{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T19:16:02Z","timestamp":1792696562452,"version":"4.5.0"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2015,3,30]],"date-time":"2015-03-30T00:00:00Z","timestamp":1427673600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Methods"],"published-print":{"date-parts":[[2015,5]]},"DOI":"10.1038\/nmeth.3337","type":"journal-article","created":{"date-parts":[[2015,3,30]],"date-time":"2015-03-30T11:34:56Z","timestamp":1427715296000},"page":"453-457","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12022,"title":["Robust enumeration of cell subsets from tissue expression profiles"],"prefix":"10.1038","volume":"12","author":[{"given":"Aaron M","family":"Newman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chih Long","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6309-9472","authenticated-orcid":false,"given":"Michael R","family":"Green","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0941-9858","authenticated-orcid":false,"given":"Andrew J","family":"Gentles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiguo","family":"Feng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuong D","family":"Hoang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maximilian","family":"Diehn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5153-5625","authenticated-orcid":false,"given":"Ash A","family":"Alizadeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2015,3,30]]},"reference":[{"key":"BFnmeth3337_CR1","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1016\/j.cell.2011.02.013","volume":"144","author":"D Hanahan","year":"2011","unstructured":"Hanahan, D. & Weinberg, R.A. Hallmarks of cancer: the next generation. Cell 144, 646\u2013674 (2011).","journal-title":"Cell"},{"key":"BFnmeth3337_CR2","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1126\/science.1232227","volume":"339","author":"LM Coussens","year":"2013","unstructured":"Coussens, L.M., Zitvogel, L. & Palucka, A.K. Neutralizing tumor-promoting chronic inflammation: a magic bullet? Science 339, 286\u2013291 (2013).","journal-title":"Science"},{"key":"BFnmeth3337_CR3","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1016\/j.coi.2013.09.015","volume":"25","author":"SS Shen-Orr","year":"2013","unstructured":"Shen-Orr, S.S. & Gaujoux, R. Computational deconvolution: extracting cell type-specific information from heterogeneous samples.. Curr. Opin. Immunol. 25, 571\u2013578 (2013).","journal-title":"Curr. Opin. Immunol."},{"key":"BFnmeth3337_CR4","doi-asserted-by":"publisher","first-page":"e6098","DOI":"10.1371\/journal.pone.0006098","volume":"4","author":"AR Abbas","year":"2009","unstructured":"Abbas, A.R., Wolslegel, K., Seshasayee, D., Modrusan, Z. & Clark, H.F. Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS ONE 4, e6098 (2009).","journal-title":"PLoS ONE"},{"key":"BFnmeth3337_CR5","doi-asserted-by":"publisher","first-page":"e27156","DOI":"10.1371\/journal.pone.0027156","volume":"6","author":"T Gong","year":"2011","unstructured":"Gong, T. et al. Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS ONE 6, e27156 (2011).","journal-title":"PLoS ONE"},{"key":"BFnmeth3337_CR6","doi-asserted-by":"publisher","first-page":"e1002838","DOI":"10.1371\/journal.pcbi.1002838","volume":"8","author":"W Qiao","year":"2012","unstructured":"Qiao, W. et al. PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions. PLoS Comput. Biol. 8, e1002838 (2012).","journal-title":"PLoS Comput. Biol."},{"key":"BFnmeth3337_CR7","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1093\/bioinformatics\/btt566","volume":"30","author":"DA Liebner","year":"2014","unstructured":"Liebner, D.A., Huang, K. & Parvin, J.D. MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples. Bioinformatics 30, 682\u2013689 (2014).","journal-title":"Bioinformatics"},{"key":"BFnmeth3337_CR8","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1186\/1471-2105-14-89","volume":"14","author":"Y Zhong","year":"2013","unstructured":"Zhong, Y., Wan, Y.-W., Pang, K., Chow, L. & Liu, Z. Digital sorting of complex tissues for cell type-specific gene expression profiles. BMC Bioinformatics 14, 89 (2013).","journal-title":"BMC Bioinformatics"},{"key":"BFnmeth3337_CR9","doi-asserted-by":"publisher","first-page":"e1003189","DOI":"10.1371\/journal.pcbi.1003189","volume":"9","author":"NS Zuckerman","year":"2013","unstructured":"Zuckerman, N.S., Noam, Y., Goldsmith, A.J. & Lee, P.P. A self-directed method for cell-type identification and separation of gene expression microarrays. PLoS Comput. Biol. 9, e1003189 (2013).","journal-title":"PLoS Comput. Biol."},{"key":"BFnmeth3337_CR10","doi-asserted-by":"publisher","first-page":"1207","DOI":"10.1162\/089976600300015565","volume":"12","author":"B Sch\u00f6lkopf","year":"2000","unstructured":"Sch\u00f6lkopf, B., Smola, A.J., Williamson, R.C. & Bartlett, P.L. New support vector algorithms. Neural Comput. 12, 1207\u20131245 (2000).","journal-title":"Neural Comput."},{"key":"BFnmeth3337_CR11","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1038\/nbt0410-322","volume":"28","author":"M Lukk","year":"2010","unstructured":"Lukk, M. et al. A global map of human gene expression.. Nat. Biotechnol. 28, 322\u2013324 (2010).","journal-title":"Nat. Biotechnol."},{"key":"BFnmeth3337_CR12","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1038\/nmeth.1439","volume":"7","author":"SS Shen-Orr","year":"2010","unstructured":"Shen-Orr, S.S. et al. Cell type\u2013specific gene expression differences in complex tissues. Nat. Methods 7, 287\u2013289 (2010).","journal-title":"Nat. Methods"},{"key":"BFnmeth3337_CR13","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1038\/nmeth.1710","volume":"8","author":"A Kuhn","year":"2011","unstructured":"Kuhn, A., Thu, D., Waldvogel, H.J., Faull, R.L.M. & Luthi-Carter, R. Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain. Nat. Methods 8, 945\u2013947 (2011).","journal-title":"Nat. Methods"},{"key":"BFnmeth3337_CR14","doi-asserted-by":"publisher","first-page":"2612","DOI":"10.1038\/ncomms3612","volume":"4","author":"K Yoshihara","year":"2013","unstructured":"Yoshihara, K. et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat. Commun. 4, 2612 (2013).","journal-title":"Nat. Commun."},{"key":"BFnmeth3337_CR15","doi-asserted-by":"publisher","first-page":"92","DOI":"10.2307\/1937887","volume":"49","author":"DE Farrar","year":"1967","unstructured":"Farrar, D.E. & Glauber, R.R. Multicollinearity in regression analysis: the problem revisited. Rev. Econ. Stat. 49, 92\u2013107 (1967).","journal-title":"Rev. Econ. Stat."},{"key":"BFnmeth3337_CR16","doi-asserted-by":"publisher","first-page":"74ra22","DOI":"10.1126\/scitranslmed.3001620","volume":"3","author":"B Burington","year":"2011","unstructured":"Burington, B. et al. CD40 pathway activation status predicts response to CD40 therapy in diffuse large B cell lymphoma. Sci. Transl. Med. 3, 74ra22 (2011).","journal-title":"Sci. Transl. Med."},{"key":"BFnmeth3337_CR17","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1093\/bioinformatics\/btt090","volume":"29","author":"T Gong","year":"2013","unstructured":"Gong, T. & Szustakowski, J.D. DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data.. Bioinformatics 29, 1083\u20131085 (2013).","journal-title":"Bioinformatics"},{"key":"BFnmeth3337_CR18","doi-asserted-by":"publisher","first-page":"1797","DOI":"10.1200\/JCO.2012.43.9273","volume":"32","author":"R Levy","year":"2014","unstructured":"Levy, R. et al. Active idiotypic vaccination versus control immunotherapy for follicular lymphoma. J. Clin. Oncol. 32, 1797\u20131803 (2014).","journal-title":"J. Clin. Oncol."},{"key":"BFnmeth3337_CR19","doi-asserted-by":"publisher","first-page":"10370","DOI":"10.1073\/pnas.1832361100","volume":"100","author":"P Lu","year":"2003","unstructured":"Lu, P., Nakorchevskiy, A. & Marcotte, E.M. Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc. Natl. Acad. Sci. USA 100, 10370\u201310375 (2003).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFnmeth3337_CR20","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1038\/nmeth.1830","volume":"9","author":"Y Zhong","year":"2012","unstructured":"Zhong, Y. & Liu, Z. Gene expression deconvolution in linear space. Nat. Methods 9, 8\u20139 (2012).","journal-title":"Nat. Methods"},{"key":"BFnmeth3337_CR21","first-page":"1157","volume":"3","author":"I Guyon","year":"2003","unstructured":"Guyon, I. & Elisseeff, A. An introduction to variable and feature selection. J. Mach. Learn. Res. 3, 1157\u20131182 (2003).","journal-title":"J. Mach. Learn. Res."},{"key":"BFnmeth3337_CR22","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/S0893-6080(03)00169-2","volume":"17","author":"V Cherkassky","year":"2004","unstructured":"Cherkassky, V. & Ma, Y. Practical selection of SVM parameters and noise estimation for SVM regression. Neural Netw. 17, 113\u2013126 (2004).","journal-title":"Neural Netw."},{"key":"BFnmeth3337_CR23","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1080\/00401706.1970.10488634","volume":"12","author":"AE Hoerl","year":"1970","unstructured":"Hoerl, A.E. & Kennard, R.W. Ridge regression: biased estimation for nonorthogonal problems. Technometrics 12, 55\u201367 (1970).","journal-title":"Technometrics"},{"key":"BFnmeth3337_CR24","doi-asserted-by":"crossref","unstructured":"Hastie, T., Tibshirani, R. & Friedman, J. The Elements of Statistical Learning 2nd edn. (Springer, 2009).","DOI":"10.1007\/978-0-387-84858-7"},{"key":"BFnmeth3337_CR25","first-page":"589","volume":"16","author":"L Wang","year":"2006","unstructured":"Wang, L., Zhu, J. & Zou, H. The doubly regularized support vector machine. Statist. Sinica 16, 589\u2013615 (2006).","journal-title":"Statist. Sinica"},{"key":"BFnmeth3337_CR26","first-page":"155","volume":"9","author":"H Drucker","year":"1997","unstructured":"Drucker, H., Burges, C.J.C., Kaufman, L., Smola, A. & Vapnik, V. in Adv. Neural Inf. Process. Syst. (eds. Mozer, M.C., Jordan, M.I. & Petsche, T.) 9, 155\u2013161 (MIT Press, 1997).","journal-title":"Adv. Neural Inf. Process. Syst."},{"key":"BFnmeth3337_CR27","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/1471-2164-8-140","volume":"8","author":"LJ Su","year":"2007","unstructured":"Su, L.J. et al. Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme. BMC Genomics 8, 140 (2007).","journal-title":"BMC Genomics"},{"key":"BFnmeth3337_CR28","doi-asserted-by":"publisher","first-page":"e1651","DOI":"10.1371\/journal.pone.0001651","volume":"3","author":"MT Landi","year":"2008","unstructured":"Landi, M.T. et al. Gene expression signature of cigarette smoking and its role in lung adenocarcinoma development and survival. PLoS One 3, e1651 (2008).","journal-title":"PLoS One"},{"key":"BFnmeth3337_CR29","doi-asserted-by":"publisher","first-page":"9440","DOI":"10.1073\/pnas.1530509100","volume":"100","author":"JD Storey","year":"2003","unstructured":"Storey, J.D. & Tibshirani, R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100, 9440\u20139445 (2003).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFnmeth3337_CR30","doi-asserted-by":"publisher","first-page":"5376","DOI":"10.1182\/blood-2010-01-263855","volume":"115","author":"Y Benita","year":"2010","unstructured":"Benita, Y. et al. Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor. Blood 115, 5376\u20135384 (2010).","journal-title":"Blood"},{"key":"BFnmeth3337_CR31","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1182\/blood-2008-06-162958","volume":"113","author":"NA Watkins","year":"2009","unstructured":"Watkins, N.A. et al. A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood 113, e1\u2013e9 (2009).","journal-title":"Blood"},{"key":"BFnmeth3337_CR32","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/sj.gene.6364173","volume":"6","author":"AR Abbas","year":"2005","unstructured":"Abbas, A.R. et al. Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data. Genes Immun. 6, 319\u2013331 (2005).","journal-title":"Genes Immun."}],"container-title":["Nature Methods"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nmeth.3337.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nmeth.3337","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nmeth.3337.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T19:30:55Z","timestamp":1684438255000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nmeth.3337"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,3,30]]},"references-count":32,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2015,5]]}},"alternative-id":["BFnmeth3337"],"URL":"https:\/\/doi.org\/10.1038\/nmeth.3337","relation":{},"ISSN":["1548-7091","1548-7105"],"issn-type":[{"value":"1548-7091","type":"print"},{"value":"1548-7105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,30]]},"assertion":[{"value":"23 May 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 February 2015","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 March 2015","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}