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Professor Peter Waterhouse

Science and Engineering Faculty,
Earth, Environmental and Biological Sciences,


Professor Peter Waterhouse
Professor of Molecular Genetics
Science and Engineering Faculty,
Earth, Environmental and Biological Sciences,
Discipline *
Other Biological Sciences
+61 7 3138 7793
View location details (QUT staff and student access only)

PhD (in Plant Virology) (University of Dundee)


Gene Silencing, RNAi, Epigenetics, Genomics, Nicotiana benthamiana, Virology, Mobile Silencing, RNA binding proteins, Biotechnology, Plants

* Field of Research code, Australian and New Zealand Standard Research Classification (ANZSRC), 2008


Peter Waterhouse, FAA, is Professor of Molecular Genetics.

Research interests

  • Gene Silencing (RNAi)
  • Genomics
  • Epigenetics
  • Virology
  • Recombinant Antibodies

He has led research teams and made fundamental discoveries, many of which have been translated into intellectual property and commercial applications. He is internationally known for his research on RNA interference (RNAi) and his expertise ranges from viral gene regulation to plant genomics. His ~ 130 peer-reviewed publications have so far received about 13,000 citations and give him an h factor of 50. He receives numerous invitations to give keynote and plenary presentations nationally and internationally and, in recognition of the transformative nature of his research, he has been awarded many of the highest scientific honours in Australia, including the Prime Minister’s Prize for Science, CSIRO Chairman’s medal, the Victor Chang Medal, and election to the Australian Academy of Science.


Academic Record

1977 Bachelor of Science (with honours) in Plant Biology

University of Newcastle upon Tyne, England

1981 Ph.D. in Plant Virology

Scottish Crop Research Institute/ University of Dundee



Employment history:

1978-79   Stagiaire, University of Cambridge, England.

1979-82   PhD. Student, Scottish Crop Research Institute, Scotland.

1982-2008 Research Officer through to Chief Research Officer, CSIRO Plant Industry, Australia.

1992-3         Visiting Fellow MRC / U. of Cambridge / CAT Ltd, England

1997-9         Program Leader CRC for Plant Sciences, CSIRO/ANU, Canberra, Australia.

2008-2013 ARC Federation Fellow, University of Sydney, Australia.

2008-2013 Honorary Fellow, CSIRO Plant Industry, Australia.

2014-          Honorary Professor, University of Sydney, Australia.

2014-          Professor of Molecular Genetics, CTCB, QUT


Patent Portfolio (Named Inventor)

A suite of 11 families of patents (granted/in contest/provisional) on RNAi (CSIRO and Bayer)

Two granted patents on recombinant antibodies  (MRC and Cambridge Antibody Technology Ltd)

One granted patent on virus resistant plants (CSIRO and GRDC)

Two granted patents on promoters and gene signals for plant biotechnology (CSIRO/ANU/RhoBio Ltd)

Many provisional and published patent applications




This information has been contributed by Professor Peter Waterhouse.











2002 Victor Chang Medal.

2003 The Bulletin: Smart 100: Science – Top Ten – Finalist.

2003 IMTC-ISI/Thomson “Most Highly Cited in Field” Award.

2005 CSIRO Chairman’s Medal.

2007 The Bulletin: Smart 100: Science -Top Ten – Winner.

2007 ARC Federation Fellowship.

2007 Prime Minister’s Prize for Science.

2009 Fellow of Australian Academy of Science.


Scientific Advisory, Editorial, or Review Boards

Prime Minister’s Science Council (Keating, 1995)

Prime Minister’s Science, Engineering and Innovation Council (Howard, 2007)

Prime Minister’s Science, Engineering and Innovation Council (Rudd, 2008)

Scientific Advisory Board: Nemgenix Pty, Australia (2008-2011)

Ed. Plant Methods http://www.plantmethods.com/ (2004- )

Ed. Molecular Plant Pathology (Wiley-Blackwell, 2003-8)

Ed. Functional Plant Biology (CSIRO Publishing, 2004-9),

Ed. Silence (BMC, 2009-2013 )

Guest Editor x 2 PloS Pathogens (2011)

Review Board for Scottish Crop Research Institute, Genetics Program (2009)

Ramaciotti Centre for Gene Function Analysis – Ramaciotti Management Committee (2009-13 ).



Competitive Grants:

ARC FF, Discovery & Linkage/Industry/CSIRO-external, since 2008 : ~ $8M


Membership of Recent International Research Efforts

European Cooperation in the Field of Scientific and Technical Research – FA0806

Epigenomics of Plants International Consortium (EPIC).

Nicotiana benthamiana Genome Sequencing Consortium


Publications and Presentations

Waterhouse has published one book, more than 30 book chapters or invited reviews and more than 130 papers in refereed international journals. Many of these papers and reviews have been in top echelon journals including: Nature, Science, Nature Genetics, Nature Biotechnology, Nature Reviews: Genetics, EMBO, EMBO Reports, Current Biology, PNAS, Trends in Plant Science, Blood and RNA. Three of these papers has been cited >1000 times, five > 950 times, and twenty nine >100 times.



Top ten publications

1. Fusaro AF, Matthew L, Smith NA, Curtin SJ, Dedic-Hagan J, Ellacott GA, Watson JM, Wang M-B, Brosnan C, Carroll BJ, and Waterhouse PM. (2006). RNAi-inducing hairpin RNAs in plants act through the viral defence pathway. EMBO Reports 7 1168-1175 (IF 7.2) This paper was the first to show that RNAi-inducing hpRNA and viral dsRNA are processed in plants by three different Dicer enzymes.

2. Wang M-B, Bian X-Y, Wu L-M, Liu L-X, Smith NA, Isenegger D, Wu RM, Masuta C, Vance VB, Watson JM, Rezaian A, Dennis ES and Waterhouse PM. (2004) On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proc Natl Acad Sci USA 101, 3275-3280. (IF 9.6) This paper was the first to propose and show that pathogens caused symptoms through siRNAs and the RNAi pathway.

3. Waterhouse PM and Helliwell CA. (2003) Exploring plant genomes by RNA-induced gene silencing. Nature Reviews: Genetics 4, 29-38. (IF 24.1) This invited review described and compared the various ways of delivering RNAi and discussed how they could be used for functional genomics research.

4. Finnegan EJ, Margis R and Waterhouse PM. (2003). Posttranscriptional Gene Silencing Is Not Compromised in the Arabidopsis Carpel Factory (Dicer-like1) Mutant, a Homolog of Dicer-1 from Drosophila. Current Biology.13, 236-40. (IF 10.8) This paper showed that, unlike humans which posses a single Dicer, plants have multiple Dicers.

5. Waterhouse PM, Wang M-B and Lough T. (2001) Gene silencing as an adaptive defence against viruses. Nature 411, 834-842.(IF 31.4) This invited review brought together many previously confusing elements to give a largely cohesive picture of the nature and function of gene silencing (now termed RNAi) in plants, and was the first to draw the parallel with the mammalian immune system.

6. Wesley SV, Helliwell, C, Smith NA, Wang M-B, Rouse D, Liu Q, Gooding P, Singh S, Abbott D, Stoutjesdijk P, Robinson S, Gleave A, Green A and Waterhouse PM. (2001) Constructs for Efficient, Effective and High Throughput Gene Silencing in Plants. The Plant Journal 27, 581-590. (IF 6.4) Describes the application of intron-spliced hairpin RNA constructs to silence a wide range of genes in a wide range of species, reducing the theory to practice. It also describes the production of a recombinase vector for high throughput silencing such as needed for large scale genomic projects. Doubly cited in Faculty of 1000.

7. Smith NA, Singh SP,Wang M-B, Stoutjesdijk P, Green A and Waterhouse PM. (2000) Total silencing by intron-spliced hairpin RNAs. Nature 407, 319-320. (IF 31.4) This was the first demonstration that intron-spliced hairpin RNAs direct very efficient gene silencing.

8. Waterhouse PM, Graham MW and Wang M-B. (1998) Virus resistance and gene silencing in plants can be induced by simultaneous expression of sense and antisense RNA. Proc Natl Acad Sci USA 95, 13959-13964. (IF 9.6) This was the first demonstration that double stranded RNA and hairpin RNA caused gene silencing in plants. This independent study was published only months after the paper by Fire and Mello that showed that double stranded RNA causes gene silencing (RNA interference; RNAi) in nematodes and for which they were awarded the Nobel Prize in 2006.

9. Waterhouse P, Griffiths AD, Johnstone K & Winter G. (1993) Combinatorial infection and in vivo recombination: a strategy for making large phage antibody repertoires. Nucleic Acids Research 21, 2265 – 2266 (IF 6.8) Describes the invention of an in vivo recombination system which generates combinatorial heavy and light chain antibody libraries. It is a key prior art paper in GatewayTM patents and facilitated the work described in the paper below (10).


10. Griffiths AD, Williams SC, Hartley O, Tomlinson IM, Waterhouse P, Crosby WL, Kontermann RE, Jones PT, Low NM, Allison TJ, Prospero TD, Hoogenboom, HR, Nissim A, Cox JPL, Harrison, JL, Zaccolo M, Gherardi E and Winter, G. (1994) Isolation of high affinity human antibodies directly from large synthetic repertoires. The EMBO Journal 13, 3245 – 3260. (IF 8.9) Describes the production of a very large library of synthetic antibodies, using the strategy and vectors from (9), and the isolation of high affinity antibodies from it to a number of different antigens.


Five recent significant publications

1. Liang D, White RG, Waterhouse PM. Gene Silencing in Arabidopsis Spreads from the Root to the Shoot, through a Gating Barrier, by Template-Dependent, Nonvascular, Cell-to-Cell Movement Plant Physiology 2012 Jul;159(3):984-1000. Epub 2012 May 11. (IF 7.1). Recommended by four Faculty1000 members and ranks FFa =10 (must read/outstanding), showing that anti-viral signals in Arabidopsis grafts do not move upwards via the vasculature.

2. Nakasugi K, Crowhurst RN, Bally J, Wood CC, Hellens RP, Waterhouse PM. De novo transcriptome sequence assembly and analysis of RNA silencing genes of Nicotiana benthamiana. PLoS One. 2013;8(3):e59534. doi: 10.1371/journal.pone.0059534. Epub 2013 Mar 28. (IF 4.2). This paper has been viewed >6000 times and our website (www.benthgenome.com ) providing access to and interrogation of the genome and transcriptome has in less than 1 year has received 284,434 hits and given 1,667Gb of downloads.

3. Eamens AL, Smith NA, Curtin SJ, Wang M-B, and Waterhouse PM (2009) The Arabidopsis thaliana double-stranded RNA binding protein DRB1 directs guide strand selection from microRNA duplexes. RNA epub doi:10.1261/rna.1646909 (IF 5.0). This identified the protein that ensured the correct strand of a miRNA is loaded onto Argonaute.

4. Pase L, Layton JE, Kloosterman WP, Carradice D, Waterhouse PM, Lieschke GJ. (2009) miR-451 regulates zebrafish erythroid maturation in vivo via its target gata2. Blood. 113 :1794-804. ( IF 10.4) This identified the miRNA that regulates erythroid maturation

5. 5.Brosnan CA, Mitter N, Christie M, Smith NA, Waterhouse PM and Carroll BJ. (2007) Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc Natl Acad Sci USA 104, 14741-14746 (IF 9.6). This showed the involvement of nuclear proteins in post transcriptional gene silencing and its tissue mobility.


Five invited opinion pieces

1. Gordon KHJ and Waterhouse PM (2007). RNAi for insect-proof plants.
Nature Biotechnology 25, 1233-1234. (IF 22.2)

2. Waterhouse PM and Fusaro AF (2006). Viruses face a double defence by plant small RNAs. Science 313 :54-5. (IF 28.1)

3. Waterhouse PM (2006) Defense and counterdefense in the plant world.
Nature Genetics. 38:138-9 (IF 30.2)

4. Hetherington, A and Waterhouse PM (2002). The complexity of signals and levels of gene regulation in plants.
Current Opinion in Plant Biology 5, 373-375 (IF 8.7)

5. Finnegan, E.J., Wang, M-B. and Waterhouse PM (2001) Gene Silencing: Fleshing out the bones. Current Biology 11, 99-102. (IF 10.8)


Five recent plenary talks:

• Molecular Plant Microbe Interactions, Rhodos, Greece, 2014.

• Illumina Asia Symposium, Penang, Malaysia 2014.

• Biovision 2013, Lyon, France, 2013.

• Epigenetics 2013, Shoal Bay, NSW, 2013

• 12th VCCRI International Symposium: Charting the depths of RNA, Sydney, Australia, 2010.


Five recent keynote talks:

• 24th International Conference on Arabidopsis Research, Sydney, Australia 2013

• Lorne Genome Conference, Lorne, Australia, 2013

• QMB Plant Biology, Queenstown New Zealand, 2010.

• Big ideas Small things Big Ideas, NZMS & NZSBMB, Auckland, New Zealand, 2010.

• Plant and Animal Genome Conference, San Diego, USA, 2008.

This information has been contributed by Professor Peter Waterhouse.


For publications by this staff member, visit QUT ePrints, the University's research repository.


Awards and recognition

Fellowship of a Learned Academy or Membership of AIATSIS
Reference year
Election as Fellow to the Australian Academy of Science (2009)
Recipient of a Nationally Competitive Research Fellowship
Reference year
Awarded ARC Federation Fellowship in 2007 and taken up at the University of Sydney 2008 - 2013. The project title was: Small RNAs: What makes a plant, a plant
Academic Honours, Prestigious Awards or Prizes
Reference year
The Bulletin: Smart 100: Science -Top Scientist - co-winner, with colleague Dr MingBo Wang.
Academic Honours, Prestigious Awards or Prizes
Reference year
Prime Minister's Prize for Science (2007)
Academic Honours, Prestigious Awards or Prizes
Reference year
CSIRO Chairmans Medal. Awarded to the RNAi team,led by Peter Waterhouse, for the discovery and development of RNAi gene silencing.