Marcel Dinger

From GroupWiki

Marcel completed his PhD in 2003 at the University of Waikato (New Zealand) and joined the Mattick group in June 2005. His major research interests are with the annotation and functional characterization of long noncoding RNAs. Marcel manages this wiki and the group websites listed below. He also regularly updates and helps to maintain the long noncoding RNA entry in the Wikipedia. You can find his Epernicus profile at http://www.epernicus.com/med. Email: m.dinger@uq.edu.au [edit] Websites ABA ncRNA Expression Database Public database containing expression data from the Allen Brain Atlas (Instructions also available). ncRNA Expression Database Database containing expression data from the v1 noncoding array and the Allen Brain Atlas. RNAdb Database of mammalian noncoding RNAs.

[edit] Microarray Analysis Tutorials

The Mattick Lab designed the NCode microarrays for analysing the expression of long noncoding RNAs in mouse and human. These arrays are based on the Agilent platform. Below are descriptions of the procedures we developed for analysing data from one and two colour high-density Agilent microarrays using the Limma library (part of Bioconductor) in R.

Single channel analysis of Agilent microarray data with Limma

Two channel analysis of Agilent microarray data with Limma

[edit] Publications

Taft RJ, Pang KC, Mercer TR, Dinger ME, Mattick JS (2009). Non-coding RNAs: regulators of disease. J Pathol. Oct 30. Epub ahead of print.

Dinger ME, Amaral PP, Mercer TR, Mattick JS (2009). Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Brief Funct Genomic Proteomic. 8: 407-23 Free access preprint (15 June 2009).

Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chan W, Mattick JS (2009). Genome-wide identification of long noncoding RNAs in CD8+ T cells. J Immunol. 182: 7738-7748.

Mercer TR, Dinger ME, Mattick JS (2009). Long noncoding RNAs: insights into function. Nature Rev Genet. 10: 155-159.

Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL (2009). MEN ϵ/β nuclear retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19: 347-359.

Dinger ME, Pang KC, Mercer TR, Crowe ML, Grimmond SM, Mattick JS (2009). NRED: a database of long noncoding RNA expression. Nucleic Acid Res 37: D122-6.

Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF (2009). RNA regulation of epigenetic processes. Bioessays. 31: 51-59.

Mercer TR, Dinger ME, Mariani J, Kosik KS, Mehler MF, Mattick JS (2008). Noncoding RNAs in long-term memory formation. Neuroscientist. 14: 434-445.

Dinger ME, Pang KC, Mercer TR, Mattick JS (2008). Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comp Biol 4: e1000176.

Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Soldà G, Simons C, Sunkin SM, Crowe ML, Grimmond SM, Perkins AC, Mattick JS (2008). Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18: 1433-1445.

Amaral PP, Dinger ME, Mercer TR, Mattick JS (2008). The eukaryotic genome as an RNA machine. Science 319: 1787-1789.

Dinger ME, Mercer TR, Mattick JS (2008). RNAs as extracellular signaling molecules. J Mol Endocrinol 40: 151-159.

Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008). Specific expression of long noncoding RNAs in the adult mouse brain. Proc Natl Acad Sci USA 105: 716-721.

Pang, KC, Stephen, S, Dinger, ME, Engstrom, PG, Lenhard, B, Mattick, JS (2007). RNAdb 2.0--an expanded database of mammalian non-coding RNAs. Nucleic Acids Res 35: D178-182.

Musgrave DR, Zhang X, Dinger ME (2002). Archaeal genome organization and stress responses: implications for the origin and evolution of cellular life. Astrobiology 2: 241-253.

Dinger ME, Baillie GJ, Musgrave DR (2000). Growth phase-dependent expression and degradation of histones in the thermophilic archaeon Thermococcus zilligii. Mol Microbiol 36: 876-885.

Dinger ME, Musgrave DR (2000). Identification of archaeal genes encoding a novel stationary phase-response protein. Biochim Biophys Acta 1490: 115-120.