Curriculum Vitae
Dr. Gabriel Kolle
Bioinformatics application specialist
- SOLiD
Life Technologies
10/60 MacGregor Tce.
Bardon, Q, Australia
Ph: +61 (0)419-748-633
Email: gabriel.kolle@lifetech.com
Summary:
I am partnered with the Institute for Molecular Bioscience/University of
Queensland to provide understanding and analysis of data derived through the use
of next-generation high throughput sequencing systems in the International Cancer
Genome Sequencing (ICGC) programme. This involves the bioinformatics support
of a variety of applications including whole genome resequencing of cancer,
methylation, transcriptome and small RNA sequencing.
I also support various
groups with Australia and New Zealand, consulting on experimental design, data
analysis and troubleshooting bioinformatics problems. My previous experience as
a post-doctoral researcher focused on the transcriptional programs that underlie the
human embryonic stem cell state, and I co-authored the first whole transcriptome
publication using the SOLiD system.
Education:
PhD
BSc (Hons)
University of Queensland
University of Queensland
2003
1998
Postdoctoral experience:
Research Officer
Guest Scientist
Institute for Molecular Bioscience, Brisbane, Australia
German Cancer Research Centre, Heidelberg, Germany
2005-9
2003-4
Detailed History:
Previous professional Experience:
2005-2009:
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Research Officer/Genome Bioinformatician
Expression Genomics Laboratory headed by A/Prof Sean Grimmond
Institute for Molecular Bioscience, University of Queensland, Brisbane,
Australia
Next generation sequencing of the transcriptome (RNA-seq). Matching and postmatching analysis of transcriptome data, generated in high throughput from ABi
SOLiD sequencing, including gene expression, alternative splicing and expressed
SNP analysis and characterization.
Microarray platform analysis (Illumina and Affymetrix microarray, Affymetrix allexon array, CGH arrays).
Collaboration with a number of groups within the Australian Stem Cell Centre
providing genomic and bio-informatic support
2003-2004:
Guest Scientist Postdoctoral Position:
Division Molecular Embryology headed by Prof. Christof Niehrs.
German Cancer Research Centre (DKFZ), Heidelberg Germany
1999-2003:
PhD Thesis: Functional analysis of a novel gene, Crim1, in vertebrate
development.
Supervised by A/Prof Melissa Little and Dr. Toshiya Yamada
Institute for Molecular Bioscience, University of Queensland, Brisbane,
Australia
1998:
Honours degree: Characterization of a novel gene, s52, in
development of the vertebrate central nervous system - Supervised by
Dr. Toshiya Yamada
Centre for Molecular and Cellular Biology, University of Queensland,
Brisbane, Australia
Publications:
Kolle G*, Cloonan N*, Forrest AR*, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF,
Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade
SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM. Stem cell transcriptome
profiling via massive-scale mRNA sequencing. Nat Methods. (2008), 5, 613-19. (* Cofirst authors)
Kolle G, Ho M, Zhou Q, Chy HS, Krishnan K, Cloonan N, Bertoncello I, Laslett AL,
Grimmond SM., Identification of human embryonic stem cell surface markers by
combined membrane-polysome translation state array analysis and
immunotranscriptional profiling. Stem Cells. (2009) Oct;27(10):2446-56.
Lin SA, Kolle G, Grimmond SM, Zhou Q, Doust E, Little MH, Aronow B, Ricardo SD,
Pera MF, Bertram JF, Laslett AL, Subfractionation of differentiating hES cell populations
allows the isolation of a mesodermal population enriched for intermediate mesoderm and
putative renal progenitors. Stem Cells Dev. (2010) [Epub ahead of print]
Hough SR, Laslett AL, Grimmond SB, Kolle G, Pera MF. A continuum of cell states
spans pluripotency and lineage commitment in human embryonic stem cells. PLoS One.
(2009) Nov 5;4(11):e7708.
Grandela C, Pera MF, Grimmond SM, Kolle G, Wolvetang EJ. p53 is required for
etoposide-induced apoptosis of human embryonic stem cells. Stem Cell Res. (2008) 116128.
Cloonan N, Xu Q, Faulkner GJ, Taylor DF, Tang DT, Kolle G, Grimmond SM.
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data.
Bioinformatics. 2009 Oct 1;25(19):2615-6. Epub 2009 Jul 30
Cloonan, N., Brown, M.K, Steptoe, A.L., Wani, S., Chan, W.L., Forrest, A.R.R., Kolle,
G., Gabrielli, B., Grimmond, S.M., The miR-17-5p microRNA is a key regulator of the
G1/S phase cell cycle transition, Genome Biol. (2008), 9, R127.
Grandela, C., Pera, M.F., Grimmond, S.M., Kolle, G., Wolvetang, E.J., p53 is required
for etoposide-induced apoptosis of human embryonic stem cells, Stem Cell Research
(2008), 1, 116–128.
Ogata, S., Morokuma, J, Hayata, T., Kolle, G., Niehrs, C., Ueno, N., Cho, KW., TGFbeta signaling-mediated morphogenesis: modulation of cell adhesion via cadherin
endocytosis, Genes Dev. (2007) 21:1817-31.
Pennisi DJ, Wilkinson L, Kolle G, Sohaskey ML, Gillinder K, Piper MJ, McAvoy JW,
Lovicu FJ, Little MH. Crim1KST264/KST264 mice display a disruption of the Crim1
gene resulting in perinatal lethality with defects in multiple organ systems. Dev Dyn.
(2007) 236, 502-11.
Forrest, A.R., Taylor, D.F., Crowe, M.L., Chalk, A.M., Waddell, N.J., Kolle, G.,
Faulkner, G.J., Kodzius, R., Katayama, S., Wells, C., Kai, C., Kawai, J., Carninci, P.,
Hayashizaki, Y., Grimmond, S.M., 2006, Genome-wide review of transcriptional
complexity in mouse protein kinases and phosphatises, Genome Biol (2006) 7: R5.
Kinna, G., Kolle, G., Carter, A., Key, B., Lieschke, G.J., Perkins, A., Little, M.H,
Knockdown of zebrafish crim1 results in a bent tail phenotype with defects in somite and
vascular development, Mech Dev. (2006) 123, 277-287
Wilkinson, L., Kolle G., Wen, D., Piper, M., Scott, J., Little, M.H. CRIM1 regulates the
rate of processing and delivery of bone morphogenetic proteins to the cell surface, J.
Biol. Chem. (2003), 278, 34181-34188.
Kolle, G., Jansen, A, Yamada, T., Little, M.H. In ovo electroporation of Crim1 in the
chick developing spinal cord, Dev Dyn. (2003), 226, 107-111.
Poh, A., Karunaratne, A., Kolle G., Huang, N., Smith, E., Starkey, J., Wilson, I.,
Yamada, T., Hargrave, M. Patterning of the vertebrate spinal cord. Int J Dev Biol. (2002)
46, 597-608.
Lovicu, F., Kolle, G., Yamada, T., Little, M.H., McAvoy, J.W. Expression of Crim1
during murine ocular development. Mech Dev. (2000) 94, 261-265.
Kolle, G., Georgas, K., Holmes, G. P., Little, M. H., Yamada, T. CRIM1, a novel gene
encoding a cysteine-rich repeat protein, is developmentally regulated and implicated in
vertebrate CNS development and organogenesis. Mech Dev. (2000) 90, 181-193.