Preprints

Cahn J*, Lloyd JPB*, Karemaker ID, Jansen PWTC, Pflueger J, Duncan O, Petereit J, Bogdanovic O, Millar H, Vermeulen M, Lister R^# (2023) Characterization of DNA methylation reader proteins of Arabidopsis thaliana. bioRxiv 10.1101/2023.12.05.570080

Liew LC*, You Y*, Oliva M, Peirats-Llobet M, Ng S, Tamiru-Oli M, Berkowitz O, Hong UVT, Haslem A, Stuart T, Ritchie ME, Bassel GW, Lister R, Whelan J^#, Gouil Q^#, Lewsey MG^# (2023) Establishment of cell transcriptional identity during seed germination. bioRxiv 10.1101/2023.01.21.523180

Bestry M, Larcombe AN, Kresoje N, Chivers EK, Bakker C, Fitzpatrick JP, Elliott EJ, Craig JM, Muggli E, Halliday J, Hutchinson D, Buckberry S, Lister R, Symons M, Martino D^# (2023) The influence of prenatal alcohol exposure and maternal diet on offspring DNA methylation: a cross-species study. bioRxiv 10.1101/2023.06.15.544516

Khan MA, Herring G, Oliva M, Fourie E, Zhu JY, Johnston B, Pflüger J, Swain T, Pflüger C, Lloyd J, Secco D, Small I, Kidd B^#, Lister R^# (2022) CRISPRi-based circuits for genetic computation in plants. bioRxiv 10.1101/2022.07.01.498372

Oliva M^#, Stuart T, Tang D, Pflueger J, Poppe D, Jabbari JS, Gigante S, Dragwidge JM, Whelan J, Lewsey MG, Lister R^# (2022) An environmentally-responsive transcriptional state modulates cell identities during root development. bioRxiv 10.1101/2022.03.04.483008

Publications

Swain T*, Pflueger C*^#, Freytag S, Poppe D, Pflueger J, Nguyen T, Li JK, Lister R^# (2023) A modular dCas9-based recruitment platform for combinatorial epigenome editing. Nucleic Acids Research 10.1093/nar/gkad1108

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 10.1038/s41586-023-06424-7

Nobori T^#, Oliva M, Lister R, Ecker JR^# (2023) Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap. Nature Plants 10.1038/s41477-023-01439-4

Oliva M, Lister R^# (2023) Exploring the identity of individual plant cells in space and time. New Phytologist 10.1111/nph.19153

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 10.3390/genes14050957

Carlessi R^#, Denisenko E, Boslem E, Köhn-Gaone J, Main N, Bakar NDBA, Shirolkar GD, Jones M, Beasley AB, Poppe D, Dwyer BJ, Jackaman C, Tjiam MC, Lister R, Karin M, Fallowfield JA, Kendall TJ, Forbes SJ, Gray ES, Olynyk JK, Yeoh G, Forrest ARR, Ramm GA, Febbraio MA, Tirnitz-Parker JEE^# (2023) Single-nucleus RNA sequencing of pre-malignant liver reveals disease-associated hepatocyte state with HCC prognostic potential. Cell Genomics 10.1016/j.xgen.2023.100301

Waryah C, Cursons J, Foroutan M, Pflueger C, Wang E, Molania R, Sorolla A, Wallis C, Moses C, Glas I, Magalhães L, Thompson EW, Fearnley LG, Chaffer CL, Davis M, Papenfuss AT, Redfern A, Lister R, Esteller M, Blancafort P^# (2023) Synthetic Epigenetic Reprogramming of Mesenchymal to Epithelial States Using the CRISPR/dCas9 Platform in Triple Negative Breast Cancer. Advanced Science 10.1002/advs.202301802

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 Physiology 10.1093/treephys/tpac146

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. Nature Communications 10.1038/s41467-022-35180-x

Herring CA*, Simmons RK*, Freytag S*, Poppe D*, Moffet JJD, Pflueger J, Buckberry S, Vargas-Landin BD, 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 10.1016/j.cell.2022.09.039, pdf

de Mendoza A*^#, Nguyen TV*, Ford E*, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanović 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 Biology 10.1186/s13059-022-02728-5, pdf

Lloyd JPB, Ly F, Gong P, Pflueger J, Swain T, Pflueger C, Fourie E, Khan MA, Kidd B, Lister R^# (2022) Synthetic memory circuits for stable cell reprogramming in plants. Nature Biotechnology 10.1038/s41587-022-01383-2, pdf

Nefzger CM, Jardé T, Srivastava A, Schroeder J, Rossello FJ, Horvay K, Prasko M, Paynter JM, Chen J, Weng C-F, Sun YBY, Liu X, Chan E, Deshpande N, Chen X, Li YJ, Pflueger J, Engel RM, Knaupp AS, Tsyganov K, Nilsson SK, Lister R, Rackham OJL, Abud HE^#, Polo JM^# (2022) Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential. NPJ Regenerative Medicine 10.1038/s41536-022-00226-7, pdf

Lloyd JPB, Lister R^# (2022) Epigenome plasticity in plants. Nature Reviews Genetics 10.1038/s41576-021-00407-y, pdf

Sutton GJ, Poppe D, Simmons RK, Walsh K, Nawaz U, Lister R, Gagnon-Bartsch JA, Voineagu I^# (2022) Comprehensive evaluation of deconvolution methods for human brain gene expression. Nature Communications 10.1038/s41467-022-28655-4, pdf

Grubman A, Choo XY, Chew G, Ouyang JF, Sun G, Croft NP, Rossello FJ, Simmons RK, Buckberry S, Vargas Landin DB, 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 associatedwith Aβ plaque phagocytosis. Nature Communications 10.1038/s41467-021-23111-1, pdf

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 10.1038/s41586-021-03372-y

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. Nature Ecology & Evolution 10.1038/s41559-020-01371-2

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 10.1093/braincomms/fcaa235

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 10.1016/j.stemcr.2020.11.005

Geng F-S, 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. microPublication Biology 2020(12) 10.17912/micropub.biology.000341

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 10.1038/s41586-020-2734-6

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. Nature Communications 10.1038/s41467-020-17397-w

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 Physiology 10.1104/pp.20.00136

Denisenko E, Guo BB, Jones M, Hou R, de Kock L, Lassmann T, Poppe D, Clement 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 Biology 10.1186/s13059-020-02048-6

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, and Casares F^# (2020) Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications 10.1038/s41467-020-16284-8

Freytag S^#, Lister R^# (2019) schex avoids overplotting for large single cell RNA-sequencing datasets. Bioinformatics 10.1093/bioinformatics/btz907

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. Nature Neuroscience 10.1038/s41593-019-0539-4

Pflueger C, Swain T, Lister R^# (2019) Harnessing targeted DNA methylation and demethylation using dCas9. Essays in Biochemistry 10.1042/EBC20190029

de Mendoza A^#, Lister R, Bogdanovic O^# (2019) Evolution of DNA methylome diversity in eukaryotes. Journal of Molecular Biology 10.1016/j.jmb.2019.11.003

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. Nature Ecology and Evolution 10.1038/s41559-019-0983-2

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. Nature Communications 10.1038/s41467-019-10895-6

de Mendoza A^#, Pflueger J, Lister R^# (2019) Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family. Genome Research 10.1101/gr.243774.118

Sanchez-Luque FJ^#, Kempen M-J, Gerdes P, Vargas-Landin DB, Richardson SR, Troskie R-L, Jesuadian JS, Cheetham SW, Carreira PE, Salvador-Palomeque C, García-Cañadas Mm 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. Molecular Cell 10.1016/j.molcel.2019.05.024

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 10.1186/s12859-019-2845-y, pdf

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 10.1038/s41586-018-0734-6, pdf

Pflueger C*, Tan D*, Swain T, Nguyen TV, 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 Research 10.1101/gr.233049.117

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. Nature Communications 10.1038/s41467-018-03724-9, pdf

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 10.1016/j.stem.2017.11.007

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 Reports 10.1016/j.celrep.2017.11.029, pdf

Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I, Bogdanović 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 Biology 10.1186/s13059-017-1335-7, pdf

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. Nature Methods 10.1038/nmeth.4436, paper

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 Biology 10.1186/s13059-017-1302-3, pdf

Valensisi C, Andrus C, Buckberry S, Jayavelu ND, Lund RJ, Lister R, Hawkins RD (2017) Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases. Cell Reports 20(6):1448-1462, pdf

Crisp PA, Ganguly D, Smith AB, Murray KD, Estavillo GM, Searle IR, 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 10.1105/tpc.16.00828, pdf

Bogdanović O and Lister R (2017) DNA methylation and the preservation of cell identity. Current Opinion in Genetics and Development 10.1016/j.gde.2017.06.007

Secco D, Whelan J, Rouached H, Lister R (2017) Nutrient stress-induced chromatin changes in plants. Current Opinion in Plant Biology 39:1-7, pdf

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. Chemical Science 8(4):2923-2930, pdf

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. The Plant Journal 10.1111/tpj.13418. pubmed

Stuart T, Eichten SR, Cahn J, Karpievitch YK, Borevitz JO, Lister R (2016) Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation. eLife 10.7554/eLife.20777, pdf

Eichten SR, Stuart T, Srivastava A, Lister R, Borevitz JO (2016) DNA methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity. Genome Research 10.1101/gr.205468.116. pdf, pubmed

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, Bogdanović 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 538:336-43. pdf

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. The Plant Journal 10.1111/tpj.13276. pubmed

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. Nature Plants 10.1038/nplants.2016.58. journal

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 10.7554/eLife.11613. journal

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 GJC, 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. Nature Genetics 10.1038/ng.3522. journal

Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanović O, Lister R, Veenstra GJ (2015) Embryonic transcription is controlled by maternally defined chromatin state. Nature Communications 10.1038/ncomms10148. pdf

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 10.1186/s12859-015-0742-6. pdf

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 10.7554/eLife.09343, pdf

Lister R and Mukamel EA (2015) Turning over DNA methylation in the mind. Frontiers in Neuroscience 10.3389/fnins.2015.00252. pdf

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 86:1369–84. pdf

Roadmap Epigenomics Consortium (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317-30. pdf

Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR (2015) MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nature Protocols 10:475-83. pdf

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 Research, gr.172015.114. pubmed

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 Research, advanced online publication. pdf

Welch MD, Lister R (2014) Epigenomics and the control of fate, form and function in social insects. Current Opinion in Insect Science 1:31-8. COIS

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−/− MEFs is associated with de novo H3K4me1 formation and altered cellular plasticity. PNAS 111(16):5890-5. pubmed

Looney T, Lee JH, Zhang L, Chen CH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker S, Fernandes C, Gaetz J, Foshay K, Clift K, Zhang Z, Li WQ, Vallender E, Wagner U, Qin JY, Michelini K, Bugarija B, Park D, Aryee E, Stricker T, White K, Ren B, Schroth G, Ecker J, Xiang AP, Zhou J, Lahn B. (2013) Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. Genome Research 24(2):267-80. pubmed

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. (2013) STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics 29(24):3204-10. pubmed

Lister R*^#, Mukamel EA*, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork A, Schultz MD, Tonti-Filippini J, Yu M, 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. pubmed abstract perspective

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. pubmed abstract

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 and Development 26(16):2461825-36. pubmed pdf

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. PNAS 109(32):E2183-91. pubmed pdf

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 Research 22(2):246-58. pubmed pdf

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):394-397. pubmed pmc

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. pubmed pdf

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. Nature Biotechnology 28(10):1026-1028. pubmed pmc

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. pubmed pdf

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):315-22. pubmed pmc

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 Journal 58(1):53-68. pubmed pdf

Lister R, Ecker JR. (2009) Finding the fifth base: Genome-wide sequencing of cytosine methylation. Genome Research 19(6):959-66. pubmed pdf

Lister R, Gregory BD, Ecker JR. (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Current Opinions in Plant Biology 12(2):107-18. pubmed pdf

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. pubmed pdf

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. Developmental Cell 14(6):854-66. pubmed pdf

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 Physiology 147(4):1858-73. pubmed pdf

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. pubmed pdf

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 Physiology 143(1):199-212. pubmed pdf

Ho LHM, Giraud E, Lister R, Thirkettle-Watts D, Low J, Clifton R, Howell KA, Carrie C, Donald T, Whelan J. (2007) Characterisation of the regulatory and expression context of an alternative oxidase gene provides insights into cyanide insensitive respiration during growth and development. Plant Physiology 143(1):199-212. pubmed pdf

Lister R, Whelan J. (2006) Mitochondrial protein import: convergent solutions for receptor structure. Current Biology 21;16(6):R197-9. pubmed pdf

Lister R, Hulett J, Lithgow T, Whelan J. (2005) Protein import into mitochondria: origins and functions today. Molecular Membrane Biology 22(1-2):87-100. pubmed

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 Molecular Biology 58:193-212. pubmed

Lister R, Chew O, Lee MN, Heazlewood JL, Clifton, R., Parker KL, Millar AH, Whelan J. (2004) A Transcriptomic and Proteomic Characterization of the Arabidopsis Mitochondrial Protein Import Apparatus and Its Response to Mitochondrial Dysfunction. Plant Physiology 134:777-789. pubmed pdf

Chew O, Lister R, Qbadou S, Heazlewood JL, Soll J, Schleiff E, Millar AH, Whelan, J. (2004) A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor. FEBS Letters 557:109-114. pubmed pdf

Murcha MW, Lister R, Ho AY, Whelan, J. (2003) Identification, expression, and import of components 17 and 23 of the inner mitochondrial membrane translocase from Arabidopsis. Plant Physiology 131:1737-1747. pubmed pdf

Lister R, Murcha MW, Whelan J (2003) The mitochondrial protein import machinery of plants (MPIMP) database. Nucleic Acids Research 31:325-327. pubmed pdf

Lister R, Mowday B, Whelan J, Millar AH (2002) Zinc dependent intermembrane space proteins stimulate carrier import into plant mitochondria. The Plant Journal 30:555-566. pubmed pdf

Lister R, Chew O, Rudhe C, Lee MN, Whelan J. (2001) Arabidopsis thaliana ferrochelatase-I and -II are not imported into Arabidopsis mitochondria. FEBS Letters 506: 291-295. pubmed pdf

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