Prof Ryan Lister
- Chief Investigator, The University Of Western Australia
Biography:
Ryan Lister completed his Bachelor's degree in Biochemistry and Genetics at The University of Western Australia (UWA) in 2000, and undertook his Ph.D. studies in plant mitochondrial biogenesis at UWA from 2001 - 2005. After completing his PhD, Ryan was awarded a Human Frontiers Science Program Postdoctoral Fellowship in 2006 to undertake his postdoctoral studies at The Salk Institute for Biological Studies, in California. There, he developed methodologies for utilizing new high-throughput DNA sequencing technologies to map the epigenome in a variety of systems, including plants, the brain, and stem cells. Ryan returned to Perth in 2012 to establish his own research group, and is currently a Sylvia and Charles Viertel Senior Medical Research Fellow and head of the Epigenetics and Genomics laboratories at the Harry Perkins Institute of Medical Research and the ARC Centre of Excellence in Plant Energy Biology.
Research:
Professor of Computational Systems Biology
Contact Info:
- hover or click to show email address
- https://listerlab.org
PEB Media Appearances:
- Plants in space research gets funding boost
- UWA launches International Space Centre
- Study provides insight into how the brain may have evolved
- PEB’S 2020 Highly Cited Researchers
- Professor Ryan Lister: the on/off switch for our genes
- Ryan Lister a WA Scientist of the Year
- UWA finalists announced in Premier's Science Awards
- Three UWA scientists named Fellows of the Australian Academy of Science
- Professor Ryan Lister named Premier’s Science Award 2019 Finalist
Year | Publication | Online |
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2024
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(2024)
CRISPRi-based circuits to control gene expression in plants.
Nat Biotechnol
(in press).
|
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2024
|
(2024)
A modular dCas9-based recruitment platform for combinatorial epigenome editing.
Nucleic Acids Res
52(1):474-491.
|
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2024
|
(2024)
Approaches for the Analysis and Interpretation of Whole-Genome Bisulfite Sequencing Data.
Methods Mol Biol
2842:391-403.
|
|
2024
|
(2024)
Generation of Whole-Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis.
Methods Mol Biol
2842:383-390.
|
|
2024
|
(2024)
RNA variant assessment using transactivation and transdifferentiation.
Am J Hum Genet
111(8):1673-1699.
|
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2024
|
(2024)
Characterization of DNA methylation reader proteins of <i>Arabidopsis thaliana</i>.
Genome Res
(in press).
|
|
2024
|
(2024)
Establishment of single-cell transcriptional states during seed germination.
Nat Plants
10(9):1418-1434.
|
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2024
|
(2024)
Early moderate prenatal alcohol exposure and maternal diet impact offspring DNA methylation across species.
Elife
12:.
|
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2023
|
(2023)
Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap.
Nat Plants
9(7):1026-1033.
|
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2023
|
(2023)
Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds.
Tree Physiol
43(4):675-689.
|
|
2023
|
(2023)
Transient naive reprogramming corrects hiPS cells functionally and epigenetically.
Nature
620(7975):863-872.
|
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2023
|
(2023)
Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development.
Genes (Basel)
14(5):.
|
|
2023
|
(2023)
Exploring the identity of individual plant cells in space and time.
New Phytol
240(1):61-67.
|
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2022
|
(2022)
Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.
Genome Biol
23(1):163.
|
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2022
|
(2022)
Synthetic memory circuits for stable cell reprogramming in plants.
Nat Biotechnol
40(12):1862-1872.
|
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2022
|
(2022)
Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells.
Nat Commun
13(1):7470.
|
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2022
|
(2022)
Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution.
Cell
185(23):4428-4447.e28.
|
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2021
|
(2021)
Cerebrospinal fluid liquid biopsy for detecting somatic mosaicism in brain
BRAIN COMMUNICATIONS
|
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2021
|
(2021)
The emergence of the brain non-CpG methylation system in vertebrates.
Nat Ecol Evol
5(3):369-378.
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2021
|
(2021)
Genomic Targeting of TET Activity for Targeted Demethylation Using CRISPR/Cas9
METHODS MOL. BIOL.
2272:181-194.
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2021
|
(2021)
Modelling human blastocysts by reprogramming fibroblasts into iBlastoids.
NATURE
591(7851):627-632.
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2021
|
(2021)
Transcriptional signature in microglia associated with Aβ plaque phagocytosis.
NAT COMMUN
12(1):3015.
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2020
|
(2020)
Mitochondrial CLPP2 Assists Coordination and Homeostasis of Respiratory Complexes.
Plant Physiol
184(1):148-164.
|
|
2020
|
(2020)
Conserved and divergent features of DNA methylation in embryonic stem cell-derived neurons
BIORXIV
|
|
2020
|
(2020)
TINC- A Method to Dissect Regulatory Complexes at Single-Locus Resolution- Reveals an Extensive Protein Complex at the Nanog Promoter.
STEM CELL REPORTS
15(6):1246-1259.
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2020
|
(2020)
schex avoids overplotting for large single cell RNA-sequencing datasets.
BIOINFORMATICS
36(7):2291-2292.
|
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2020
|
(2020)
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows.
GENOME BIOL
21(1):130.
|
|
2020
|
(2020)
Reprogramming roadmap reveals route to human induced trophoblast stem cells.
NATURE
586(7827):101-107.
|
|
2020
|
(2020)
Evolution of DNA Methylome Diversity in Eukaryotes.
J MOL BIOL
432(6):1687-1705.
|
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2020
|
(2020)
Depletion of Foxk transcription factors causes genome-wide transcriptional misregulation and developmental arrest in zebrafish embryos.
MicroPubl Biol
2020():.
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2020
|
(2020)
Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings.
NAT COMMUN
11(1):2631.
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2020
|
(2020)
Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri.
NAT COMMUN
11(1):3676.
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2019
|
(2019)
Convergent evolution of a vertebrate-like methylome in a marine sponge.
NAT ECOL EVOL
3(10):1464-1473.
|
|
2019
|
(2019)
A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation.
NAT. NEUROSCI.
22(12):2087-2097.
|
|
2019
|
(2019)
Systematic bias assessment in solid tissue 10x scRNA-seq workflows
BIORXIV
|
|
2019
|
(2019)
Harnessing targeted DNA methylation and demethylation using dCas9.
ESSAYS BIOCHEM.
63(6):813-825.
|
|
2019
|
(2019)
HOME: a histogram based machine learning approach for effective identification of differentially methylated regions.
BMC BIOINFORMATICS
20(1):253.
|
|
2019
|
(2019)
Retention of paternal DNA methylome in the developing zebrafish germline.
NAT COMMUN
10(1):3054.
|
|
2019
|
(2019)
Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family.
GENOME RES
29(8):1277-1286.
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2019
|
(2019)
LINE-1 Evasion of Epigenetic Repression in Humans.
MOL CELL
75(3):590-604.e12.
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2018
|
(2018)
Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.
NAT COMMUN
9(1):1341.
|
|
2018
|
(2018)
Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data.
Methods Mol Biol
1767:299-310.
|
|
2018
|
(2018)
Generation of Whole Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis.
Methods Mol Biol
1767():291-298.
|
|
2018
|
(2018)
A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs.
GENOME RES
28(8):1193-1206.
|
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2018
|
(2018)
Author Correction: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.
NAT COMMUN
9(1):1811.
|
|
2018
|
(2018)
Amphioxus functional genomics and the origins of vertebrate gene regulation.
Nature
564(7734):64-70.
|
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2017
|
(2017)
Nutrient stress-induced chromatin changes in plants.
Curr Opin Plant Biol
39:1-7.
|
|
2017
|
(2017)
Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases.
CELL REP
20(6):1448-1462.
|
|
2017
|
(2017)
Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis.
Plant Cell
29(8):1836-1863.
|
|
2017
|
(2017)
DNA methylation and the preservation of cell identity.
CURR. OPIN. GENET. DEV.
46:9-14.
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2017
|
(2017)
Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA.
CHEM SCI
8(4):2923-2930.
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2017
|
(2017)
Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.
Genome Biol
18(1):172.
|
|
2017
|
(2017)
Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming.
NAT METHODS
14(11):1055-1062.
|
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2017
|
(2017)
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.
GENOME BIOL
18(1):198.
|
|
2017
|
(2017)
Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming.
CELL STEM CELL
21(6):834-845.e6.
|
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2017
|
(2017)
Cell Type of Origin Dictates the Route to Pluripotency.
CELL REP
21(10):2649-2660.
|
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2017
|
(2017)
Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.
Plant J
89(4):805-824.
|
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2016
|
(2016)
Active DNA demethylation at enhancers during the vertebrate phylotypic period.
NAT GENET
48(4):417-26.
|
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2016
|
(2016)
Epigenomic landscapes of retinal rods and cones.
ELIFE
5:e11613.
|
|
2016
|
(2016)
Erratum: Embryonic transcription is controlled by maternally defined chromatin state.
NAT COMMUN
7:12208.
|
|
2016
|
(2016)
Unique cell-type-specific patterns of DNA methylation in the root meristem.
NAT PLANTS
2(5):16058.
|
|
2016
|
(2016)
Retrograde signalling caused by heritable mitochondrial dysfunction is partially mediated by ANAC017 and improves plant performance.
PLANT J.
88(4):542-558.
|
|
2016
|
(2016)
DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity.
GENOME RES
26(11):1520-1531.
|
|
2016
|
(2016)
Genome evolution in the allotetraploid frog Xenopus laevis.
Nature
538(7625):336-343.
|
|
2016
|
(2016)
Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation.
ELIFE
5. pii: e20777.
|
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2015
|
(2015)
Integrative analysis of 111 reference human epigenomes.
NATURE
518(7539):317-30.
|
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2015
|
(2015)
MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.
NAT PROTOC
10(3):475-83.
|
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2015
|
(2015)
Of Mice and Man: Differential DNMT Dependence in Mammalian ESCs.
CELL STEM CELL
16(5):459-60.
|
|
2015
|
(2015)
The effect of paranoia on the judging of harmful events.
COGN NEUROPSYCHIATRY
20(2):122-7.
|
|
2015
|
(2015)
Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.
Elife
4:.
|
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2015
|
(2015)
Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.
NEURON
86(6):1369-84.
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2015
|
(2015)
methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.
BMC Bioinformatics
16():313.
|
|
2015
|
(2015)
Turning over DNA methylation in the mind.
Front Neurosci
9():252.
|
|
2015
|
(2015)
Embryonic transcription is controlled by maternally defined chromatin state.
NAT COMMUN
18;6:10148.
|
|
2014
|
(2014)
Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells.
GENOME RES
24(2):267-80.
|
|
2014
|
(2014)
CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity.
Proc Natl Acad Sci U S A
111(16):5890-5.
|
|
2014
|
(2014)
Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation.
NUCLEIC ACIDS RES
42(16):10856-68.
|
|
2014
|
(2014)
Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways.
GENOME RES
24(10):1613-23.
|
|
2014
|
(2014)
Epigenomics and the control of fate, form and function in social insects
CURR OPIN INSECT SCI
Jul(1):31-38.
|
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2013
|
(2013)
Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells
CELL
153(5):1134-48.
|
|
2013
|
(2013)
Global Epigenomic Reconfiguration During Mammalian Brain Development
SCIENCE
341(6146):1237905.
|
|
2013
|
(2013)
STAR: An Integrated Solution to Management and Visualization of Sequencing Data.
BIOINFORMATICS
29(24):3204-10.
|
|
2012
|
(2012)
Widespread dynamic DNA methylation in response to biotic stress.
Proc Natl Acad Sci U S A
109(32):E2183-91.
|
|
2012
|
(2012)
Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome.
GENES DEV
Aug 15;26(16):1825-36.
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2011
|
(2011)
Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer.
GENOME RES
22(2):246-58.
|
|
2011
|
(2011)
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.
NATURE
473(7347):39.
|
|
2011
|
(2011)
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.
NATURE
471(7336):68-73.
|
|
2010
|
(2010)
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
NAT BIOTECHNOL
28(10):1026-1028.
|
|
2010
|
(2010)
Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.
CELL STEM CELL
7;6(5):479-91.
|
|
2009
|
(2009)
Finding the fifth base: Genome-wide sequencing of cytosine methylation.
GENOME RES
19(6):959-66.
|
|
2009
|
(2009)
Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond.
CURR OPIN PLANT BIOL
12(2):107-18.
|
|
2009
|
(2009)
The Arabidopsis glutathione transferase gene family displays complex stress regulation and co-silencing multiple genes results in altered metabolic sensitivity to oxidative stress.
Plant J
58(1):53-68.
|
|
2009
|
(2009)
Human DNA methylomes at base resolution show widespread epigenomic differences
NATURE
462(7271): 315-322.
|
|
2008
|
(2008)
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
CELL
133(3):523-36.
|
|
2008
|
(2008)
A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development
DEV CELL
14(6):854-866.
|
|
2008
|
(2008)
Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis.
Plant Physiol
147(4):1858-73.
|
|
2007
|
(2007)
Characterization of the preprotein and amino acid transporter gene family in Arabidopsis.
Plant Physiol
143(1):199-212.
|
|
2007
|
(2007)
Characterization of the regulatory and expression context of an alternative oxidase gene provides insights into cyanide-insensitive respiration during growth and development.
Plant Physiol
143(4):1519-33.
|
|
2007
|
(2007)
Functional definition of outer membrane proteins involved in preprotein import into mitochondria.
Plant Cell
19(11):3739-59.
|
|
2006
|
(2006)
Mitochondrial protein import: convergent solutions for receptor structure
CURR BIOL
16(6): R197-9.
|
|
2005
|
(2005)
Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana.
Plant Mol Biol
58(2):193-212.
|
|
2005
|
(2005)
Protein import into mitochondria: endosymbiotic origins and functions today
MOL MEMBR BIOL
22(1-2):87-100.
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106