• The University of Western Australia (M519), 35 Stirling Highway,

    6009 Perth


  • The University of Western Australia (M316), 35 Stirling Highway,

    6009 Perth


  • 13086 Citations
  • 34 h-Index
If you made any changes in Pure these will be visible here soon.

Personal profile

Previous positions

2009-2011: California Institute for Regenerative Medicine Postdoctoral Trainee (Joseph Ecker), The Salk Institute for Biological Studies, La Jolla, CA, USA.

2006-2009: Human Frontier Science Project Postdoctoral Fellow (Joseph Ecker), The Salk Institute for Biological Studies, La Jolla, CA, USA.

2005-2006: Postdoctoral Fellow (James Whelan), Department of Biochemistry and Molecular Biology, The University of Western Australia, Perth, Australia.

2001-2005: Ph.D. (James Whelan), Department of Biochemistry and Molecular Biology, The University of Western Australia, Perth, Australia.


Exploring the Epigenome

Just as the fixed notes of a musical instrument can be played in different combinations, orders and strengths to create unique songs, different cells in a complex multicellular organism can produce their distinctive form and function by each expressing particular combinations of genes from the genome. By modulating accessibility to the information encoded in the genome, epigenetic modifications can affect gene activation and repression to execute distinct transcriptional programs and impart a heritable state of transcriptional activity. In essence, the epigenome is a regulatory code that is superimposed upon the genome that can modify the cellular readout of the underlying information encoded in the DNA sequence. Developing a comprehensive understanding of how the cell utilizes epigenetic modifications is essential in order to both understand the critical roles it plays in eukaryotic development and stress response, and to develop effective strategies to remedy its disruption in disease states.

We use advanced DNA sequencing, molecular, genetic and computational techniques in a diverse range of complex multicellular organisms, including plants, humans, mice, and social insects, to study the epigenome and epigenetic mechanisms at the molecular scale. Recent advances in DNA sequencing technology now enable us to rapidly identify precisely where epigenetic modifications, such as DNA methylation and histone modifications, occur throughout entire plant and animal genomes1-3. The research in my laboratory aims to understand how the information encoded in the DNA of plant and animal genomes is controlled by epigenetic mechanisms during development, how the epigenome may be altered by the surrounding environment, and to develop molecular tools to reprogram it.


  • Epigenetics
  • Epigenomics
  • DNA methylation
  • Genomics (plant, animal)
  • Stem cells
  • Induced pluripotent stem cells

Fingerprint Fingerprint is based on mining the text of the person's scientific documents to create an index of weighted terms, which defines the key subjects of each individual researcher.

  • 4 Similar Profiles
DNA Methylation Medicine & Life Sciences
Arabidopsis Medicine & Life Sciences
Epigenomics Medicine & Life Sciences
Genome Medicine & Life Sciences
Mitochondrial Proteins Medicine & Life Sciences
Genes Medicine & Life Sciences
Cytosine Medicine & Life Sciences
Methylation Medicine & Life Sciences

Network Recent external collaboration on country level. Dive into details by clicking on the dots.

Research Output 2001 2019

HOME: A histogram based machine learning approach for effective identification of differentially methylated regions

Srivastava, A., Karpievitch, Y. V., Eichten, S. R., Borevitz, J. O. & Lister, R., 16 May 2019, In : BMC Bioinformatics. 20, 1, 253.

Research output: Contribution to journalArticle

Open Access
Learning systems
Identification (control systems)
Machine Learning
11 Citations (Scopus)

A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs

Pflueger, C., Tan, D., Swain, T., Nguyen, T. V., Pflueger, J., Nefzger, C., Polo, J. M., Ford, E. & Lister, R., Aug 2018, In : Genome Research. 28, 8, p. 1193-1206

Research output: Contribution to journalArticle

Open Access
DNA Methylation
Catalytic Domain
Binding Sites
4 Citations (Scopus)

Amphioxus functional genomics and the origins of vertebrate gene regulation

Marlétaz, F., Firbas, P. N., Maeso, I., Tena, J. J., Bogdanovic, O., Perry, M., Wyatt, C. D. R., de la Calle-Mustienes, E., Bertrand, S., Burguera, D., Acemel, R. D., van Heeringen, S. J., Naranjo, S., Herrera-Ubeda, C., Skvortsova, K., Jimenez-Gancedo, S., Aldea, D., Marquez, Y., Buono, L., Kozmikova, I. & 41 othersPermanyer, J., Louis, A., Albuixech-Crespo, B., Le Petillon, Y., Leon, A., Subirana, L., Balwierz, P. J., Duckett, P. E., Farahani, E., Aury, J. M., Mangenot, S., Wincker, P., Albalat, R., Benito-Gutiérrez, È., Cañestro, C., Castro, F., D’Aniello, S., Ferrier, D. E. K., Huang, S., Laudet, V., Marais, G. A. B., Pontarotti, P., Schubert, M., Seitz, H., Somorjai, I., Takahashi, T., Mirabeau, O., Xu, A., Yu, J. K., Carninci, P., Martinez-Morales, J. R., Crollius, H. R., Kozmik, Z., Weirauch, M. T., Garcia-Fernàndez, J., Lister, R., Lenhard, B., Holland, P. W. H., Escriva, H., Gómez-Skarmeta, J. L. & Irimia, M., 6 Dec 2018, In : Nature. 564, 7734, p. 64-70 7 p.

Research output: Contribution to journalArticle

Open Access
Gene expression
1 Citation (Scopus)

Approaches for the analysis and interpretation of whole genome bisulfite sequencing data

Stuart, T., Buckberry, S. & Lister, R., 2018, Epigenome Editing: Methods and Protocols. Jeltsch, A. & Rots, M. G. (eds.). New York: Springer, Vol. 1767. p. 299-310 12 p. (Methods in Molecular Biology).

Research output: Chapter in Book/Conference paperChapter

DNA Methylation
DNA Transposable Elements

Cell culture-generated neurons show non-physiological DNA methylation signatures

Poppe, D., Martin, S., Pflueger, J., Wolvetang, E. & Lister, R., 22 Jun 2018.

Research output: Contribution to conferencePoster

DNA Methylation
Cell culture
Cell Culture Techniques


GSM1977638: xl_st10.5_MethylC-seq

Bogdanovic, O. (Creator), Lister, R. (Creator), Gene Expression Omnibus (NCBI), 26 Aug 2016


Data from: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

Secco, D. (Creator), Wang, C. (Creator), Shou, H. (Creator), Schultz, M. D. (Creator), Chiarenza, S. (Creator), Nussaume, L. (Creator), Ecker, J. R. (Creator), Whelan, J. (Creator), Lister, R. (Creator), Dryad Digital Repository, 6 Aug 2015


Projects 2013 2022