Michael Clark

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Mike completed his BSc(Hons) and MSc at the University of Otago (New Zealand) with Prof Warren Tate before joining the Mattick group to do his PhD. He completed his PhD in January 2012 on the "Transcriptional complexity and post-transcriptional regulation of long noncoding RNAs". Mike's PhD looked into a number of different aspects of long noncoding RNA biology including their expression, sub-cellular localisation, stability and function. Much of his PhD research made use of custom microarrays containing thousands of long noncoding RNAs as well as the usual set of protein coding genes.

In 2013 Mike joined the lab of Marcel Dinger at the Garvan Institute of Medical Research in Sydney. Before moving Chris Ponting's group at Oxford University in 2014 on a NHMRC CJ Martin fellowship.

Mike's postdoctoral work focuses on transcriptomics, especially the use of Capture Sequencing, to investigate RNA processing and splicing, the expression of long noncoding RNAs and role of intergenic disease-associated regions in the human genome.


Email: m.clark'at'garvan.org.au

Twitter: @ClarksysCorner


Contents

Websites

LncRNAdb.org: A manually curated database of known long noncoding RNAs

RNA stability browser: LncRNA and mRNA stability clusters from Clark et al, 2012

Noncodarnia: Noncoding RNA blog from members of the Mattick and Rinn labs

Publications

  1. Clark MB*, Mercer TR*, Bussotti G, Leonardi T, Haynes KR, Crawford J, Lê Cao K, Brunck ME, Thomas GP, Taft RJ, Nielsen LK, Enright AJ, Mattick JS and Dinger ME (2015). Quantitative profiling of long noncoding RNAs with targeted RNA sequencing. Nat Methods 12: 339-342
  2. Mercer TR*, Clark MB*, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS (2015). Genome-wide discovery of human splicing branchpoints. Genome Res. 25: 290-303
  3. The RNAcentral Consortium (2015). RNAcentral: an international database of ncRNA sequences Nucleic Acids Res. 43(Database issue): D123-D129
  4. Quek XC, Thomson DW, Maag JL, Bartonicek N, Signal B, Clark MB, Gloss BS, Dinger ME (2015). lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res. 43(Database issue): D168-173
  5. Mercer TR*, Clark MB*, Crawford J*, Brunck ME, Gerhardt DJ, Taft RJ, Nielsen LK, Dinger ME, Mattick JS (2014). Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nat Protoc. 9: 989-1009
  6. Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen L, Mattick JS, Stamatoyannopoulos JA (2013). DNaseI-hypersensitive exons co-localize with promoters and distal regulatory elements. Nat Genet. 45: 852-9
  7. Clark MB, Choudhary A, Smith, MA, Taft RJ, Mattick JS (2013). The dark matter rises: The expanding world of regulatory RNAs. Essays Biochem. 54: 1–16
  8. Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, Wilhelm D, Dinger ME, Mattick JS (2012). Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. Bioinformatics 28:3042-50
  9. Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P, Dinger ME, Mattick JS (2012). Genome-wide analysis of long noncoding RNA stability. Genome Res. 22: 885-898
  10. Mattick JS, Clark MB (2011) RNA lights up Nat Biotech. 29: 883–884.
  11. Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, et al. (2011) The Reality of Pervasive Transcription. PLoS Biol 9:e1000625.
  12. Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA, Dinger ME, Mattick JS (2011). SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA. 17:878-91.
  13. Clark MB, Mattick JS (2011) Long noncoding RNAs in cell biology. Semin Cell Dev Biol 22:366-376.
  14. Amaral PP*, Clark MB*, Gascoigne DK*, Dinger ME, Mattick JS (2011). lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res. 39: D146-151.
  15. Clark MB, Jänicke M, Gottesbühren U, Kleffmann T, Legge M, Poole ES, Tate WP (2007). Mammalian gene PEG10 expresses two reading frames by high efficiency -1 frameshifting in embryonic-associated tissues. J Biol Chem. 282:37359-69.


(*) Joint first authors.

Genome-wide analysis of long noncoding RNA stability

An updated version of Supplementary Table 2 which includes the column explanations can be found here.

The column explanation table itself can be found here.


For reasons unknown, the resolution of Figure 4 in the published version of Clark et al (2012) Genome-wide analysis of long noncoding RNA stability is low. A copy of the original high resolution image can be found here.

The Reality of Pervasive Transcription

Comment on van Bakel et al. (2011)

Our critique of van Bakel et al. (2010) "Most "dark matter" transcripts are associated with known genes" was recently published in PLoS Biology. van Bakel et al. (2011) replied to our critique. Some comments on their reply can be found here: Comments on van Bakel et al. (2011) Response to “The Reality of Pervasive Transcription”.

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