DeconRNASeq: A statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data

Bioinformatics

Volumn 29, Issue 8, 2013, Pages 1083-1085

  Gong, Ting ^a   Szustakowski, Joseph D ^a  

^a NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SEQUENCING; METABOLISM; METHODOLOGY; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LINEAR MODELS; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84876213240     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt090     Document Type: Article

References (12)

1. Bertsekas, D.P. (1999) Nonlinear Programming, 2nd edn. Athena Scientific, Belmont, MA.
2. Cibulskis, K. et al. (2011) ContEst: estimating cross-contamination of human sam- ples in next-generation sequencing data. Bioinformatics, 27, 2601-2602.
3. Gong, T. et al. (2011) Optimal deconvolution oftranscriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS One, 6, e27156.
4. Haas, B.J. and Zody, M.C. (2010) Advancing RNA-Seq analysis. Nat. Biotechnol., 28, 421-423.
5. Huang, W. et al. (2011) Efficiently identifying genome-wide changes with next-generation sequencing data. Nucleic Acids Res., 39, e130.
6. Knights, D. et al. (2011) Bayesian community-wide culture-independent microbial source tracking. Nat. Methods, 8, 761-763.
7. Kuhn, A. et al. (2011) Population-specific expression analysis (PSEA) reveals mo- lecular changes in diseased brain. Nat. Methods, 8, 945-947.
8. Mackey, M.D. et al. (1996) CHEMTAX\-a program for estimating class abun- dances from chemical markers: application to HPLC measurements of phyto- plankton. Mar. Ecol. Prog. Ser., 144, 265-283.
9. Pan, Q. et al. (2008) Deep surveying ofalternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet., 40, 1413-1415.
10. Quon, G. and Morris, Q. (2009) ISOLATE: a computational strategy for identifying the primary origin ofcancers using high-throughput sequencing. Bioinformatics, 25, 2882-2889.
11. Tang, F. et al. (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods, 6, 377-382.
12. Zhao, Y. and Simon, R. (2010) Gene expression deconvolution in clinical samples. Genome Med., 2, 93.