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Items: 1 to 50 of 255

1.

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.

Linker SM, Urban L, Clark SJ, Chhatriwala M, Amatya S, McCarthy DJ, Ebersberger I, Vallier L, Reik W, Stegle O, Bonder MJ.

Genome Biol. 2019 Feb 11;20(1):30. doi: 10.1186/s13059-019-1644-0.

2.

Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program.

Eckersley-Maslin M, Alda-Catalinas C, Blotenburg M, Kreibich E, Krueger C, Reik W.

Genes Dev. 2019 Feb 1;33(3-4):194-208. doi: 10.1101/gad.321174.118. Epub 2019 Jan 28.

3.

Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.

Messmer T, von Meyenn F, Savino A, Santos F, Mohammed H, Lun ATL, Marioni JC, Reik W.

Cell Rep. 2019 Jan 22;26(4):815-824.e4. doi: 10.1016/j.celrep.2018.12.099.

4.

The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome.

Gdula MR, Nesterova TB, Pintacuda G, Godwin J, Zhan Y, Ozadam H, McClellan M, Moralli D, Krueger F, Green CM, Reik W, Kriaucionis S, Heard E, Dekker J, Brockdorff N.

Nat Commun. 2019 Jan 3;10(1):30. doi: 10.1038/s41467-018-07907-2.

5.

Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity.

Hahn O, Stubbs TM, Reik W, Grönke S, Beyer A, Partridge L.

PLoS Genet. 2018 Nov 21;14(11):e1007766. doi: 10.1371/journal.pgen.1007766. eCollection 2018 Nov.

6.

Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development.

Boroviak T, Stirparo GG, Dietmann S, Hernando-Herraez I, Mohammed H, Reik W, Smith A, Sasaki E, Nichols J, Bertone P.

Development. 2018 Nov 9;145(21). pii: dev167833. doi: 10.1242/dev.167833.

7.

5-Formylcytosine organizes nucleosomes and forms Schiff base interactions with histones in mouse embryonic stem cells.

Raiber EA, Portella G, Martínez Cuesta S, Hardisty R, Murat P, Li Z, Iurlaro M, Dean W, Spindel J, Beraldi D, Liu Z, Dawson MA, Reik W, Balasubramanian S.

Nat Chem. 2018 Dec;10(12):1258-1266. doi: 10.1038/s41557-018-0149-x. Epub 2018 Oct 22.

PMID:
30349137
8.

Transgenerational transmission of hedonic behaviors and metabolic phenotypes induced by maternal overnutrition.

Sarker G, Berrens R, von Arx J, Pelczar P, Reik W, Wolfrum C, Peleg-Raibstein D.

Transl Psychiatry. 2018 Oct 12;8(1):195. doi: 10.1038/s41398-018-0243-2.

9.

Publisher Correction: Cold-induced epigenetic programming of the sperm enhances brown adipose tissue activity in the offspring.

Sun W, Dong H, Becker AS, Dapito DH, Modica S, Grandl G, Opitz L, Efthymiou V, Straub LG, Sarker G, Balaz M, Balazova L, Perdikari A, Kiehlmann E, Bacanovic S, Zellweger C, Peleg-Raibstein D, Pelczar P, Reik W, Burger IA, von Meyenn F, Wolfrum C.

Nat Med. 2018 Nov;24(11):1777. doi: 10.1038/s41591-018-0163-y.

PMID:
30087436
10.

Author Correction: Cold-induced epigenetic programming of the sperm enhances brown adipose tissue activity in the offspring.

Sun W, Dong H, Becker AS, Dapito DH, Modica S, Grandl G, Opitz L, Efthymiou V, Straub LG, Sarker G, Balaz M, Balazova L, Perdikari A, Kiehlmann E, Bacanovic S, Zellweger C, Peleg-Raibstein D, Pelczar P, Reik W, Burger IA, von Meyenn F, Wolfrum C.

Nat Med. 2018 Nov;24(11):1776. doi: 10.1038/s41591-018-0162-z.

PMID:
30087435
11.

Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency.

Rulands S, Lee HJ, Clark SJ, Angermueller C, Smallwood SA, Krueger F, Mohammed H, Dean W, Nichols J, Rugg-Gunn P, Kelsey G, Stegle O, Simons BD, Reik W.

Cell Syst. 2018 Jul 25;7(1):63-76.e12. doi: 10.1016/j.cels.2018.06.012.

12.

Cold-induced epigenetic programming of the sperm enhances brown adipose tissue activity in the offspring.

Sun W, Dong H, Becker AS, Dapito DH, Modica S, Grandl G, Opitz L, Efthymiou V, Straub LG, Sarker G, Balaz M, Balazova L, Perdikari A, Kiehlmann E, Bacanovic S, Zellweger C, Peleg-Raibstein D, Pelczar P, Reik W, Burger IA, von Meyenn F, Wolfrum C.

Nat Med. 2018 Sep;24(9):1372-1383. doi: 10.1038/s41591-018-0102-y. Epub 2018 Jul 9. Erratum in: Nat Med. 2018 Aug 7;:. Nat Med. 2018 Aug 7;:.

PMID:
29988127
13.

Defective germline reprogramming rewires the spermatogonial transcriptome.

Vasiliauskaitė L, Berrens RV, Ivanova I, Carrieri C, Reik W, Enright AJ, O'Carroll D.

Nat Struct Mol Biol. 2018 May;25(5):394-404. doi: 10.1038/s41594-018-0058-0. Epub 2018 Apr 30.

14.

Dynamics of the epigenetic landscape during the maternal-to-zygotic transition.

Eckersley-Maslin MA, Alda-Catalinas C, Reik W.

Nat Rev Mol Cell Biol. 2018 Jul;19(7):436-450. doi: 10.1038/s41580-018-0008-z. Review.

PMID:
29686419
15.

Correction: Epigenetic resetting of human pluripotency (doi:10.1242/dev.146811).

Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A.

Development. 2018 Apr 18;145(8). pii: dev166397. doi: 10.1242/dev.166397. No abstract available.

16.

Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

Olova N, Krueger F, Andrews S, Oxley D, Berrens RV, Branco MR, Reik W.

Genome Biol. 2018 Mar 15;19(1):33. doi: 10.1186/s13059-018-1408-2.

17.

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.

Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W.

Nat Commun. 2018 Feb 22;9(1):781. doi: 10.1038/s41467-018-03149-4.

18.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

19.

Coupling shRNA screens with single-cell RNA-seq identifies a dual role for mTOR in reprogramming-induced senescence.

Aarts M, Georgilis A, Beniazza M, Beolchi P, Banito A, Carroll T, Kulisic M, Kaemena DF, Dharmalingam G, Martin N, Reik W, Zuber J, Kaji K, Chandra T, Gil J.

Genes Dev. 2017 Oct 15;31(20):2085-2098. doi: 10.1101/gad.297796.117. Epub 2017 Nov 14.

20.

An endosiRNA-Based Repression Mechanism Counteracts Transposon Activation during Global DNA Demethylation in Embryonic Stem Cells.

Berrens RV, Andrews S, Spensberger D, Santos F, Dean W, Gould P, Sharif J, Olova N, Chandra T, Koseki H, von Meyenn F, Reik W.

Cell Stem Cell. 2017 Nov 2;21(5):694-703.e7. doi: 10.1016/j.stem.2017.10.004.

21.

cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.

Martin-Herranz DE, Ribeiro AJM, Krueger F, Thornton JM, Reik W, Stubbs TM.

Nucleic Acids Res. 2017 Nov 16;45(20):11559-11569. doi: 10.1093/nar/gkx814.

22.

Establishment of mouse expanded potential stem cells.

Yang J, Ryan DJ, Wang W, Tsang JC, Lan G, Masaki H, Gao X, Antunes L, Yu Y, Zhu Z, Wang J, Kolodziejczyk AA, Campos LS, Wang C, Yang F, Zhong Z, Fu B, Eckersley-Maslin MA, Woods M, Tanaka Y, Chen X, Wilkinson AC, Bussell J, White J, Ramirez-Solis R, Reik W, Göttgens B, Teichmann SA, Tam PPL, Nakauchi H, Zou X, Lu L, Liu P.

Nature. 2017 Oct 19;550(7676):393-397. doi: 10.1038/nature24052. Epub 2017 Oct 11.

23.

Single-cell epigenomics: Recording the past and predicting the future.

Kelsey G, Stegle O, Reik W.

Science. 2017 Oct 6;358(6359):69-75. doi: 10.1126/science.aan6826. Review.

PMID:
28983045
24.

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.

Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W.

Cell Rep. 2017 Aug 1;20(5):1215-1228. doi: 10.1016/j.celrep.2017.07.009.

25.

Epigenetic resetting of human pluripotency.

Guo G, von Meyenn F, Rostovskaya M, Clarke J, Dietmann S, Baker D, Sahakyan A, Myers S, Bertone P, Reik W, Plath K, Smith A.

Development. 2017 Aug 1;144(15):2748-2763. doi: 10.1242/dev.146811. Erratum in: Development. 2018 Apr 18;145(8):.

26.

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment.

Kirschner K, Chandra T, Kiselev V, Flores-Santa Cruz D, Macaulay IC, Park HJ, Li J, Kent DG, Kumar R, Pask DC, Hamilton TL, Hemberg M, Reik W, Green AR.

Cell Rep. 2017 May 23;19(8):1503-1511. doi: 10.1016/j.celrep.2017.04.074.

27.

A MILI-independent piRNA biogenesis pathway empowers partial germline reprogramming.

Vasiliauskaitė L, Vitsios D, Berrens RV, Carrieri C, Reik W, Enright AJ, O'Carroll D.

Nat Struct Mol Biol. 2017 Jul;24(7):604-606. doi: 10.1038/nsmb.3413. Epub 2017 May 22.

28.

Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.

Angermueller C, Lee HJ, Reik W, Stegle O.

Genome Biol. 2017 May 12;18(1):90. doi: 10.1186/s13059-017-1233-z. No abstract available.

29.

Multi-tissue DNA methylation age predictor in mouse.

Stubbs TM, Bonder MJ, Stark AK, Krueger F; BI Ageing Clock Team, von Meyenn F, Stegle O, Reik W.

Genome Biol. 2017 Apr 11;18(1):68. doi: 10.1186/s13059-017-1203-5.

30.

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.

Angermueller C, Lee HJ, Reik W, Stegle O.

Genome Biol. 2017 Apr 11;18(1):67. doi: 10.1186/s13059-017-1189-z. Erratum in: Genome Biol. 2017 May 12;18(1):90.

31.

Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism.

Hahn O, Grönke S, Stubbs TM, Ficz G, Hendrich O, Krueger F, Andrews S, Zhang Q, Wakelam MJ, Beyer A, Reik W, Partridge L.

Genome Biol. 2017 Mar 28;18(1):56. doi: 10.1186/s13059-017-1187-1.

32.

SC3: consensus clustering of single-cell RNA-seq data.

Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M.

Nat Methods. 2017 May;14(5):483-486. doi: 10.1038/nmeth.4236. Epub 2017 Mar 27.

33.

DNA methylation homeostasis in human and mouse development.

Iurlaro M, von Meyenn F, Reik W.

Curr Opin Genet Dev. 2017 Apr;43:101-109. doi: 10.1016/j.gde.2017.02.003. Epub 2017 Mar 2. Review.

PMID:
28260631
34.

The Ageing Brain: Effects on DNA Repair and DNA Methylation in Mice.

Langie SA, Cameron KM, Ficz G, Oxley D, Tomaszewski B, Gorniak JP, Maas LM, Godschalk RW, van Schooten FJ, Reik W, von Zglinicki T, Mathers JC.

Genes (Basel). 2017 Feb 17;8(2). pii: E75. doi: 10.3390/genes8020075.

35.

Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq).

Clark SJ, Smallwood SA, Lee HJ, Krueger F, Reik W, Kelsey G.

Nat Protoc. 2017 Mar;12(3):534-547. doi: 10.1038/nprot.2016.187. Epub 2017 Feb 9.

PMID:
28182018
36.

Tracking the embryonic stem cell transition from ground state pluripotency.

Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS, Nichols J, Reik W, Bertone P, Smith A.

Development. 2017 Apr 1;144(7):1221-1234. doi: 10.1242/dev.142711. Epub 2017 Feb 7.

37.

Gender Differences in Global but Not Targeted Demethylation in iPSC Reprogramming.

Milagre I, Stubbs TM, King MR, Spindel J, Santos F, Krueger F, Bachman M, Segonds-Pichon A, Balasubramanian S, Andrews SR, Dean W, Reik W.

Cell Rep. 2017 Jan 31;18(5):1079-1089. doi: 10.1016/j.celrep.2017.01.008.

38.

A Hox-Embedded Long Noncoding RNA: Is It All Hot Air?

Selleri L, Bartolomei MS, Bickmore WA, He L, Stubbs L, Reik W, Barsh GS.

PLoS Genet. 2016 Dec 15;12(12):e1006485. doi: 10.1371/journal.pgen.1006485. eCollection 2016 Dec. No abstract available.

39.

Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase.

Stepper P, Kungulovski G, Jurkowska RZ, Chandra T, Krueger F, Reinhardt R, Reik W, Jeltsch A, Jurkowski TP.

Nucleic Acids Res. 2017 Feb 28;45(4):1703-1713. doi: 10.1093/nar/gkw1112.

40.

The H3K9 dimethyltransferases EHMT1/2 protect against pathological cardiac hypertrophy.

Thienpont B, Aronsen JM, Robinson EL, Okkenhaug H, Loche E, Ferrini A, Brien P, Alkass K, Tomasso A, Agrawal A, Bergmann O, Sjaastad I, Reik W, Roderick HL.

J Clin Invest. 2017 Jan 3;127(1):335-348. doi: 10.1172/JCI88353. Epub 2016 Nov 28.

41.

Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms.

Hore TA, von Meyenn F, Ravichandran M, Bachman M, Ficz G, Oxley D, Santos F, Balasubramanian S, Jurkowski TP, Reik W.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12202-12207. Epub 2016 Oct 11.

42.

Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification.

von Meyenn F, Berrens RV, Andrews S, Santos F, Collier AJ, Krueger F, Osorno R, Dean W, Rugg-Gunn PJ, Reik W.

Dev Cell. 2016 Oct 10;39(1):104-115. doi: 10.1016/j.devcel.2016.09.015.

43.

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs.

Eckersley-Maslin MA, Svensson V, Krueger C, Stubbs TM, Giehr P, Krueger F, Miragaia RJ, Kyriakopoulos C, Berrens RV, Milagre I, Walter J, Teichmann SA, Reik W.

Cell Rep. 2016 Sep 27;17(1):179-192. doi: 10.1016/j.celrep.2016.08.087.

44.

In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine.

Iurlaro M, McInroy GR, Burgess HE, Dean W, Raiber EA, Bachman M, Beraldi D, Balasubramanian S, Reik W.

Genome Biol. 2016 Jun 29;17(1):141. doi: 10.1186/s13059-016-1001-5.

45.

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells.

von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, Reik W, Stunnenberg HG.

Mol Cell. 2016 Jun 16;62(6):983. doi: 10.1016/j.molcel.2016.06.005. Epub 2016 Jun 16. No abstract available.

46.

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells.

von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, Reik W, Stunnenberg HG.

Mol Cell. 2016 Jun 16;62(6):848-861. doi: 10.1016/j.molcel.2016.04.025. Epub 2016 May 26. Erratum in: Mol Cell. 2016 Jun 16;62(6):983.

47.

Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity.

Clark SJ, Lee HJ, Smallwood SA, Kelsey G, Reik W.

Genome Biol. 2016 Apr 18;17:72. doi: 10.1186/s13059-016-0944-x. Review.

48.

Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass.

Guo G, von Meyenn F, Santos F, Chen Y, Reik W, Bertone P, Smith A, Nichols J.

Stem Cell Reports. 2016 Apr 12;6(4):437-446. doi: 10.1016/j.stemcr.2016.02.005. Epub 2016 Mar 3.

49.

Maternal DNA Methylation Regulates Early Trophoblast Development.

Branco MR, King M, Perez-Garcia V, Bogutz AB, Caley M, Fineberg E, Lefebvre L, Cook SJ, Dean W, Hemberger M, Reik W.

Dev Cell. 2016 Jan 25;36(2):152-63. doi: 10.1016/j.devcel.2015.12.027.

50.

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.

Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W.

Nat Methods. 2016 Mar;13(3):229-232. doi: 10.1038/nmeth.3728. Epub 2016 Jan 11.

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