{"name":"Computational Biology Unit, Department of Informatics, University of Bergen , Postboks 7803 , Bergen NO-5020,","place":["Norway"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6509-2143","authenticated-orcid":false,"given":"Tim","family":"Beissbarth","sequence":"additional","affiliation":[{"name":"Department of Medical Bioinformatics, University Medical Center G\u00f6ttingen , G\u00f6ttingen 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