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Items: 1 to 50 of 269

1.

Retention of paternal DNA methylome in the developing zebrafish germline.

Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E, Bogdanovic O.

Nat Commun. 2019 Jul 11;10(1):3054. doi: 10.1038/s41467-019-10895-6.

2.

Capture of a functionally active methyl-CpG binding domain by an arthropod retrotransposon family.

de Mendoza A, Pflueger J, Lister R.

Genome Res. 2019 Jun 25. pii: gr.243774.118. doi: 10.1101/gr.243774.118. [Epub ahead of print]

PMID:
31239280
3.

LINE-1 Evasion of Epigenetic Repression in Humans.

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.

Mol Cell. 2019 Jun 20. pii: S1097-2765(19)30396-X. doi: 10.1016/j.molcel.2019.05.024. [Epub ahead of print]

PMID:
31230816
4.

HOME: a histogram based machine learning approach for effective identification of differentially methylated regions.

Srivastava A, Karpievitch YV, Eichten SR, Borevitz JO, Lister R.

BMC Bioinformatics. 2019 May 16;20(1):253. doi: 10.1186/s12859-019-2845-y.

5.

The Dunn Worry Questionnaire and the Paranoia Worries Questionnaire: new assessments of worry.

Freeman D, Bird JC, Loe BS, Kingdon D, Startup H, Clark DM, Ehlers A, Černis E, Wingham G, Evans N, Lister R, Pugh K, Cordwell J, Dunn G.

Psychol Med. 2019 Apr 5:1-10. doi: 10.1017/S0033291719000588. [Epub ahead of print]

PMID:
30947766
6.
7.

Amphioxus functional genomics and the origins of vertebrate gene regulation.

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.

Nature. 2018 Dec;564(7734):64-70. doi: 10.1038/s41586-018-0734-6. Epub 2018 Nov 21.

8.

A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs.

Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J, Nefzger C, Polo JM, Ford E, Lister R.

Genome Res. 2018 Aug;28(8):1193-1206. doi: 10.1101/gr.233049.117. Epub 2018 Jun 15.

9.

Author Correction: Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.

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.

Nat Commun. 2018 May 1;9(1):1811. doi: 10.1038/s41467-018-04260-2.

10.

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons.

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.

Nat Commun. 2018 Apr 9;9(1):1341. doi: 10.1038/s41467-018-03724-9. Erratum in: Nat Commun. 2018 May 1;9(1):1811.

11.

Approaches for the Analysis and Interpretation of Whole Genome Bisulfite Sequencing Data.

Stuart T, Buckberry S, Lister R.

Methods Mol Biol. 2018;1767:299-310. doi: 10.1007/978-1-4939-7774-1_17.

PMID:
29524143
12.

Generation of Whole Genome Bisulfite Sequencing Libraries for Comprehensive DNA Methylome Analysis.

Vargas-Landin DB, Pflüger J, Lister R.

Methods Mol Biol. 2018;1767:291-298. doi: 10.1007/978-1-4939-7774-1_16.

PMID:
29524142
13.

Evaluation of a method for measuring the radioprotective metabolite WR-1065 in plasma using chemical derivatization combined with UHPLC-MS/MS.

Simon ES, Reyna D, Lister RJ, Harteg C, Lipka E.

J Chromatogr B Analyt Technol Biomed Life Sci. 2018 Mar 30;1080:82-89. doi: 10.1016/j.jchromb.2018.02.030. Epub 2018 Feb 20.

PMID:
29482122
14.

Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming.

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.

Cell Stem Cell. 2017 Dec 7;21(6):834-845.e6. doi: 10.1016/j.stem.2017.11.007.

15.

Cell Type of Origin Dictates the Route to Pluripotency.

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.

Cell Rep. 2017 Dec 5;21(10):2649-2660. doi: 10.1016/j.celrep.2017.11.029.

16.

The effects of cannabidiol on persecutory ideation and anxiety in a high trait paranoid group.

Hundal H, Lister R, Evans N, Antley A, Englund A, Murray RM, Freeman D, Morrison PD.

J Psychopharmacol. 2018 Mar;32(3):276-282. doi: 10.1177/0269881117737400. Epub 2017 Oct 31.

PMID:
29086614
17.

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.

Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I, Bogdanovic O, Gibeaux R, Heald R, Lister R, Huynen MA, van Heeringen SJ, Veenstra GJC.

Genome Biol. 2017 Oct 24;18(1):198. doi: 10.1186/s13059-017-1335-7.

18.

Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming.

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.

Nat Methods. 2017 Nov;14(11):1055-1062. doi: 10.1038/nmeth.4436. Epub 2017 Sep 25.

PMID:
28945704
19.

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination.

Narsai R, Gouil Q, Secco D, Srivastava A, Karpievitch YV, Liew LC, Lister R, Lewsey MG, Whelan J.

Genome Biol. 2017 Sep 15;18(1):172. doi: 10.1186/s13059-017-1302-3.

20.

Epigenomic Landscapes of hESC-Derived Neural Rosettes: Modeling Neural Tube Formation and Diseases.

Valensisi C, Andrus C, Buckberry S, Doni Jayavelu N, Lund RJ, Lister R, Hawkins RD.

Cell Rep. 2017 Aug 8;20(6):1448-1462. doi: 10.1016/j.celrep.2017.07.036.

21.

Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis.

Crisp PA, Ganguly DR, Smith AB, Murray KD, Estavillo GM, Searle I, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ.

Plant Cell. 2017 Aug;29(8):1836-1863. doi: 10.1105/tpc.16.00828. Epub 2017 Jul 13.

22.

DNA methylation and the preservation of cell identity.

Bogdanović O, Lister R.

Curr Opin Genet Dev. 2017 Oct;46:9-14. doi: 10.1016/j.gde.2017.06.007. Epub 2017 Jun 24. Review.

PMID:
28651214
23.

Synthetically controlling dendrimer flexibility improves delivery of large plasmid DNA.

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.

Chem Sci. 2017 Apr 1;8(4):2923-2930. doi: 10.1039/c7sc00097a. Epub 2017 Jan 27.

24.

Nutrient stress-induced chromatin changes in plants.

Secco D, Whelan J, Rouached H, Lister R.

Curr Opin Plant Biol. 2017 Oct;39:1-7. doi: 10.1016/j.pbi.2017.04.001. Epub 2017 Apr 22. Review.

25.

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation.

Stuart T, Eichten SR, Cahn J, Karpievitch YV, Borevitz JO, Lister R.

Elife. 2016 Dec 2;5. pii: e20777. doi: 10.7554/eLife.20777.

26.

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.

Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J.

Plant J. 2017 Feb;89(4):805-824. doi: 10.1111/tpj.13418. Epub 2017 Feb 11.

27.

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity.

Eichten SR, Stuart T, Srivastava A, Lister R, Borevitz JO.

Genome Res. 2016 Nov;26(11):1520-1531. Epub 2016 Sep 9.

28.

Retrograde signalling caused by heritable mitochondrial dysfunction is partially mediated by ANAC017 and improves plant performance.

Van Aken O, Ford E, Lister R, Huang S, Millar AH.

Plant J. 2016 Nov;88(4):542-558. doi: 10.1111/tpj.13276. Epub 2016 Oct 17.

29.

Genome evolution in the allotetraploid frog Xenopus laevis.

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.

Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.

30.

Erratum: Embryonic transcription is controlled by maternally defined chromatin state.

Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJ.

Nat Commun. 2016 Jul 5;7:12208. doi: 10.1038/ncomms12208. No abstract available.

31.

Unique cell-type-specific patterns of DNA methylation in the root meristem.

Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR.

Nat Plants. 2016 Apr 29;2(5):16058. doi: 10.1038/nplants.2016.58.

32.

Targeting Recovery in Persistent Persecutory Delusions: A Proof of Principle Study of a New Translational Psychological Treatment (the Feeling Safe Programme).

Freeman D, Bradley J, Waite F, Sheaves B, DeWeever N, Bourke E, McInerney J, Evans N, Černis E, Lister R, Garety P, Dunn G.

Behav Cogn Psychother. 2016 Sep;44(5):539-52. doi: 10.1017/S1352465816000060. Epub 2016 Apr 5.

33.

Epigenomic landscapes of retinal rods and cones.

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.

Elife. 2016 Mar 7;5:e11613. doi: 10.7554/eLife.11613.

34.

Active DNA demethylation at enhancers during the vertebrate phylotypic period.

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.

Nat Genet. 2016 Apr;48(4):417-26. doi: 10.1038/ng.3522. Epub 2016 Feb 29.

35.

Embryonic transcription is controlled by maternally defined chromatin state.

Hontelez S, van Kruijsbergen I, Georgiou G, van Heeringen SJ, Bogdanovic O, Lister R, Veenstra GJC.

Nat Commun. 2015 Dec 18;6:10148. doi: 10.1038/ncomms10148. Erratum in: Nat Commun. 2016 Jul 05;7:12208.

36.

Genetic moderation of the effects of cannabis: catechol-O-methyltransferase (COMT) affects the impact of Δ9-tetrahydrocannabinol (THC) on working memory performance but not on the occurrence of psychotic experiences.

Tunbridge EM, Dunn G, Murray RM, Evans N, Lister R, Stumpenhorst K, Harrison PJ, Morrison PD, Freeman D.

J Psychopharmacol. 2015 Nov;29(11):1146-51. doi: 10.1177/0269881115609073. Epub 2015 Oct 13.

PMID:
26464454
37.

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.

Kishore K, de Pretis S, Lister R, Morelli MJ, Bianchi V, Amati B, Ecker JR, Pelizzola M.

BMC Bioinformatics. 2015 Sep 29;16:313. doi: 10.1186/s12859-015-0742-6.

38.

Efficacy of cognitive behavioural therapy for sleep improvement in patients with persistent delusions and hallucinations (BEST): a prospective, assessor-blind, randomised controlled pilot trial.

Freeman D, Waite F, Startup H, Myers E, Lister R, McInerney J, Harvey AG, Geddes J, Zaiwalla Z, Luengo-Fernandez R, Foster R, Clifton L, Yu LM.

Lancet Psychiatry. 2015 Nov;2(11):975-83. doi: 10.1016/S2215-0366(15)00314-4. Epub 2015 Sep 9.

39.

The Perseverative Thinking Questionnaire in Patients with Persecutory Delusions.

Černis E, Dunn G, Startup H, Kingdon D, Wingham G, Evans N, Lister R, Pugh K, Cordwell J, Mander H, Freeman D.

Behav Cogn Psychother. 2016 Jul;44(4):472-81. doi: 10.1017/S1352465815000533. Epub 2015 Aug 24.

PMID:
26301705
40.

The patient experience of sleep problems and their treatment in the context of current delusions and hallucinations.

Waite F, Evans N, Myers E, Startup H, Lister R, Harvey AG, Freeman D.

Psychol Psychother. 2016 Jun;89(2):181-93. doi: 10.1111/papt.12073. Epub 2015 Aug 18.

41.

Turning over DNA methylation in the mind.

Lister R, Mukamel EA.

Front Neurosci. 2015 Jul 30;9:252. doi: 10.3389/fnins.2015.00252. eCollection 2015. Review.

42.

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.

Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R.

Elife. 2015 Jul 21;4. doi: 10.7554/eLife.09343.

43.

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

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.

Neuron. 2015 Jun 17;86(6):1369-84. doi: 10.1016/j.neuron.2015.05.018.

44.

Of Mice and Man: Differential DNMT Dependence in Mammalian ESCs.

Bogdanović O, Lister R.

Cell Stem Cell. 2015 May 7;16(5):459-60. doi: 10.1016/j.stem.2015.04.009.

45.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium, 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.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

46.

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.

Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR.

Nat Protoc. 2015 Mar;10(3):475-83. doi: 10.1038/nprot.2014.114. Epub 2015 Feb 18.

47.

An early Phase II randomised controlled trial testing the effect on persecutory delusions of using CBT to reduce negative cognitions about the self: the potential benefits of enhancing self confidence.

Freeman D, Pugh K, Dunn G, Evans N, Sheaves B, Waite F, Cernis E, Lister R, Fowler D.

Schizophr Res. 2014 Dec;160(1-3):186-92. doi: 10.1016/j.schres.2014.10.038. Epub 2014 Nov 11.

48.

Self-Confidence and Paranoia: An Experimental Study Using an Immersive Virtual Reality Social Situation.

Atherton S, Antley A, Evans N, Cernis E, Lister R, Dunn G, Slater M, Freeman D.

Behav Cogn Psychother. 2016 Jan;44(1):56-64. doi: 10.1017/S1352465814000496. Epub 2014 Nov 11.

PMID:
25384608
49.

The effect of paranoia on the judging of harmful events.

Freeman D, Evans N, Černis E, Lister R, Dunn G.

Cogn Neuropsychiatry. 2015;20(2):122-7. doi: 10.1080/13546805.2014.976307. Epub 2014 Oct 27.

PMID:
25345664
50.

Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways.

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 Res. 2014 Oct;24(10):1613-23. doi: 10.1101/gr.172015.114. Epub 2014 Aug 28.

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