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Analysis and simulation of gene expression profiles in pure and mixed cell populations.

Hebenstreit D, Teichmann SA.

Phys Biol. 2011 Jun;8(3):035013. doi: 10.1088/1478-3975/8/3/035013. Epub 2011 May 13. Review.


Defining the transcriptome and proteome in three functionally different human cell lines.

Lundberg E, Fagerberg L, Klevebring D, Matic I, Geiger T, Cox J, Algenäs C, Lundeberg J, Mann M, Uhlen M.

Mol Syst Biol. 2010 Dec 21;6:450. doi: 10.1038/msb.2010.106.


EpiChIP: gene-by-gene quantification of epigenetic modification levels.

Hebenstreit D, Gu M, Haider S, Turner DJ, Liò P, Teichmann SA.

Nucleic Acids Res. 2011 Mar;39(5):e27. doi: 10.1093/nar/gkq1226. Epub 2010 Dec 3.


Differentiation of effector CD4 T cell populations (*).

Zhu J, Yamane H, Paul WE.

Annu Rev Immunol. 2010;28:445-89. doi: 10.1146/annurev-immunol-030409-101212. Review.


Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.

Bullard JH, Purdom E, Hansen KD, Dudoit S.

BMC Bioinformatics. 2010 Feb 18;11:94. doi: 10.1186/1471-2105-11-94.


An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.

Ramsköld D, Wang ET, Burge CB, Sandberg R.

PLoS Comput Biol. 2009 Dec;5(12):e1000598. doi: 10.1371/journal.pcbi.1000598. Epub 2009 Dec 11.


PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification.

Spandidos A, Wang X, Wang H, Seed B.

Nucleic Acids Res. 2010 Jan;38(Database issue):D792-9. doi: 10.1093/nar/gkp1005. Epub 2009 Nov 11.


Computation for ChIP-seq and RNA-seq studies.

Pepke S, Wold B, Mortazavi A.

Nat Methods. 2009 Nov;6(11 Suppl):S22-32. doi: 10.1038/nmeth.1371. Review.


An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems.

Lu C, King RD.

Bioinformatics. 2009 Aug 15;25(16):2020-7. doi: 10.1093/bioinformatics/btp360. Epub 2009 Jun 17.


Single-molecule approaches to stochastic gene expression.

Raj A, van Oudenaarden A.

Annu Rev Biophys. 2009;38:255-70. doi: 10.1146/annurev.biophys.37.032807.125928. Review.


Transcript length bias in RNA-seq data confounds systems biology.

Oshlack A, Wakefield MJ.

Biol Direct. 2009 Apr 16;4:14. doi: 10.1186/1745-6150-4-14.


Characterization of human epigenomes.

Wang Z, Schones DE, Zhao K.

Curr Opin Genet Dev. 2009 Apr;19(2):127-34. doi: 10.1016/j.gde.2009.02.001. Epub 2009 Mar 18. Review.


Histone modifications at human enhancers reflect global cell-type-specific gene expression.

Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, Ching KA, Antosiewicz-Bourget JE, Liu H, Zhang X, Green RD, Lobanenkov VV, Stewart R, Thomson JA, Crawford GE, Kellis M, Ren B.

Nature. 2009 May 7;459(7243):108-12. doi: 10.1038/nature07829. Epub 2009 Mar 18.


Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead B, Trapnell C, Pop M, Salzberg SL.

Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4.


Statistical inferences for isoform expression in RNA-Seq.

Jiang H, Wong WH.

Bioinformatics. 2009 Apr 15;25(8):1026-32. doi: 10.1093/bioinformatics/btp113. Epub 2009 Feb 25.


Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells.

Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, Schones DE, Peng W, Sun HW, Paul WE, O'Shea JJ, Zhao K.

Immunity. 2009 Jan 16;30(1):155-67. doi: 10.1016/j.immuni.2008.12.009.


Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.

Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K.

Cell Stem Cell. 2009 Jan 9;4(1):80-93. doi: 10.1016/j.stem.2008.11.011.


RNA-Seq: a revolutionary tool for transcriptomics.

Wang Z, Gerstein M, Snyder M.

Nat Rev Genet. 2009 Jan;10(1):57-63. doi: 10.1038/nrg2484. Review.


Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum.

Mudge J, Miller NA, Khrebtukova I, Lindquist IE, May GD, Huntley JJ, Luo S, Zhang L, van Velkinburgh JC, Farmer AD, Lewis S, Beavis WD, Schilkey FD, Virk SM, Black CF, Myers MK, Mader LC, Langley RJ, Utsey JP, Kim RW, Roberts RC, Khalsa SK, Garcia M, Ambriz-Griffith V, Harlan R, Czika W, Martin S, Wolfinger RD, Perrone-Bizzozero NI, Schroth GP, Kingsmore SF.

PLoS One. 2008;3(11):e3625. doi: 10.1371/journal.pone.0003625. Epub 2008 Nov 5.


Alternative isoform regulation in human tissue transcriptomes.

Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB.

Nature. 2008 Nov 27;456(7221):470-6. doi: 10.1038/nature07509.

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