| Year |
Citation |
Score |
| 2024 |
Cahn J, Lloyd JPB, Karemaker ID, Jansen PWTC, Pflueger J, Duncan O, Petereit J, Bogdanovic O, Millar AH, Vermeulen M, Lister R. Characterization of DNA methylation reader proteins of . Genome Research. PMID 39632087 DOI: 10.1101/gr.279379.124 |
0.441 |
|
| 2024 |
Liew LC, You Y, Auroux L, 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, et al. Establishment of single-cell transcriptional states during seed germination. Nature Plants. PMID 39256563 DOI: 10.1038/s41477-024-01771-3 |
0.679 |
|
| 2024 |
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. Early moderate prenatal alcohol exposure and maternal diet impact offspring DNA methylation across species. Elife. 12. PMID 39239947 DOI: 10.7554/eLife.92135 |
0.334 |
|
| 2024 |
Stuart T, Buckberry S, Nguyen TV, Lister R. Approaches for the Analysis and Interpretation of Whole-Genome Bisulfite Sequencing Data. Methods in Molecular Biology (Clifton, N.J.). 2842: 391-403. PMID 39012607 DOI: 10.1007/978-1-0716-4051-7_20 |
0.47 |
|
| 2024 |
Vargas-Landin DB, Pflüger J, Nguyen TV, Lister R. Generation of Whole-Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis. Methods in Molecular Biology (Clifton, N.J.). 2842: 383-390. PMID 39012606 DOI: 10.1007/978-1-0716-4051-7_19 |
0.364 |
|
| 2023 |
Swain T, Pflueger C, Freytag S, Poppe D, Pflueger J, Nguyen TV, Li JK, Lister R. A modular dCas9-based recruitment platform for combinatorial epigenome editing. Nucleic Acids Research. PMID 38000387 DOI: 10.1093/nar/gkad1108 |
0.686 |
|
| 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, ... ... Lister R, et al. Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature. 620: 863-872. PMID 37587336 DOI: 10.1038/s41586-023-06424-7 |
0.758 |
|
| 2023 |
Nobori T, Oliva M, Lister R, Ecker JR. Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap. Nature Plants. PMID 37308583 DOI: 10.1038/s41477-023-01439-4 |
0.741 |
|
| 2023 |
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, ... ... Lister R, et al. Synthetic Epigenetic Reprogramming of Mesenchymal to Epithelial States Using the CRISPR/dCas9 Platform in Triple Negative Breast Cancer. Advanced Science (Weinheim, Baden-Wurttemberg, Germany). e2301802. PMID 37217832 DOI: 10.1002/advs.202301802 |
0.303 |
|
| 2023 |
Hermawaty D, Cahn J, Lister R, Considine MJ. Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds. Tree Physiology. PMID 36637421 DOI: 10.1093/treephys/tpac146 |
0.336 |
|
| 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, ... ... Lister R, et al. Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution. Cell. PMID 36318921 DOI: 10.1016/j.cell.2022.09.039 |
0.789 |
|
| 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. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biology. 23: 163. PMID 35883107 DOI: 10.1186/s13059-022-02728-5 |
0.833 |
|
| 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, ... ... Lister R, et al. Transcriptional signature in microglia associated with Aβ plaque phagocytosis. Nature Communications. 12: 3015. PMID 34021136 DOI: 10.1038/s41467-021-23111-1 |
0.692 |
|
| 2021 |
Nguyen TV, Lister R. Genomic Targeting of TET Activity for Targeted Demethylation Using CRISPR/Cas9. Methods in Molecular Biology (Clifton, N.J.). 2272: 181-194. PMID 34009614 DOI: 10.1007/978-1-0716-1294-1_10 |
0.427 |
|
| 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, ... ... Lister R, et al. The emergence of the brain non-CpG methylation system in vertebrates. Nature Ecology & Evolution. PMID 33462491 DOI: 10.1038/s41559-020-01371-2 |
0.821 |
|
| 2020 |
Geng FS, de la Calle-Mustienes E, Gómez-Skarmeta JL, Lister R, Bogdanovic O. Depletion of Foxk transcription factors causes genome-wide transcriptional misregulation and developmental arrest in zebrafish embryos. Micropublication Biology. 2020. PMID 33313487 DOI: 10.17912/micropub.biology.000341 |
0.682 |
|
| 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, ... ... Lister R, et al. Reprogramming roadmap reveals route to human induced trophoblast stem cells. Nature. PMID 32939092 DOI: 10.1038/S41586-020-2734-6 |
0.751 |
|
| 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, et al. Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri. Nature Communications. 11: 3676. PMID 32719321 DOI: 10.1038/S41467-020-17397-W |
0.413 |
|
| 2020 |
Denisenko E, Guo BB, Jones M, Hou R, de Kock L, Lassmann T, Poppe D, Clément O, Simmons RK, Lister R, Forrest ARR. Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows. Genome Biology. 21: 130. PMID 32487174 DOI: 10.1186/S13059-020-02048-6 |
0.324 |
|
| 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, ... ... Lister R, et al. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications. 11: 2631. PMID 32457347 DOI: 10.1038/S41467-020-16284-8 |
0.373 |
|
| 2019 |
Freytag S, Lister R. schex avoids overplotting for large single cell RNA-sequencing datasets. Bioinformatics (Oxford, England). PMID 31794001 DOI: 10.1093/Bioinformatics/Btz907 |
0.678 |
|
| 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. A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nature Neuroscience. PMID 31768052 DOI: 10.1038/S41593-019-0539-4 |
0.717 |
|
| 2019 |
de Mendoza A, Lister R, Bogdanovic O. Evolution of DNA methylome diversity in eukaryotes. Journal of Molecular Biology. PMID 31726061 DOI: 10.1016/J.Jmb.2019.11.003 |
0.746 |
|
| 2019 |
Pflueger C, Swain T, Lister R. Harnessing targeted DNA methylation and demethylation using dCas9. Essays in Biochemistry. PMID 31724704 DOI: 10.1042/Ebc20190029 |
0.528 |
|
| 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. Convergent evolution of a vertebrate-like methylome in a marine sponge. Nature Ecology & Evolution. 3: 1464-1473. PMID 31558833 DOI: 10.1038/S41559-019-0983-2 |
0.834 |
|
| 2019 |
Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E, Bogdanovic O. Retention of paternal DNA methylome in the developing zebrafish germline. Nature Communications. 10: 3054. PMID 31296860 DOI: 10.1038/S41467-019-10895-6 |
0.765 |
|
| 2019 |
de Mendoza A, Pflueger J, Lister R. Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family. Genome Research. PMID 31239280 DOI: 10.1101/Gr.243774.118 |
0.493 |
|
| 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, ... ... Lister R, et al. LINE-1 Evasion of Epigenetic Repression in Humans. Molecular Cell. PMID 31230816 DOI: 10.1016/J.Molcel.2019.05.024 |
0.365 |
|
| 2019 |
Srivastava A, Karpievitch YV, Eichten SR, Borevitz JO, Lister R. HOME: a histogram based machine learning approach for effective identification of differentially methylated regions. Bmc Bioinformatics. 20: 253. PMID 31096906 DOI: 10.1186/S12859-019-2845-Y |
0.826 |
|
| 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, ... ... Lister R, et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. PMID 30464347 DOI: 10.1038/S41586-018-0734-6 |
0.753 |
|
| 2018 |
Pflueger C, Tan D, Swain T, Nguyen TV, Pflueger J, Nefzger C, Polo JM, Ford E, Lister R. A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Research. PMID 29907613 DOI: 10.1101/Gr.233049.117 |
0.528 |
|
| 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. Author Correction: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nature Communications. 9: 1811. PMID 29717194 DOI: 10.1038/S41467-018-04260-2 |
0.678 |
|
| 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. Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nature Communications. 9: 1341. PMID 29632298 DOI: 10.1038/S41467-018-03724-9 |
0.805 |
|
| 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 |
0.836 |
|
| 2018 |
Vargas-Landin DB, Pflüger J, Lister R. Generation of Whole Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis. Methods in Molecular Biology (Clifton, N.J.). 1767: 291-298. PMID 29524142 DOI: 10.1007/978-1-4939-7774-1_16 |
0.471 |
|
| 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, et al. Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming. Cell Stem Cell. 21: 834-845.e6. PMID 29220667 DOI: 10.1016/J.Stem.2017.11.007 |
0.757 |
|
| 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, et al. Cell Type of Origin Dictates the Route to Pluripotency. Cell Reports. 21: 2649-2660. PMID 29212013 DOI: 10.1016/J.Celrep.2017.11.029 |
0.723 |
|
| 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. Regulatory remodeling in the allo-tetraploid frog Xenopus laevis. Genome Biology. 18: 198. PMID 29065907 DOI: 10.1186/S13059-017-1335-7 |
0.704 |
|
| 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, ... ... Lister R, et al. Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming. Nature Methods. PMID 28945704 DOI: 10.1038/Nmeth.4436 |
0.337 |
|
| 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 |
0.79 |
|
| 2017 |
Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R, Hawkins RD. Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases. Cell Reports. 20: 1448-1462. PMID 28793267 DOI: 10.1016/J.Celrep.2017.07.036 |
0.741 |
|
| 2017 |
Crisp PA, Ganguly D, Smith AB, Murray KD, Estavillo GM, Searle IR, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ. Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis. The Plant Cell. PMID 28705956 DOI: 10.1105/Tpc.16.00828 |
0.747 |
|
| 2017 |
Bogdanović O, Lister R. DNA methylation and the preservation of cell identity. Current Opinion in Genetics & Development. 46: 9-14. PMID 28651214 DOI: 10.1016/J.Gde.2017.06.007 |
0.777 |
|
| 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. Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA. Chemical Science. 8: 2923-2930. PMID 28451358 DOI: 10.1039/C7Sc00097A |
0.31 |
|
| 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 |
0.397 |
|
| 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 |
0.792 |
|
| 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 |
0.626 |
|
| 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, ... ... Lister R, et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 538: 336-343. PMID 27762356 DOI: 10.1038/Nature19840 |
0.699 |
|
| 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 |
0.84 |
|
| 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 |
0.302 |
|
| 2016 |
Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJ. Erratum: Embryonic transcription is controlled by maternally defined chromatin state. Nature Communications. 7: 12208. PMID 27378471 DOI: 10.1038/ncomms12208 |
0.653 |
|
| 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 |
0.835 |
|
| 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 |
0.788 |
|
| 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 |
0.797 |
|
| 2016 |
Stuart T, Eichten SR, Cahn J, Karpievitch YV, Borevitz JO, Lister R. Author response: Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation Elife. DOI: 10.7554/Elife.20777.056 |
0.316 |
|
| 2015 |
Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJ. Embryonic transcription is controlled by maternally defined chromatin state. Nature Communications. 6: 10148. PMID 26679111 DOI: 10.1038/Ncomms10148 |
0.707 |
|
| 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 |
0.777 |
|
| 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 |
0.517 |
|
| 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 |
0.644 |
|
| 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 |
0.754 |
|
| 2015 |
Bogdanović O, Lister R. Of Mice and Man: Differential DNMT Dependence in Mammalian ESCs. Cell Stem Cell. 16: 459-60. PMID 25957900 DOI: 10.1016/J.Stem.2015.04.009 |
0.695 |
|
| 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 |
0.625 |
|
| 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 |
0.806 |
|
| 2015 |
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. Author response: Epigenomic landscapes of retinal rods and cones Elife. DOI: 10.7554/Elife.11613.056 |
0.67 |
|
| 2015 |
Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R. Author response: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements Elife. DOI: 10.7554/Elife.09343.035 |
0.609 |
|
| 2015 |
Lister R, Mukamel EA. Turning over DNA methylation in the mind Frontiers in Neuroscience. 9. DOI: 10.3389/fnins.2015.00252 |
0.388 |
|
| 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 |
0.492 |
|
| 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 |
0.705 |
|
| 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 |
0.403 |
|
| 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 |
0.652 |
|
| 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 |
0.774 |
|
| 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 |
0.705 |
|
| 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 |
0.462 |
|
| 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 |
0.647 |
|
| 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 |
0.68 |
|
| 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 |
0.731 |
|
| 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 |
0.826 |
|
| 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 |
0.777 |
|
| 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 |
0.68 |
|
| 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 |
0.837 |
|
| 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 |
0.802 |
|
| 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 |
0.805 |
|
| 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 |
0.849 |
|
| 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 |
0.642 |
|
| 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 |
0.734 |
|
| 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 |
0.337 |
|
| 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 |
0.756 |
|
| 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 |
0.839 |
|
| 2008 |
Ecker JR, Lister R, O'Malley RC, Tonti-Filippini J, Berry CC, Millar AH. Genome meets epigenome: Sequencing and analysis of the DNA methylome Developmental Biology. 319: 462. DOI: 10.1016/J.Ydbio.2008.05.004 |
0.762 |
|
| 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 |
0.38 |
|
| 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 DOI: 10.1080/09687860500041247 |
0.316 |
|
| 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 |
0.333 |
|
| 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 |
0.306 |
|
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