Ryan Lister - Publications

Affiliations: 
University of Western Australia, Crawley, Western Australia, Australia 
Website:
http://www.web.uwa.edu.au/people/ryan.lister

54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Petereit J, Duncan O, Murcha MW, Fenske R, Cincu E, Cahn J, Pruzinska A, Ivanova A, Kollipara L, Wortelkamp S, Sickmann A, Lee J, Lister R, Millar AH, Huang S. Mitochondrial CLPP2 assists coordination and homeostasis of respiratory complexes. Plant Physiology. PMID 32571844 DOI: 10.1104/pp.20.00136  0.4
2018 Stuart T, Buckberry S, Lister R. Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data. Methods in Molecular Biology (Clifton, N.J.). 1767: 299-310. PMID 29524143 DOI: 10.1007/978-1-4939-7774-1_17  0.32
2017 Narsai R, Gouil Q, Secco D, Srivastava A, Karpievitch YV, Liew LC, Lister R, Lewsey MG, Whelan J. Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination. Genome Biology. 18: 172. PMID 28911330 DOI: 10.1186/s13059-017-1302-3  0.4
2017 Secco D, Whelan J, Rouached H, Lister R. Nutrient stress-induced chromatin changes in plants. Current Opinion in Plant Biology. 39: 1-7. PMID 28441589 DOI: 10.1016/j.pbi.2017.04.001  0.4
2016 Stuart T, Eichten S, Cahn J, Karpievitch Y, Borevitz J, Lister R. Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. Elife. 5. PMID 27911260 DOI: 10.7554/eLife.20777  0.32
2016 Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J. Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. The Plant Journal : For Cell and Molecular Biology. PMID 27859855 DOI: 10.1111/tpj.13418  0.48
2016 Eichten SR, Stuart T, Srivastava A, Lister R, Borevitz JO. DNA methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity. Genome Research. PMID 27613611 DOI: 10.1101/gr.205468.116  0.32
2016 Van Aken O, Ford E, Lister R, Huang S, Millar AH. Retrograde signalling caused by heritable mitochondrial dysfunction is partially mediated by ANAC017 and improves plant performance. The Plant Journal : For Cell and Molecular Biology. PMID 27425258 DOI: 10.1111/tpj.13276  0.4
2016 Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR. Unique cell-type-specific patterns of DNA methylation in the root meristem. Nature Plants. 2: 16058. PMID 27243651 DOI: 10.1038/nplants.2016.58  0.48
2016 Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J. Epigenomic landscapes of retinal rods and cones. Elife. 5. PMID 26949250 DOI: 10.7554/eLife.11613  0.48
2016 Bogdanović O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I, Rayon T, Gnerlich F, Carell T, Veenstra GJ, Manzanares M, ... ... Lister R, et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nature Genetics. PMID 26928226 DOI: 10.1038/ng.3522  0.48
2015 Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M. methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. Bmc Bioinformatics. 16: 313. PMID 26415965 DOI: 10.1186/s12859-015-0742-6  0.48
2015 Lister R, Mukamel EA. Turning over DNA methylation in the mind. Frontiers in Neuroscience. 9: 252. PMID 26283895 DOI: 10.3389/fnins.2015.00252  0.32
2015 Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R. Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife. 4. PMID 26196146 DOI: 10.7554/eLife.09343  0.48
2015 Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron. 86: 1369-84. PMID 26087164 DOI: 10.1016/j.neuron.2015.05.018  0.48
2015 Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Lister R, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/nature14248  0.48
2015 Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols. 10: 475-83. PMID 25692984 DOI: 10.1038/nprot.2014.114  0.48
2015 Lister R, Mukamel EA. Turning over DNA methylation in the mind Frontiers in Neuroscience. 9. DOI: 10.3389/fnins.2015.00252  0.48
2015 Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing Nature Protocols. 10: 475-483. DOI: 10.1038/nprot.2014.114  0.48
2015 Hontelez S, Van Kruijsbergen I, Georgiou G, Van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJC. Embryonic transcription is controlled by maternally defined chromatin state Nature Communications. 6. DOI: 10.1038/ncomms10148  0.48
2014 Yu W, McIntosh C, Lister R, Zhu I, Han Y, Ren J, Landsman D, Lee E, Briones V, Terashima M, Leighty R, Ecker JR, Muegge K. Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways. Genome Research. 24: 1613-23. PMID 25170028 DOI: 10.1101/gr.172015.114  0.48
2014 Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ. Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. Nucleic Acids Research. 42: 10856-68. PMID 25122745 DOI: 10.1093/nar/gku708  0.48
2014 Yu W, Briones V, Lister R, McIntosh C, Han Y, Lee EY, Ren J, Terashima M, Leighty RM, Ecker JR, Muegge K. CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity. Proceedings of the National Academy of Sciences of the United States of America. 111: 5890-5. PMID 24711395 DOI: 10.1073/pnas.1320945111  0.48
2014 Looney TJ, Zhang L, Chen CH, Lee JH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker SW, Fernandes CJ, Gaetz J, Foshay KM, Clift KL, Zhang Z, et al. Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. Genome Research. 24: 267-80. PMID 24310002 DOI: 10.1101/gr.143891.112  0.48
2014 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Corrigendum: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells Nature. 514: 126. DOI: 10.1038/nature13843  0.48
2014 Welch M, Lister R. Epigenomics and the control of fate, form and function in social insects Current Opinion in Insect Science. 1: 31-38. DOI: 10.1016/j.cois.2014.04.005  0.48
2013 Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics (Oxford, England). 29: 3204-3210. PMID 24078702 DOI: 10.1093/bioinformatics/btt558  0.48
2013 Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, et al. Global epigenomic reconfiguration during mammalian brain development. Science (New York, N.Y.). 341: 1237905. PMID 23828890 DOI: 10.1126/science.1237905  0.48
2013 Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 153: 1134-48. PMID 23664764 DOI: 10.1016/j.cell.2013.04.022  0.48
2012 Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Jordan Rowley M, Gregory BD, Ecker JR, Tang H, Pikaard CS. Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome Genes and Development. 26: 1825-1836. PMID 22855789 DOI: 10.1101/gad.197772.112  0.48
2012 Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the National Academy of Sciences of the United States of America. 109: E2183-91. PMID 22733782 DOI: 10.1073/pnas.1209329109  0.48
2012 Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research. 22: 246-58. PMID 22156296 DOI: 10.1101/gr.125872.111  0.48
2011 Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. 473: 394-7. PMID 21552279 DOI: 10.1038/nature10102  0.48
2011 Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 471: 68-73. PMID 21289626 DOI: 10.1038/nature09798  0.48
2010 Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, ... ... Lister R, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/nbt.1682  0.48
2010 Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, Pelizzola M, Edsall LE, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell. 6: 479-91. PMID 20452322 DOI: 10.1016/j.stem.2010.03.018  0.48
2009 Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462: 315-22. PMID 19829295 DOI: 10.1038/nature08514  0.48
2009 Lister R, Ecker JR. Finding the fifth base: Genome-wide sequencing of cytosine methylation Genome Research. 19: 959-966. PMID 19273618 DOI: 10.1101/gr.083451.108  0.48
2009 Lister R, Gregory BD, Ecker JR. Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond Current Opinion in Plant Biology. 12: 107-118. PMID 19157957 DOI: 10.1016/j.pbi.2008.11.004  0.48
2009 Sappl PG, Carroll AJ, Clifton R, Lister R, Whelan J, Harvey Millar A, Singh KB. The Arabidopsis glutathione transferase gene family displays complex stress regulation and co-silencing multiple genes results in altered metabolic sensitivity to oxidative stress. The Plant Journal : For Cell and Molecular Biology. 58: 53-68. PMID 19067976 DOI: 10.1111/j.1365-313X.2008.03761.x  0.4
2008 Ho LH, Giraud E, Uggalla V, Lister R, Clifton R, Glen A, Thirkettle-Watts D, Van Aken O, Whelan J. Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis. Plant Physiology. 147: 1858-73. PMID 18567827 DOI: 10.1104/pp.108.121384  0.4
2008 Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR. A link between RNA metabolism and silencing affecting Arabidopsis development. Developmental Cell. 14: 854-66. PMID 18486559 DOI: 10.1016/j.devcel.2008.04.005  0.48
2008 Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 133: 523-36. PMID 18423832 DOI: 10.1016/j.cell.2008.03.029  0.48
2007 Lister R, Carrie C, Duncan O, Ho LH, Howell KA, Murcha MW, Whelan J. Functional definition of outer membrane proteins involved in preprotein import into mitochondria. The Plant Cell. 19: 3739-59. PMID 17981999 DOI: 10.1105/tpc.107.050534  0.4
2007 Ho LH, Giraud E, Lister R, Thirkettle-Watts D, Low J, Clifton R, Howell KA, Carrie C, Donald T, Whelan J. Characterization of the regulatory and expression context of an alternative oxidase gene provides insights into cyanide-insensitive respiration during growth and development. Plant Physiology. 143: 1519-33. PMID 17322330 DOI: 10.1104/pp.106.091819  0.4
2007 Murcha MW, Elhafez D, Lister R, Tonti-Filippini J, Baumgartner M, Philippar K, Carrie C, Mokranjac D, Soll J, Whelan J. Characterization of the preprotein and amino acid transporter gene family in Arabidopsis. Plant Physiology. 143: 199-212. PMID 17098851 DOI: 10.1104/pp.106.090688  0.4
2006 Lister R, Whelan J. Mitochondrial protein import: convergent solutions for receptor structure. Current Biology : Cb. 16: R197-9. PMID 16546069 DOI: 10.1016/j.cub.2006.02.024  0.4
2005 Lister R, Hulett JM, Lithgow T, Whelan J. Protein import into mitochondria: origins and functions today (review). Molecular Membrane Biology. 22: 87-100. PMID 16092527  0.4
2005 Clifton R, Lister R, Parker KL, Sappl PG, Elhafez D, Millar AH, Day DA, Whelan J. Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Molecular Biology. 58: 193-212. PMID 16027974 DOI: 10.1007/s11103-005-5514-7  0.48
2004 Chew O, Lister R, Qbadou S, Heazlewood JL, Soll J, Schleiff E, Millar AH, Whelan J. A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor. Febs Letters. 557: 109-14. PMID 14741350  0.4
2004 Lister R, Chew O, Lee MN, Heazlewood JL, Clifton R, Parker KL, Millar AH, Whelan J. A transcriptomic and proteomic characterization of the Arabidopsis mitochondrial protein import apparatus and its response to mitochondrial dysfunction. Plant Physiology. 134: 777-89. PMID 14730085 DOI: 10.1104/pp.103.033910  0.48
2003 Murcha MW, Lister R, Ho AY, Whelan J. Identification, expression, and import of components 17 and 23 of the inner mitochondrial membrane translocase from Arabidopsis. Plant Physiology. 131: 1737-47. PMID 12692332 DOI: 10.1104/pp.102.016808  0.4
2003 Lister R, Murcha MW, Whelan J. The Mitochondrial Protein Import Machinery of Plants (MPIMP) database. Nucleic Acids Research. 31: 325-7. PMID 12520014  0.4
2002 Lister R, Mowday B, Whelan J, Millar AH. Zinc-dependent intermembrane space proteins stimulate import of carrier proteins into plant mitochondria. The Plant Journal : For Cell and Molecular Biology. 30: 555-66. PMID 12047630  0.4
Show low-probability matches.