Ryan J. Taft

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Research Interests

My work is currently focused on two broad questions: how is the amazing adaptive plasticity and developmental complexity of animals encoded in the genome, and how can we use the emerging evidence that the answer to this is question is non-protein-coding RNAs to improve diagnostics, prognostics and therapeutics.

Using high throughput sequencing I have recently led teams in the discovery of three new classes of small RNAs which we are pursuing as potential epigentic modulators. We suspect that as we gain more insight into these RNA species, and into epigenetics generally, we will eventually be able to fine tune gene expression without interfering with the gene itself.

If you'd like to collaborate or get in touch for any reason you can email me (r.taft AT imb.uq.edu.au), or reach me through my profile on the scientific networking site Epernicus (http://www.epernicus.com/rjt).

Brief Biography

I completed a Bachelor of Science in Biochemistry and Molecular Biology at The University of California, Davis. While there I was a University of California Regent's Scholar, a member of the Golden Key national honor society, and in the founding class of the Davis Honors Challenge program.

After completing my degree I worked at the California Pacific Medical Center for four years before joining the Mattick Lab where I was supported by a National Science Foundation Graduate Research Fellowship and University of Queensland International Research Tuition Award. My PhD thesis, "The discovery and characterization of novel classes of small noncoding RNAs", was awarded a Dean's Award for Outstanding Higher Degree Theses. In 2010 I was named as a finalist in the Australia Museum Eureka Prizes in the People's Choice and the Early Career Researcher categories. I am currently supported by a University of Queensland Postdoctoral Fellowship

Selected Publications

Fernandez-Valverde SL, Taft RJ, Mattick JS (2010). Dynamic isomiR regulation in Drosophila development. RNA 16: 1881-1888.

Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, Holst J, Ritchie W, Wong JJ, Rasko JE, Rokhsar DS, Degnan BM, Mattick JS (2010). Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol 17: 1030-1034.

de Hoon MJ, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M, Kishima M, Lassmann T, Faulkner GJ, Mattick JS, Daub CO, Carninci P, Kawai J, Suzuki H, Hayashizaki Y (2010). Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 20: 257-264.

Mattick JS, Taft RJ, Faulkner GJ (2010). A global view of genomic information--moving beyond the gene and the master regulator. Trends Genet 26: 21-8.

Taft RJ, Pang KC, Mercer TR, Dinger ME, Mattick JS (2010). Non-coding RNAs: regulators of disease. J Pathol 220: 126-39.

Nahkuri S, Taft RJ, Mattick JS (2009). Nucleosomes are preferentially positioned at exons in somatic and sperm cells. Cell Cycle 8: 3420-4.

Taft RJ, Kaplan CD, Simons C, Mattick JS (2009). Evolution, biogenesis and function of promoter-associated RNAs. Cell Cycle 8: 2332-8.

Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, Mattick JS (2009). Small RNAs derived from snoRNAs. RNA. 8: 2332-8

Guffanti A, Iacono M, Pelucchi P, Kim N, Solda G, Croft LJ, Taft RJ, Rizzi E, Askarian-Amiri M, Bonnal RJ, Callari M, Mignone F, Pesole G, Bertalot G, Rossi Bernardi L, Albertini A, Lee C, Mattick JS, Zucchi I, De Bellis G (2009). A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics. 10: 163

Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS (2009). Tiny RNAs associated with transcription start sites in animals. Nat Genet. Epub Apr 19.

Nahkuri S, Taft RJ, Korbie DJ, Mattick JS (2008). Molecular evolution of the HBII-52 snoRNA cluster. J Mol Biol 381: 810-815.

Taft, RJ, Pheasant, M, Mattick, JS (2007). The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29: 288-299.

Yount G, Taft RJ, Luu T, Rachlin K, Moore D, Zhang W. Independent motile microplast formation correlates with glioma cell invasiveness. J Neurooncol 81: 113-121.

McAllister SD, Chan C, Taft RJ, Luu T, Abood ME, Moore DH, Aldape K, Yount G. Cannabinoids selectively inhibit proliferation and induce death of cultured human glioblastoma multiforme cells. J Neurooncol 74: 31-40.

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