Paul Berkman - Revision history

Appbio at 00:09, 21 August 2012

2012-08-21T00:09:07Z

Appbio: /* Publications */

2011-11-15T00:00:20Z

‎Publications

Appbio: /* Publications */

2011-09-27T23:15:42Z

‎Publications

Appbio: /* Qualifications */

2011-04-01T01:52:08Z

‎Qualifications

Appbio at 07:15, 22 March 2011

2011-03-22T07:15:08Z

Appbio: /* What I'm Working On */

2011-03-22T07:14:32Z

‎What I'm Working On

Appbio at 07:05, 22 March 2011

2011-03-22T07:05:45Z

Appbio: /* Address */

2011-03-22T06:55:47Z

‎Address

Appbio: Created page with "==Qualifications== * BSc in Genetics, University of Queensland, Brisbane, Australia * BSc (Honours - First Class) in Biology, University of Southern Queensland, Toowoomba, Austra..."

2010-09-21T11:24:10Z

Created page with "==Qualifications== * BSc in Genetics, University of Queensland, Brisbane, Australia * BSc (Honours - First Class) in Biology, University of Southern Queensland, Toowoomba, Austra..."

New page

==Qualifications==
* BSc in Genetics, University of Queensland, Brisbane, Australia
* BSc (Honours - First Class) in Biology, University of Southern Queensland, Toowoomba, 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. I'm also working on integrating SNP marker data generated by others within the group for use within the infrastructure of an industry partner of the group.

==Contact Details==
===Address===

Paul Berkman

Room S425, Hartley Teakle Building (83)

University of Queensland

St Lucia, QLD, 4072

===Work Phone===

+61 (0)7 334 67082

===Mobile===
+61 (0)409 823 106

===Email===
[mailto:p.berkman@uq.edu.au p.berkman@uq.edu.au]

@@ Line 2: / Line 2: @@
 * 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
+* Grad. Cert. in Research Commercialisation, University of Queensland, Brisbane, Australia
-* Doctor of Philopsophy (current), University of Queensland, Brisbane, Australia
+* Doctor of Philosophy, 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.
+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 became absorbed in my PhD, looking at the complexities of plant genomics.
+==Publications (from Edwards lab)==
 * Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, <b>Berkman PJ</b>, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D (2010) [http://www.plantmethods.com/content/6/1/19 Targeted identification of genomic regions using TAGdb]. Plant Methods 6:19.
 * Duran C, Eales D, Marshall D, Imelfort M, Stiller J, <b>Berkman PJ</b>, Clark T, McKenzie M, Appleby N, Batley J, Basford K and Edwards D (2010) [http://rparticle.web-p.cisti.nrc.ca/rparticle/RpArticleViewer?_handler_=HandleInitialGet&journal=gen&volume=53&calyLang=eng&media=html&articleFile=g10-057.pdf Future tools for association mapping in crop plants]. Genome 53:1017-1023.
 * <b>Berkman PJ</b>, 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) [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract 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) [http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.919.html The genome of the mesopolyploid crop species <i>Brassica rapa</i>]. Nature Genetics 43:1035-1039
-* <b>Berkman PJ</b>, 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) [http://www.springerlink.com/content/uk508r17832pkht8/ Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation]. TAG Theoretical and Applied Genetics Accepted: In Press.
+* <b>Berkman PJ</b>, 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 (2012) [http://www.springerlink.com/content/uk508r17832pkht8/ Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation]. TAG Theoretical and Applied Genetics 124:423-432.
-* Lai K, <b>Berkman PJ</b>, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, and Edwards D (2011) [http://pcp.oxfordjournals.org/content/early/2011/10/18/pcp.pcr141.abstract WheatGenome.info: An integrated database and portal for wheat genome information]. Plant & Cell Physiology Accepted: In Press.
+* Lai K, <b>Berkman PJ</b>, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, and Edwards D (2012) [http://pcp.oxfordjournals.org/content/early/2011/10/18/pcp.pcr141.abstract WheatGenome.info: An integrated database and portal for wheat genome information]. Plant & Cell Physiology 53:e2.
-* <b>Berkman PJ</b>, Lai K, Lorenc MT and Edwards D (2011)  Next generation sequencing applications for wheat crop improvement. American Journal of Botany Accepted: In Press.
+* <b>Berkman PJ</b>, Lai K, Lorenc MT and Edwards D (2012)  [http://www.amjbot.org/content/99/2/365.long Next generation sequencing applications for wheat crop improvement]. American Journal of Botany 99:365-371.
 ==Contact Details==
 ===Email===
-[mailto:p.berkman@uq.edu.au p.berkman@uq.edu.au]
+[mailto:paul.berkman@csiro.au paul.berkman@csiro.au]

@@ Line 20: / Line 20: @@
 * Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, <b>Berkman PJ</b>, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D (2010) [http://www.plantmethods.com/content/6/1/19 Targeted identification of genomic regions using TAGdb]. Plant Methods 6:19.
 * Duran C, Eales D, Marshall D, Imelfort M, Stiller J, <b>Berkman PJ</b>, Clark T, McKenzie M, Appleby N, Batley J, Basford K and Edwards D (2010) [http://rparticle.web-p.cisti.nrc.ca/rparticle/RpArticleViewer?_handler_=HandleInitialGet&journal=gen&volume=53&calyLang=eng&media=html&articleFile=g10-057.pdf Future tools for association mapping in crop plants]. Genome 53:1017-1023.
-* <b>Berkman PJ</b>, 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) [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS]. Plant Biotechnol J 9:768-775.
+* <b>Berkman PJ</b>, 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) [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract 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) [http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.919.html The genome of the mesopolyploid crop species <i>Brassica rapa</i>]. Nature Genetics Accepted: In Press.
+* The Brassica rapa Genome Sequencing Project Consortium (2011) [http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.919.html The genome of the mesopolyploid crop species <i>Brassica rapa</i>]. Nature Genetics 43:1035-1039
-* <b>Berkman PJ</b>, 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.
+* <b>Berkman PJ</b>, 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) [http://www.springerlink.com/content/uk508r17832pkht8/ Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation]. TAG Theoretical and Applied Genetics Accepted: In Press.
 ==Contact Details==

@@ Line 20: / Line 20: @@
 * Marshall DJ, Hayward A, Eales D, Imelfort M, Stiller J, <b>Berkman PJ</b>, Clark T, McKenzie M, Lai K, Duran C, Batley J and Edwards D (2010) [http://www.plantmethods.com/content/6/1/19 Targeted identification of genomic regions using TAGdb]. Plant Methods 6:19.
 * Duran C, Eales D, Marshall D, Imelfort M, Stiller J, <b>Berkman PJ</b>, Clark T, McKenzie M, Appleby N, Batley J, Basford K and Edwards D (2010) [http://rparticle.web-p.cisti.nrc.ca/rparticle/RpArticleViewer?_handler_=HandleInitialGet&journal=gen&volume=53&calyLang=eng&media=html&articleFile=g10-057.pdf Future tools for association mapping in crop plants]. Genome 53:1017-1023.
-* <b>Berkman PJ</b>, Skarshewski A, Lorenc M, 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) [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS]. Plant Biotechnol J Accepted:In Press.
+* <b>Berkman PJ</b>, 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) [http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2010.00587.x/abstract Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS]. Plant Biotechnol J 9:768-775.
+* The Brassica rapa Genome Sequencing Project Consortium (2011) [http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.919.html The genome of the mesopolyploid crop species <i>Brassica rapa</i>]. Nature Genetics Accepted: In Press.
 ==Contact Details==

@@ Line 14: / Line 14: @@
 ==What I'm Working On==
 I'm predominantly working on the [http://wheatgenome.info 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 ([http://flora.acpfg.com.au/tagdb TAGdb], [http://www.ncbi.nlm.nih.gov/sra NCBI SRA]).
 ==Publications==

@@ Line 13: / Line 13: @@
 ==What I'm Working On==
-I'm predominantly working on the wheat chromosome arm assembly project.  I'm also working on integrating SNP marker data generated by others within the group for use within the infrastructure of an industry partner of the group.
+I'm predominantly working on the [http://wheatgenome.info 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 ([http://flora.acpfg.com.au/tagdb TAGdb], [http://www.ncbi.nlm.nih.gov/sra NCBI SRA]).
 ==Publications==

@@ Line 19: / Line 19: @@
 ===Address===
-Paul Berkman
+Paul J. Berkman
-Room S425, Hartley Teakle Building (83)
+Room S421, Hartley Teakle Building (83)
 University of Queensland
 St Lucia, QLD, 4072
 ===Work Phone===