Difference between revisions of "Paul Berkman"

Revision as of 00:00, 15 November 2011

Qualifications

• BSc in Genetics, University of Queensland, Brisbane, Australia
• BSc (Honours - First Class) in Biology, University of Southern Queensland, Toowoomba, Australia
• Grad. Cert. in Research Commercialisation (current), University of Queensland, Brisbane, Australia
• Doctor of Philopsophy (current), University of Queensland, Brisbane, Australia

About Me

I started with the ACPFG Bioinformatics Group in March 2009, marking my return to the University of Queensland. Genetics caught my interest early in my undergraduate career as I came to appreciate the intricacies of molecular biology and in 2005 I completed my Bachelor of Science with a Major in Genetics at UQ. After a few years away from scientific pursuits, I undertook my Honours study at the University of Southern Queensland. During Honours, I learnt basic programming while computationally investigating patterns in promoter regions and codon usage in the human genome. Commencing with the ACPFG was a change for me into plant biology where I'm now absorbed in my PhD and enjoying the complexities of plant genomics.

Research Interests

My research interests revolve around resolving assembly issues of repetitive plant genomic sequences. In particular, I am interested in producing high quality genomic sequence data that will be useful for downstream researchers and breeders.

What I'm Working On

I'm predominantly working on the wheat chromosome arm assembly project, driving the group 7 chromosome assemblies and analysis. I've also been contributing on a number of other projects within the group including integrating SNP marker data for use within the infrastructure of an industry partner, quality control of second-generation sequence (2GS) data, and integrating 2GS data into publicly accessible databases (TAGdb, NCBI SRA).

Publications

• Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D (2010) Targeted identification of genomic regions using TAGdb. Plant Methods 6:19.
• Duran C, Eales D, Marshall D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Appleby N, Batley J, Basford K and Edwards D (2010) Future tools for association mapping in crop plants. Genome 53:1017-1023.
• Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubaláková M, Šimková H, Batley J, Fleury D, Doležel J and Edwards D (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol Journal 9:768-775.
• The Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43:1035-1039
• Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubaláková M, Šimková H, Batley J, Doležel J, Hernandez P, and Edwards D (2011) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. TAG Theoretical and Applied Genetics Accepted: In Press.
• Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, and Edwards D (2011) WheatGenome.info: An integrated database and portal for wheat genome information. Plant & Cell Physiology Accepted: In Press.
• Berkman PJ, Lai K, Lorenc MT and Edwards D (2011) Next generation sequencing applications for wheat crop improvement. American Journal of Botany Accepted: In Press.

Contact Details

Address

Paul J. Berkman

Room S421, Hartley Teakle Building (83)

University of Queensland

St Lucia, QLD, 4072

Work Phone

+61 (0)7 3365 1138

Email

p.berkman@uq.edu.au