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Items: 1 to 20 of 81

1.

Gene expression deconvolution in clinical samples.

Zhao Y, Simon R.

Genome Med. 2010 Dec 29;2(12):93. doi: 10.1186/gm214.

2.

In silico microdissection of microarray data from heterogeneous cell populations.

Lähdesmäki H, Shmulevich L, Dunmire V, Yli-Harja O, Zhang W.

BMC Bioinformatics. 2005 Mar 14;6:54.

3.

MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples.

Liebner DA, Huang K, Parvin JD.

Bioinformatics. 2014 Mar 1;30(5):682-9. doi: 10.1093/bioinformatics/btt566. Epub 2013 Oct 1.

4.

A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues.

Li Y, Xie X.

BMC Bioinformatics. 2013;14 Suppl 5:S11. doi: 10.1186/1471-2105-14-S5-S11. Epub 2013 Apr 10.

5.

Computational expression deconvolution in a complex mammalian organ.

Wang M, Master SR, Chodosh LA.

BMC Bioinformatics. 2006 Jul 3;7:328.

6.

PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions.

Qiao W, Quon G, Csaszar E, Yu M, Morris Q, Zandstra PW.

PLoS Comput Biol. 2012;8(12):e1002838. doi: 10.1371/journal.pcbi.1002838. Epub 2012 Dec 20.

7.

Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: a case study.

Gaujoux R, Seoighe C.

Infect Genet Evol. 2012 Jul;12(5):913-21. doi: 10.1016/j.meegid.2011.08.014. Epub 2011 Sep 10.

PMID:
21930246
8.

Digital sorting of complex tissues for cell type-specific gene expression profiles.

Zhong Y, Wan YW, Pang K, Chow LM, Liu Z.

BMC Bioinformatics. 2013 Mar 7;14:89. doi: 10.1186/1471-2105-14-89.

9.

Strategies for aggregating gene expression data: the collapseRows R function.

Miller JA, Cai C, Langfelder P, Geschwind DH, Kurian SM, Salomon DR, Horvath S.

BMC Bioinformatics. 2011 Aug 4;12:322. doi: 10.1186/1471-2105-12-322.

10.
11.

Statistical expression deconvolution from mixed tissue samples.

Clarke J, Seo P, Clarke B.

Bioinformatics. 2010 Apr 15;26(8):1043-9. doi: 10.1093/bioinformatics/btq097. Epub 2010 Mar 4.

12.

Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14:89.

Kuhn A.

BMC Bioinformatics. 2014 Nov 28;15:347. doi: 10.1186/s12859-014-0347-5.

13.

MixChIP: a probabilistic method for cell type specific protein-DNA binding analysis.

Rautio S, Lähdesmäki H.

BMC Bioinformatics. 2015 Dec 24;16:413. doi: 10.1186/s12859-015-0834-3.

14.

CellMix: a comprehensive toolbox for gene expression deconvolution.

Gaujoux R, Seoighe C.

Bioinformatics. 2013 Sep 1;29(17):2211-2. doi: 10.1093/bioinformatics/btt351. Epub 2013 Jul 3.

PMID:
23825367
15.

UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples.

Wang N, Gong T, Clarke R, Chen L, Shih IeM, Zhang Z, Levine DA, Xuan J, Wang Y.

Bioinformatics. 2015 Jan 1;31(1):137-9. doi: 10.1093/bioinformatics/btu607. Epub 2014 Sep 10.

16.

Expression profiling of gastric cancer samples by oligonucleotide microarray analysis reveals low degree of intra-tumor variability.

Trautmann K, Steudel C, Grossmann D, Aust D, Ehninger G, Miehlke S, Thiede C.

World J Gastroenterol. 2005 Oct 14;11(38):5993-6.

17.

Gene expression analysis in clear cell renal cell carcinoma using gene set enrichment analysis for biostatistical management.

Maruschke M, Reuter D, Koczan D, Hakenberg OW, Thiesen HJ.

BJU Int. 2011 Jul;108(2 Pt 2):E29-35. doi: 10.1111/j.1464-410X.2010.09794.x. Epub 2011 Mar 16.

18.

CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations.

Chikina M, Zaslavsky E, Sealfon SC.

Bioinformatics. 2015 May 15;31(10):1584-91. doi: 10.1093/bioinformatics/btv015. Epub 2015 Jan 11.

19.

Statistical mechanics approach to the sample deconvolution problem.

Riedel N, Berg J.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Apr;87(4):042715. Epub 2013 Apr 18.

PMID:
23679457
20.

From drug response profiling to target addiction scoring in cancer cell models.

Yadav B, Gopalacharyulu P, Pemovska T, Khan SA, Szwajda A, Tang J, Wennerberg K, Aittokallio T.

Dis Model Mech. 2015 Oct 1;8(10):1255-64. doi: 10.1242/dmm.021105.

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