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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:

Year Publication Online
2024
Khan MA, Herring G, Zhu JY, Oliva M, Fourie E, Johnston B, Zhang Z, Potter J, Pineda L, Pflueger J, Swain T, Pflueger C, Lloyd JPB, Secco D, Small I, Kidd BN, Lister R (2024) CRISPRi-based circuits to control gene expression in plants. Nat Biotechnol (in press).
NCBI Pubmed DOI Link
2024
Swain T, Pflueger C, Freytag S, Poppe D, Pflueger J, Nguyen TV, Li JK, Lister R (2024) A modular dCas9-based recruitment platform for combinatorial epigenome editing. Nucleic Acids Res 52(1):474-491.
NCBI Pubmed DOI Link
2024
Stuart T, Buckberry S, Nguyen TV, Lister R (2024) Approaches for the Analysis and Interpretation of Whole-Genome Bisulfite Sequencing Data. Methods Mol Biol 2842:391-403.
NCBI Pubmed DOI Link
2024
Vargas-Landin DB, Pflüger J, Nguyen TV, Lister R (2024) Generation of Whole-Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis. Methods Mol Biol 2842:383-390.
NCBI Pubmed DOI Link
2024
Nicolas-Martinez EC, Robinson O, Pflueger C, Gardner A, Corbett MA, Ritchie T, Kroes T, Van Eyk CL, Scheffer IE, Hildebrand MS, Barnier JV, Rousseau V, Genevieve D, Haushalter V, Piton A, Denommé-Pichon AS, Bruel AL, Nambot S, Isidor B, Grigg J, Gonzalez T, Ghedia S, Marchant RG, Bournazos A, Wong WK, Webster RI, Evesson FJ, Jones KJ, Cooper ST, Lister R, Gecz J, Jolly LA (2024) RNA variant assessment using transactivation and transdifferentiation. Am J Hum Genet 111(8):1673-1699.
NCBI Pubmed DOI Link
2023
Nobori T, Oliva M, Lister R, Ecker JR (2023) Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap. Nat Plants 9(7):1026-1033.
NCBI Pubmed DOI Link
2023
Hermawaty D, Cahn J, Lister R, Considine MJ (2023) Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds. Tree Physiol 43(4):675-689.
NCBI Pubmed DOI Link
2023
Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, De Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM, Lister R (2023) Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature 620(7975):863-872.
NCBI Pubmed DOI Link
2023
Martin S, Poppe D, Olova N, O'Leary C, Ivanova E, Pflueger J, Dechka J, Simmons RK, Cooper HM, Reik W, Lister R, Wolvetang EJ (2023) Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development. Genes (Basel) 14(5):.
NCBI Pubmed DOI Link
2023
Oliva M, Lister R (2023) Exploring the identity of individual plant cells in space and time. New Phytol 240(1):61-67.
NCBI Pubmed DOI Link
2022
De Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R (2022) Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biol 23(1):163.
NCBI Pubmed DOI Link
2022
Lloyd JPB, Ly F, Gong P, Pflueger J, Swain T, Pflueger C, Fourie E, Khan MA, Kidd BN, Lister R (2022) Synthetic memory circuits for stable cell reprogramming in plants. Nat Biotechnol 40(12):1862-1872.
NCBI Pubmed DOI Link
2022
Gerdes P, Lim SM, Ewing AD, Larcombe MR, Chan D, Sanchez-Luque FJ, Walker L, Carleton AL, James C, Knaupp AS, Carreira PE, Nefzger CM, Lister R, Richardson SR, Polo JM, Faulkner GJ (2022) Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells. Nat Commun 13(1):7470.
NCBI Pubmed DOI Link
2022
Herring CA, Simmons RK, Freytag S, Poppe D, Moffet JJD, Pflueger J, Buckberry S, Vargas-Landin DB, Clément O, Echeverría EG, Sutton GJ, Alvarez-Franco A, Hou R, Pflueger C, Mcdonald K, Polo JM, Forrest ARR, Nowak AK, Voineagu I, Martelotto L, Lister R (2022) Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution. Cell 185(23):4428-4447.e28.
NCBI Pubmed DOI Link
2021
Ye Z, Chatterton Z, Pflueger J, Damiano JA, McQuillan L, Harvey AS, Malone S, Do H, Maixner W, Schneider A, Nolan B, Wood M, Lee WS, Gillies G, Pope K, Wilson M, Lockhart PJ, Dobrovic A, Scheffer IE, Bahlo M, Leventer R, Lister R, Berkovic S, Hildebrand MS (2021) Cerebrospinal fluid liquid biopsy for detecting somatic mosaicism in brain BRAIN COMMUNICATIONS
NCBI Pubmed DOI Link
2021
De Mendoza A, Poppe D, Buckberry S, Pflueger J, Albertin CB, Daish T, Bertrand S, De La Calle-Mustienes E, Gómez-Skarmeta JL, Nery JR, Ecker JR, Baer B, Ragsdale CW, Grützner F, Escriva H, Venkatesh B, Bogdanovic O, Lister R (2021) The emergence of the brain non-CpG methylation system in vertebrates. Nat Ecol Evol 5(3):369-378.
NCBI Pubmed DOI Link
2021
Nguyen TV, Lister R (2021) Genomic Targeting of TET Activity for Targeted Demethylation Using CRISPR/Cas9 METHODS MOL. BIOL. 2272:181-194.
NCBI Pubmed DOI Link
2021
Liu X, Tan JP, Schröder J, Aberkane A, Ouyang JF, Mohenska M, Lim SM, Sun YBY, Chen J, Sun G, Zhou Y, Poppe D, Lister R, Clark AT, Rackham OJL, Zenker J, Polo JM (2021) Modelling human blastocysts by reprogramming fibroblasts into iBlastoids. NATURE 591(7851):627-632.
NCBI Pubmed DOI Link
2021
Grubman A, Choo XY, Chew G, Ouyang JF, Sun G, Croft NP, Rossello FJ, Simmons R, Buckberry S, Landin DV, Pflueger J, Vandekolk TH, Abay Z, Zhou Y, Liu X, Chen J, Larcombe M, Haynes JM, McLean C, Williams S, Chai SY, Wilson T, Lister R, Pouton CW, Purcell AW, Rackham OJL, Petretto E, Polo JM (2021) Transcriptional signature in microglia associated with Aβ plaque phagocytosis. NAT COMMUN 12(1):3015.
NCBI Pubmed DOI Link
2020
Petereit J, Duncan O, Murcha MW, Fenske R, Cincu E, Cahn J, Pružinská A, Ivanova A, Kollipara L, Wortelkamp S, Sickmann A, Lee J, Lister R, Millar AH, Huang S (2020) Mitochondrial CLPP2 Assists Coordination and Homeostasis of Respiratory Complexes. Plant Physiol 184(1):148-164.
NCBI Pubmed DOI Link
2020
Martin S, Poppe D, Olova N, O'Leary C, Ivanova E, Pflueger J, Dechka J, Simmons RK, Cooper HM, Reik W, Lister R, Wolvetang EJ (2020) Conserved and divergent features of DNA methylation in embryonic stem cell-derived neurons BIORXIV
DOI Link
2020
Knaupp AS, Mohenska M, Larcombe MR, Ford E, Lim SM, Wong K, Chen J, Firas J, Huang C, Liu X, Nguyen T, Sun YBY, Holmes ML, Tripathi P, Pflueger J, Rossello FJ, Schröder J, Davidson KC, Nefzger CM, Das PP, Haigh JJ, Lister R, Schittenhelm RB, Polo JM (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.
NCBI Pubmed DOI Link
2020
Freytag S, Lister R (2020) schex avoids overplotting for large single cell RNA-sequencing datasets. BIOINFORMATICS 36(7):2291-2292.
NCBI Pubmed DOI Link
2020
Denisenko E, Guo BB, Jones M, Hou R, de Kock L, Lassmann T, Poppe D, Clément O, Simmons RK, Lister R, Forrest ARR (2020) Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows. GENOME BIOL 21(1):130.
NCBI Pubmed DOI Link
2020
Liu X, Ouyang JF, Rossello FJ, Tan JP, Davidson KC, Valdes DS, Schröder J, Sun YBY, Chen J, Knaupp AS, Sun G, Chy HS, Huang Z, Pflueger J, Firas J, Tano V, Buckberry S, Paynter JM, Larcombe MR, Poppe D, Choo XY, O'Brien CM, Pastor WA, Chen D, Leichter AL, Naeem H, Tripathi P, Das PP, Grubman A, Powell DR, Laslett AL, David L, Nilsson SK, Clark AT, Lister R, Nefzger CM, Martelotto LG, Rackham OJL, Polo JM (2020) Reprogramming roadmap reveals route to human induced trophoblast stem cells. NATURE 586(7827):101-107.
NCBI Pubmed DOI Link
2020
de Mendoza A, Lister R, Bogdanovic O (2020) Evolution of DNA Methylome Diversity in Eukaryotes. J MOL BIOL 432(6):1687-1705.
NCBI Pubmed DOI Link
2020
Geng FS, De La Calle-Mustienes E, Gómez-Skarmeta JL, Lister R, Bogdanovic O (2020) Depletion of Foxk transcription factors causes genome-wide transcriptional misregulation and developmental arrest in zebrafish embryos. MicroPubl Biol 2020():.
NCBI Pubmed DOI Link
2020
Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina-Caro A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, Davie K, Misof B, González J, Aerts S, Lister R, Paps J, Rozas J, Sánchez-Gracia A, Irimia M, Maeso I, Casares F (2020) Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. NAT COMMUN 11(1):2631.
NCBI Pubmed DOI Link
2020
Kenny NJ, Francis WR, Rivera-Vicéns RE, Juravel K, de Mendoza A, Díez-Vives C, Lister R, Bezares-Calderón LA, Grombacher L, Roller M, Barlow LD, Camilli S, Ryan JF, Wörheide G, Hill AL, Riesgo A, Leys SP (2020) Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. NAT COMMUN 11(1):3676.
NCBI Pubmed DOI Link
2019
de Mendoza A, Hatleberg WL, Pang K, Leininger S, Bogdanovic O, Pflueger J, Buckberry S, Technau U, Hejnol A, Adamska M, Degnan BM, Degnan SM, Lister R (2019) Convergent evolution of a vertebrate-like methylome in a marine sponge. NAT ECOL EVOL 3(10):1464-1473.
NCBI Pubmed DOI Link
2019
Grubman A, Chew G, Ouyang JF, Sun G, Choo XY, McLean C, Simmons RK, Buckberry S, Vargas-Landin DB, Poppe D, Pflueger J, Lister R, Rackham OJL, Petretto E, Polo JM (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.
NCBI Pubmed DOI Link
2019
Denisenko E, Guo BB, Jones M, Hou R, Kock LD, Lassmann T, Poppe D, Clement O, Simmons RK, Lister R, Forrest AR (2019) Systematic bias assessment in solid tissue 10x scRNA-seq workflows BIORXIV
DOI Link
2019
Pflueger C, Swain T, Lister R (2019) Harnessing targeted DNA methylation and demethylation using dCas9. ESSAYS BIOCHEM. 63(6):813-825.
NCBI Pubmed DOI Link
2019
Srivastava A, Karpievitch YV, Eichten SR, Borevitz JO, Lister R (2019) HOME: a histogram based machine learning approach for effective identification of differentially methylated regions. BMC BIOINFORMATICS 20(1):253.
NCBI Pubmed DOI Link
2019
Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E, Bogdanovic O (2019) Retention of paternal DNA methylome in the developing zebrafish germline. NAT COMMUN 10(1):3054.
NCBI Pubmed DOI Link
2019
de Mendoza A, Pflueger J, Lister R (2019) Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family. GENOME RES 29(8):1277-1286.
NCBI Pubmed DOI Link
2019
Sanchez-Luque FJ, Kempen MHC, Gerdes P, Vargas-Landin DB, Richardson SR, Troskie RL, Jesuadian JS, Cheetham SW, Carreira PE, Salvador-Palomeque C, García-Cañadas M, Muñoz-Lopez M, Sanchez L, Lundberg M, Macia A, Heras SR, Brennan PM, Lister R, Garcia-Perez JL, Ewing AD, Faulkner GJ (2019) LINE-1 Evasion of Epigenetic Repression in Humans. MOL CELL 75(3):590-604.e12.
NCBI Pubmed DOI Link
2018
de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Hong F, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S, Lister R (2018) Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. NAT COMMUN 9(1):1341.
NCBI Pubmed DOI Link
2018
Stuart T, Buckberry S, Lister R (2018) Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data. Methods Mol Biol 1767:299-310.
NCBI Pubmed DOI Link
2018
Vargas-Landin DB, Pflüger J, Lister R (2018) Generation of Whole Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis. Methods Mol Biol 1767():291-298.
NCBI Pubmed DOI Link
2018
Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J, Nefzger C, Polo JM, Ford E, Lister R (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.
NCBI Pubmed DOI Link
2018
de Mendoza A, Bonnet A, Vargas-Landin DB, Ji N, Li H, Yang F, Li L, Hori K, Pflueger J, Buckberry S, Ohta H, Rosic N, Lesage P, Lin S, Lister R (2018) Author Correction: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. NAT COMMUN 9(1):1811.
NCBI Pubmed DOI Link
2018
Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, De La Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, Van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D'Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M (2018) Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 564(7734):64-70.
NCBI Pubmed DOI Link
2017
Secco D, Whelan J, Rouached H, Lister R (2017) Nutrient stress-induced chromatin changes in plants. Curr Opin Plant Biol 39:1-7.
NCBI Pubmed DOI Link
2017
Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R, Hawkins RD (2017) Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases. CELL REP 20(6):1448-1462.
NCBI Pubmed DOI Link
2017
Crisp PA, Ganguly DR, Smith AB, Murray KD, Estavillo GM, Searle I, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ (2017) Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis. Plant Cell 29(8):1836-1863.
NCBI Pubmed DOI Link
2017
Bogdanović O, Lister R (2017) DNA methylation and the preservation of cell identity. CURR. OPIN. GENET. DEV. 46:9-14.
NCBI Pubmed DOI Link
2017
Kretzmann JA, Ho D, Evans CW, Plani-Lam JHC, Garcia-Bloj B, Mohamed AE, O'Mara ML, Ford E, Tan DEK, Lister R, Blancafort P, Norret M, Iyer KS (2017) Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA. CHEM SCI 8(4):2923-2930.
NCBI Pubmed DOI Link
2017
Narsai R, Gouil Q, Secco D, Srivastava A, Karpievitch YV, Liew LC, Lister R, Lewsey MG, Whelan J (2017) Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination. Genome Biol 18(1):172.
NCBI Pubmed DOI Link
2017
Liu X, Nefzger CM, Rossello FJ, Chen J, Knaupp AS, Firas J, Ford E, Pflueger J, Paynter JM, Chy HS, O'Brien CM, Huang C, Mishra K, Hodgson-Garms M, Jansz N, Williams SM, Blewitt ME, Nilsson SK, Schittenhelm RB, Laslett AL, Lister R, Polo JM (2017) Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming. NAT METHODS 14(11):1055-1062.
NCBI Pubmed DOI Link
2017
Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I, Bogdanovic O, Gibeaux R, Heald R, Lister R, Huynen MA, van Heeringen SJ, Veenstra GJC (2017) Regulatory remodeling in the allo-tetraploid frog Xenopus laevis. GENOME BIOL 18(1):198.
NCBI Pubmed DOI Link
2017
Knaupp AS, Buckberry S, Pflueger J, Lim SM, Ford E, Larcombe MR, Rossello FJ, de Mendoza A, Alaei S, Firas J, Holmes ML, Nair SS, Clark SJ, Nefzger CM, Lister R, Polo JM (2017) Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming. CELL STEM CELL 21(6):834-845.e6.
NCBI Pubmed DOI Link
2017
Nefzger CM, Rossello FJ, Chen J, Liu X, Knaupp AS, Firas J, Paynter JM, Pflueger J, Buckberry S, Lim SM, Williams B, Alaei S, Faye-Chauhan K, Petretto E, Nilsson SK, Lister R, Ramialison M, Powell DR, Rackham OJL, Polo JM (2017) Cell Type of Origin Dictates the Route to Pluripotency. CELL REP 21(10):2649-2660.
NCBI Pubmed DOI Link
2017
Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J (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.
NCBI Pubmed DOI Link
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, Sauka-Spengler T, Ecker JR, Vermeulen M, Gómez-Skarmeta JL, Lister R (2016) Active DNA demethylation at enhancers during the vertebrate phylotypic period. NAT GENET 48(4):417-26.
NCBI Pubmed DOI Link
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 (2016) Epigenomic landscapes of retinal rods and cones. ELIFE 5:e11613.
NCBI Pubmed DOI Link
2016
Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJ (2016) Erratum: Embryonic transcription is controlled by maternally defined chromatin state. NAT COMMUN 7:12208.
NCBI Pubmed DOI Link
2016
Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR (2016) Unique cell-type-specific patterns of DNA methylation in the root meristem. NAT PLANTS 2(5):16058.
NCBI Pubmed DOI Link
2016
Van Aken O, Ford E, Lister R, Huang S, Millar AH (2016) Retrograde signalling caused by heritable mitochondrial dysfunction is partially mediated by ANAC017 and improves plant performance. PLANT J. 88(4):542-558.
NCBI Pubmed DOI Link
2016
Eichten SR, Stuart T, Srivastava A, Lister R, Borevitz JO (2016) DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity. GENOME RES 26(11):1520-1531.
NCBI Pubmed DOI Link
2016
Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, Van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, Van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, Dupasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS (2016) Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538(7625):336-343.
NCBI Pubmed DOI Link
2016
Stuart T, Eichten SR, Cahn J, Karpievitch YV, Borevitz JO, Lister R (2016) Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. ELIFE 5. pii: e20777.
NCBI Pubmed DOI Link
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, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M (2015) Integrative analysis of 111 reference human epigenomes. NATURE 518(7539):317-30.
NCBI Pubmed DOI Link
2015
Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR (2015) MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. NAT PROTOC 10(3):475-83.
NCBI Pubmed DOI Link
2015
Bogdanović O, Lister R (2015) Of Mice and Man: Differential DNMT Dependence in Mammalian ESCs. CELL STEM CELL 16(5):459-60.
NCBI Pubmed DOI Link
2015
Freeman D, Evans N, Černis E, Lister R, Dunn G (2015) The effect of paranoia on the judging of harmful events. COGN NEUROPSYCHIATRY 20(2):122-7.
NCBI Pubmed DOI Link
2015
Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R (2015) Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Elife 4:.
NCBI Pubmed DOI Link
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 (2015) Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. NEURON 86(6):1369-84.
NCBI Pubmed DOI Link
2015
Kishore K, De Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M (2015) methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data. BMC Bioinformatics 16():313.
NCBI Pubmed DOI Link
2015
Lister R, Mukamel EA (2015) Turning over DNA methylation in the mind. Front Neurosci 9():252.
NCBI Pubmed DOI Link
2015
Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJ (2015) Embryonic transcription is controlled by maternally defined chromatin state. NAT COMMUN 18;6:10148.
NCBI Pubmed DOI Link
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, Li WQ, Vallender EJ, Wagner U, Qin JY, Michelini KJ, Bugarija B, Park D, Aryee E, Stricker T, Zhou J, White KP, Ren B, Schroth GP, Ecker JR, Xiang AP, Lahn BT (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.
NCBI Pubmed DOI Link
2014
Yu W, Briones V, Lister R, McIntosh C, Han Y, Lee EY, Ren J, Terashima M, Leighty RM, Ecker JR, Muegge K (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.
NCBI Pubmed DOI Link
2014
Grimmer MR, Stolzenburg S, Ford E, Lister R, Blancafort P, Farnham PJ (2014) Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation. NUCLEIC ACIDS RES 42(16):10856-68.
NCBI Pubmed DOI Link
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 (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.
NCBI Pubmed DOI Link
2014
Welch MD, Lister R (2014) Epigenomics and the control of fate, form and function in social insects CURR OPIN INSECT SCI Jul(1):31-38.
NCBI Pubmed DOI Link
2013
Xie W, Schultz M, 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, Zhu Y, Kim A, Nery J, Urich MA, Kuan S, Yen C, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W, Chi NC, Antosiewicz-Bourget J, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B (2013) Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells CELL 153(5):1134-48.
NCBI Pubmed DOI Link
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, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker JR (2013) Global Epigenomic Reconfiguration During Mammalian Brain Development SCIENCE 341(6146):1237905.
NCBI Pubmed DOI Link
2013
Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Ecker J, Millar AH, Ren B, Wang W (2013) STAR: An Integrated Solution to Management and Visualization of Sequencing Data. BIOINFORMATICS 29(24):3204-10.
NCBI Pubmed DOI Link
2012
Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A 109(32):E2183-91.
NCBI Pubmed DOI Link
2012
Wierzbicki AT, Cocklin R, Mayampurath A, Lister R, Rowley MJ, Gregory BD, Ecker JR, Tang H, Pikaard CS (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.
NCBI Pubmed DOI Link
2011
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, Simpson AJ, Ren B (2011) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. GENOME RES 22(2):246-58.
NCBI Pubmed DOI Link
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, Agarwal S, Rao A (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. NATURE 473(7347):39.
NCBI Pubmed DOI Link
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, Evans RM, Ecker JR (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. NATURE 471(7336):68-73.
NCBI Pubmed DOI Link
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, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. NAT BIOTECHNOL 28(10):1026-1028.
NCBI Pubmed DOI Link
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, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. CELL STEM CELL 7;6(5):479-91.
NCBI Pubmed DOI Link
2009
Lister R, Ecker JR (2009) Finding the fifth base: Genome-wide sequencing of cytosine methylation. GENOME RES 19(6):959-66.
NCBI Pubmed DOI Link
2009
Lister R, Gregory BD, Ecker JR (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. CURR OPIN PLANT BIOL 12(2):107-18.
NCBI Pubmed DOI Link
2009
Sappl PG, Carroll AJ, Clifton R, Lister R, Whelan J, Harvey Millar A, Singh KB (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.
NCBI Pubmed DOI Link
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, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences NATURE 462(7271): 315-322.
NCBI Pubmed DOI Link
2008
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis CELL 133(3):523-36.
NCBI Pubmed DOI Link
2008
Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, Millar AH, Ecker JR (2008) A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development DEV CELL 14(6):854-866.
NCBI Pubmed DOI Link
2008
Ho LH, Giraud E, Uggalla V, Lister R, Clifton R, Glen A, Thirkettle-Watts D, Van Aken O, Whelan J (2008) Identification of regulatory pathways controlling gene expression of stress-responsive mitochondrial proteins in Arabidopsis. Plant Physiol 147(4):1858-73.
NCBI Pubmed DOI Link
2007
Murcha MW, Elhafez D, Lister R, Tonti-Filippini J, Baumgartner M, Philippar K, Carrie C, Mokranjac D, Soll J, Whelan J (2007) Characterization of the preprotein and amino acid transporter gene family in Arabidopsis. Plant Physiol 143(1):199-212.
NCBI Pubmed DOI Link
2007
Ho LH, Giraud E, Lister R, Thirkettle-Watts D, Low J, Clifton R, Howell KA, Carrie C, Donald T, Whelan J (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.
NCBI Pubmed DOI Link
2007
Lister R, Carrie C, Duncan O, Ho LH, Howell KA, Murcha MW, Whelan J (2007) Functional definition of outer membrane proteins involved in preprotein import into mitochondria. Plant Cell 19(11):3739-59.
NCBI Pubmed DOI Link
2006
Lister R, Whelan J (2006) Mitochondrial protein import: convergent solutions for receptor structure CURR BIOL 16(6): R197-9.
NCBI Pubmed DOI Link
2005
Clifton R, Lister R, Parker KL, Sappl PG, Elhafez D, Millar AH, Day DA, Whelan J (2005) Stress-induced co-expression of alternative respiratory chain components in Arabidopsis thaliana. Plant Mol Biol 58(2):193-212.
NCBI Pubmed DOI Link
2005
Lister R, Hulett JM, Lithgow T, Whelan J (2005) Protein import into mitochondria: endosymbiotic origins and functions today MOL MEMBR BIOL 22(1-2):87-100.
NCBI Pubmed DOI Link
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