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Associate Professor Geoff Faulkner

Associate Professor Geoff Faulkner

Associate Professor Geoff Faulkner is a Principal Research Fellow and head of the Genome Plasticity and Disease group. His research seeks to elucidate functions for retrotransposons and pseudogenes, regions of the genome previously described as “junk DNA” but increasingly viewed as important factors in human biology and disease.

Dr Faulkner began his research career in 2002 as an undergraduate working in Prof. David Hume’s lab at the University of Queensland (UQ). He went on to first complete a BSc with first class honours (2004) and then a computational biology PhD (2008) working with Prof. Sean Grimmond at the Institute for Molecular Bioscience, UQ. After a brief period as a research officer he was awarded a CJ Martin NHMRC Overseas Biomedical Training Fellowship in 2009 and with this funding established an independent laboratory at the Roslin Institute, University of Edinburgh. He relocated to Australia in 2012 and was awarded an NHMRC Career Development Fellowship in early 2013.

Over the course of his career, Dr Faulkner has published 31 peer-reviewed articles (>4600 citations, h-index 22), the majority in top-tier journals, and received grant funding totalling nearly $7M. He recently published a landmark work in Nature describing somatic retrotransposition in the human brain that was selected by the US National Institute of Mental Health as the “joint No. 1 research advance of 2011”. He is a senior invited member of the Functional Annotation of Mammal (FANTOM) consortium, was awarded an ASMR Queensland Premier’s Award in 2009 and was presented the FEBS Anniversary Prize in 2011 for “outstanding achievement in the field of Molecular Biology.”

For information regarding student projects (Honours/Masters/PhD) please contact gfaulkner@mmri.mater.org.au

Publications

Key publications
Shukla, R., Upton, K.R., Muñoz-Lopez, M., Gerhardt, D.J., Fisher, M.E., Nguyen, T., Brennan P.M., Baillie, J.K., Collino, A., Ghisletti, S., Sinha, S., Iannelli, F., Radaelli, E., Dos Santos, A., Rapoud, D., Guettier, C., Samuel, D., Natoli, G., Carninci, P., Ciccarelli, F.D., Garcia-Perez, J.L., Faivre, J., Faulkner, G.J. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153, 101-111 (2013)

Baillie, J.K., Barnett, M.W., Upton, K.R., Gerhardt, D.J., Richmond, T., de Sapio, F., Brennan, P., Rizzu, P., Smith, S., Fell, M., Talbot, R.T., Gustincich, S., Freeman, T.C., Mattick., J.S., Hume, D.A., Heutink, P., Carninci, P., Jeddeloh, J.A., Faulkner, G.J. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479, 534-537 (2011)

Faulkner, G.J., Kimura, Y., Daub, C.O., Wani, S., Plessy, C., Irvine, K.M., Schroder, K., Cloonan, N., Steptoe, A.L., Lassmann, T., Waki, K., Hornig, N., Arakawa, T., Takahashi, H., Kawai, J., Forrest, A.R.R., Suzuki, H., Hayashizaki, Y., Hume, D.A., Orlando, V., Grimmond, S.M., Carninci, P. The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics 41, 563-71 (2009)

Complete publication list

Richardson, S.R., Salvador-Palomeque, C., Faulkner, G.J. Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population. Bioessays (in press)

Carreira, P.E., Richardson, S.R., Faulkner, G.J. L1 retrotransposons, cancer stem cells and oncogenesis. FEBS Journal 281 63-73 (2014)

Faulkner, G.J. Retrotransposon silencing during embryogenesis: Dicer cuts in LINE. PLoS Genetics 9 e1003944 (2013)

Reilly, M.T., Faulkner, G.J., Dubnau, J., Ponomarev, I., Gage, F.H. The role of transposable elements in health and diseases of the central nervous system. J. Neurosci. 33 17577-86 (2013)

Li, J. L., Mazar, J., Zhong, C., Faulkner, G. J., Govindarajan, S. S., Zhang, Z., Dinger, M. E., Meredith, G., Adams, C., Zhang, S., Mattick, J. S., Ray, A., Perera, R. J. Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network. Sci Rep 3, 2962-2975 (2013)

Shukla, R., Upton, K.R., Muñoz-Lopez, M., Gerhardt, D.J., Fisher, M.E., Nguyen, T., Brennan P.M., Baillie, J.K., Collino, A., Ghisletti, S., Sinha, S., Iannelli, F., Radaelli, E., Dos Santos, A., Rapoud, D., Guettier, C., Samuel, D., Natoli, G., Carninci, P., Ciccarelli, F.D., Garcia-Perez, J.L., Faivre, J., Faulkner, G.J. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153, 101-111 (2013)

Groenen, M. A., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F., et al., Analyses of pig genomes provide insight into porcine demography and evolution Nature 491, 393-8 (2012)

Solyom, S., Ewing, A.D., Rahrmann, E.P., Doucet, T.T., Nelson, H.H., Burns, M.B., et al., Extensive somatic L1 retrotransposition in colorectal tumors Genome Research 22, 2328-38 (2012)

Schroder, K., Irvine, K.M., Taylor, M.S., Bokil, N.J., Le Cao, K., Masterman, K., et al., Conservation and divergence in Toll-like Receptor 4-regulated gene expression in primary human versus mouse macrophages. PNAS 109, E944-E953 (2012)
Plessy, C., Pascarella, G., Bertin, N., Akalin, A., Carrieri, C., Vassalli, A., et al., Promoter Architecture of Mouse Olfactory Receptor Genes. Genome Research 22, 486-497 (2012)

Upton, K.R., Baillie, J.K., Faulkner, G.J. Is somatic retrotransposition a parasitic or symbiotic phenomenon? Mobile Genetic Elements 1, 279-328 (2011)

Baillie, J.K., Barnett, M.W., Upton, K.R., Gerhardt, D.J., Richmond, T., de Sapio, F., et al., Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479, 534-537 (2011)

Faulkner, G.J. Retrotransposons: mobile and mutagenic from conception to death. FEBS Letters 585, 1589-1594 (2011)

Mattick, J.S., Taft, R.T., Faulkner, G.J. A global view of genomic information – moving beyond the gene and the master regulator. Trends in Genetics 26, 21-8 (2010)

de Hoon, M.J.L., Taft, R.J., Hashimoto, T., Kanamori-Katayama, M., Kawaji, H., Kawano, M., et al., Y. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Research 20, 257-64 (2010)

Faulkner, G.J., Carninci, P. Altruistic functions for selfish DNA. Cell Cycle 8, 2895-900 (2009)

Hashimoto, T., de Hoon, M.J.L., Grimmond, S.M., Daub, C.O., Hayashizaki, Y., Faulkner, G.J. Probabilistic resolution of multi-mapping reads in next-generation sequence data using MuMRescueLite. Bioinformatics 25, 2613-4 (2009)

Cloonan, N., Xu, Q., Faulkner, G.J., Taylor, D.F., Tang, D.T.P., Grimmond, S.M. RNA-MATE: A recursive mapping strategy for high throughput RNA-sequencing data. Bioinformatics 25, 2615-6 (2009)

Faulkner, G.J., Kimura, Y., Daub, C.O., Wani, S., Plessy, C., Irvine, K.M., et al., The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics 41, 563-71 (2009)

Taft, R.J., Glazov, E.A., Cloonan, N., Simons, C., Stephen, S., Faulkner, G.,J., et al., Tiny RNAs associated with transcription start sites in animals. Nature Genetics 41, 572-8 (2009)

Suzuki, H., Forrest, A.R.R., van Nimwegen, E., et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics 41, 553-62 (2009)

Cloonan, N., Forrest, A.R.R., Kolle, G., Gardiner, B.B.A., Faulkner, G.J., Brown, M.K., et al., Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods 5, 613-9 (2008)

Faulkner, G.J., Forrest, A.R., Chalk, A.M., Schroder, K., Hayashizaki, Y., Carninci, P., et al., A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics 91, 281-8 (2008)

Meadows, N.A., Sharma, S.M., Faulkner, G.J., Ostrowski, M.C., Hume, D.A. & Cassady, A.I. The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factor. J Biol Chem 282, 1891-904 (2007)

Wells, C.A., Chalk, A.M., Forrest, A., Taylor, D., Waddell, N., Schroder, K., et al., Alternate transcription of the Toll-like receptor signaling cascade. Genome Biology 7, R10 (2006)

Forrest, A.R., Taylor, D.F., Crowe, M.L., Chalk, A.M., Waddell, N.J., Kolle, G., et al., Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biology 7, R5 (2006)

Carninci, P., et al. The transcriptional landscape of the mammalian genome. Science 309, 1559-63 (2005)

Meadows, N.A., Faulkner, G., Wells, C., Ravasi, T., Hume, D., Sankar, U., et al., Novel genes regulated by microphthalmia transcription factor in macrophages and osteoclasts. Journal of Bone and Mineral Research 19, S413-S413 (2004)

Huber, T., Faulkner, G. & Hugenholtz, P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20, 2317-9 (2004)

Wells, C.A., Ravasi, T., Sultana, R., Yagi, K., Carninci, P., Bono, H., et al., Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage. Genome Research 13, 1360-5 (2003)

Wells, C.A., Ravasi, T., Faulkner, G.J., Carninci, P., Okazaki, Y., Hayashizaki, Y., et al., Genetic control of the innate immune response. BMC Immunology 4, 5 (2003)
 

 

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