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Items: 1 to 20 of 50

1.

Estimation of Cell-Type Composition Including T and B Cell Subtypes for Whole Blood Methylation Microarray Data.

Waite LL, Weaver B, Day K, Li X, Roberts K, Gibson AW, Edberg JC, Kimberly RP, Absher DM, Tiwari HK.

Front Genet. 2016 Feb 18;7:23. doi: 10.3389/fgene.2016.00023. eCollection 2016.

2.

Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues.

Wang N, Hoffman EP, Chen L, Chen L, Zhang Z, Liu C, Yu G, Herrington DM, Clarke R, Wang Y.

Sci Rep. 2016 Jan 7;6:18909. doi: 10.1038/srep18909.

3.

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.

Levine JH, Simonds EF, Bendall SC, Davis KL, Amir el-AD, Tadmor MD, Litvin O, Fienberg HG, Jager A, Zunder ER, Finck R, Gedman AL, Radtke I, Downing JR, Pe'er D, Nolan GP.

Cell. 2015 Jul 2;162(1):184-97. doi: 10.1016/j.cell.2015.05.047. Epub 2015 Jun 18.

4.

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.

Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC.

BMC Bioinformatics. 2015 May 14;16:156. doi: 10.1186/s12859-015-0597-x.

5.

Perturbation-expression analysis identifies RUNX1 as a regulator of human mammary stem cell differentiation.

Sokol ES, Sanduja S, Jin DX, Miller DH, Mathis RA, Gupta PB.

PLoS Comput Biol. 2015 Apr 20;11(4):e1004161. doi: 10.1371/journal.pcbi.1004161. eCollection 2015 Apr.

6.

Robust enumeration of cell subsets from tissue expression profiles.

Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA.

Nat Methods. 2015 May;12(5):453-7. doi: 10.1038/nmeth.3337. Epub 2015 Mar 30.

7.

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.

8.

PDE7B is a novel, prognostically significant mediator of glioblastoma growth whose expression is regulated by endothelial cells.

Brooks MD, Jackson E, Warrington NM, Luo J, Forys JT, Taylor S, Mao DD, Leonard JR, Kim AH, Piwnica-Worms D, Mitra RD, Rubin JB.

PLoS One. 2014 Sep 9;9(9):e107397. doi: 10.1371/journal.pone.0107397. eCollection 2014.

9.

Cell cycle population effects in perturbation studies.

O'Duibhir E, Lijnzaad P, Benschop JJ, Lenstra TL, van Leenen D, Groot Koerkamp MJ, Margaritis T, Brok MO, Kemmeren P, Holstege FC.

Mol Syst Biol. 2014 Jun 21;10:732. doi: 10.15252/msb.20145172.

10.

Two-stage, in silico deconvolution of the lymphocyte compartment of the peripheral whole blood transcriptome in the context of acute kidney allograft rejection.

Shannon CP, Balshaw R, Ng RT, Wilson-McManus JE, Keown P, McMaster R, McManus BM, Landsberg D, Isbel NM, Knoll G, Tebbutt SJ.

PLoS One. 2014 Apr 14;9(4):e95224. doi: 10.1371/journal.pone.0095224. eCollection 2014.

11.

MicroRNA dysregulation in spinal cord injury: causes, consequences and therapeutics.

Nieto-Diaz M, Esteban FJ, Reigada D, Muñoz-Galdeano T, Yunta M, Caballero-López M, Navarro-Ruiz R, Del Águila A, Maza RM.

Front Cell Neurosci. 2014 Feb 25;8:53. doi: 10.3389/fncel.2014.00053. eCollection 2014. Review.

12.

Digital cell quantification identifies global immune cell dynamics during influenza infection.

Altboum Z, Steuerman Y, David E, Barnett-Itzhaki Z, Valadarsky L, Keren-Shaul H, Meningher T, Mendelson E, Mandelboim M, Gat-Viks I, Amit I.

Mol Syst Biol. 2014 Feb 28;10:720. doi: 10.1002/msb.134947. Print 2014.

13.

An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples.

Yadav VK, De S.

Brief Bioinform. 2015 Mar;16(2):232-41. doi: 10.1093/bib/bbu002. Epub 2014 Feb 20. Review.

14.

Integrated transcriptome analysis of mouse spermatogenesis.

Margolin G, Khil PP, Kim J, Bellani MA, Camerini-Otero RD.

BMC Genomics. 2014 Jan 18;15:39. doi: 10.1186/1471-2164-15-39.

15.

A method for cell type marker discovery by high-throughput gene expression analysis of mixed cell populations.

Andrade-Navarro MA, Kanji F, Palii CG, Brand M, Atkins H, Perez-Iratxeta C.

BMC Biotechnol. 2013 Oct 3;13:80. doi: 10.1186/1472-6750-13-80.

16.

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.

17.

A self-directed method for cell-type identification and separation of gene expression microarrays.

Zuckerman NS, Noam Y, Goldsmith AJ, Lee PP.

PLoS Comput Biol. 2013;9(8):e1003189. doi: 10.1371/journal.pcbi.1003189. Epub 2013 Aug 22.

18.

RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib.

Bradford JR, Farren M, Powell SJ, Runswick S, Weston SL, Brown H, Delpuech O, Wappett M, Smith NR, Carr TH, Dry JR, Gibson NJ, Barry ST.

PLoS One. 2013 Jun 19;8(6):e66003. doi: 10.1371/journal.pone.0066003. Print 2013.

19.

Systems biological approaches to measure and understand vaccine immunity in humans.

Li S, Nakaya HI, Kazmin DA, Oh JZ, Pulendran B.

Semin Immunol. 2013 Oct 31;25(3):209-18. doi: 10.1016/j.smim.2013.05.003. Epub 2013 Jun 21. Review.

20.

DeMix: deconvolution for mixed cancer transcriptomes using raw measured data.

Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, Wang W.

Bioinformatics. 2013 Aug 1;29(15):1865-71. doi: 10.1093/bioinformatics/btt301. Epub 2013 May 27.

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