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Items: 1 to 50 of 253

1.

OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development.

Hrit J, Goodrich L, Li C, Wang BA, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, Ecker JR, Goll M, Panning B.

Elife. 2018 Oct 16;7. pii: e34870. doi: 10.7554/eLife.34870.

2.

Dynamic DNA methylation: In the right place at the right time.

Luo C, Hajkova P, Ecker JR.

Science. 2018 Sep 28;361(6409):1336-1340. doi: 10.1126/science.aat6806. Review.

PMID:
30262495
3.

Robust single-cell DNA methylome profiling with snmC-seq2.

Luo C, Rivkin A, Zhou J, Sandoval JP, Kurihara L, Lucero J, Castanon R, Nery JR, Pinto-Duarte A, Bui B, Fitzpatrick C, O'Connor C, Ruga S, Van Eden ME, Davis DA, Mash DC, Behrens MM, Ecker JR.

Nat Commun. 2018 Sep 20;9(1):3824. doi: 10.1038/s41467-018-06355-2.

4.

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells.

Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J.

Elife. 2018 Sep 6;7. pii: e36187. doi: 10.7554/eLife.36187.

5.

Profiling Interactome Networks with the HaloTag-NAPPA In Situ Protein Array.

Yazaki J, Galli M, Kim AY, Ecker JR.

Curr Protoc Plant Biol. 2018 Sep;3(3):e20071. doi: 10.1002/cppb.20071. Epub 2018 Aug 14.

PMID:
30106517
6.

Author Correction: A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development.

Xie M, Chen H, Huang L, O'Neil RC, Shokhirev MN, Ecker JR.

Nat Commun. 2018 May 22;9(1):2075. doi: 10.1038/s41467-018-04514-z.

7.

A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development.

Xie M, Chen H, Huang L, O'Neil RC, Shokhirev MN, Ecker JR.

Nat Commun. 2018 Apr 23;9(1):1604. doi: 10.1038/s41467-018-03921-6. Erratum in: Nat Commun. 2018 May 22;9(1):2075.

8.

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell.

Michael TP, Jupe F, Bemm F, Motley ST, Sandoval JP, Lanz C, Loudet O, Weigel D, Ecker JR.

Nat Commun. 2018 Feb 7;9(1):541. doi: 10.1038/s41467-018-03016-2.

9.

Challenges and recommendations for epigenomics in precision health.

Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, Palmer M, Snyder MP, Tung J, Urban A, Vidal M, Wong W.

Nat Biotechnol. 2017 Dec 8;35(12):1128-1132. doi: 10.1038/nbt.4030. No abstract available.

10.

Piecing together cis-regulatory networks: insights from epigenomics studies in plants.

Huang SC, Ecker JR.

Wiley Interdiscip Rev Syst Biol Med. 2018 May;10(3):e1411. doi: 10.1002/wsbm.1411. Epub 2017 Nov 30. Review.

PMID:
29194997
11.

The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas.

Ecker JR, Geschwind DH, Kriegstein AR, Ngai J, Osten P, Polioudakis D, Regev A, Sestan N, Wickersham IR, Zeng H.

Neuron. 2017 Nov 1;96(3):542-557. doi: 10.1016/j.neuron.2017.10.007. Review.

12.

Dynamic DNA methylation reconfiguration during seed development and germination.

Kawakatsu T, Nery JR, Castanon R, Ecker JR.

Genome Biol. 2017 Sep 15;18(1):171. doi: 10.1186/s13059-017-1251-x.

13.

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.

Luo C, Keown CL, Kurihara L, Zhou J, He Y, Li J, Castanon R, Lucero J, Nery JR, Sandoval JP, Bui B, Sejnowski TJ, Harkins TT, Mukamel EA, Behrens MM, Ecker JR.

Science. 2017 Aug 11;357(6351):600-604. doi: 10.1126/science.aan3351.

14.

Mapping genome-wide transcription-factor binding sites using DAP-seq.

Bartlett A, O'Malley RC, Huang SC, Galli M, Nery JR, Gallavotti A, Ecker JR.

Nat Protoc. 2017 Aug;12(8):1659-1672. doi: 10.1038/nprot.2017.055. Epub 2017 Jul 20.

15.

CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.

Trigg SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang ZZ, Galli M, Ecker JR.

Nat Methods. 2017 Aug;14(8):819-825. doi: 10.1038/nmeth.4343. Epub 2017 Jun 26.

16.

Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection.

Hsia MM, O'Malley R, Cartwright A, Nieu R, Gordon SP, Kelly S, Williams TG, Wood DF, Zhao Y, Bragg J, Jordan M, Pauly M, Ecker JR, Gu Y, Vogel JP.

Plant J. 2017 Aug;91(3):361-370. doi: 10.1111/tpj.13582. Epub 2017 Jun 21.

17.

Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain.

Keown CL, Berletch JB, Castanon R, Nery JR, Disteche CM, Ecker JR, Mukamel EA.

Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):E2882-E2890. doi: 10.1073/pnas.1611905114. Epub 2017 Mar 20.

18.

Improved regulatory element prediction based on tissue-specific local epigenomic signatures.

He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR.

Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):E1633-E1640. doi: 10.1073/pnas.1618353114. Epub 2017 Feb 13.

19.

Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors.

Shani E, Salehin M, Zhang Y, Sanchez SE, Doherty C, Wang R, Mangado CC, Song L, Tal I, Pisanty O, Ecker JR, Kay SA, Pruneda-Paz J, Estelle M.

Curr Biol. 2017 Feb 6;27(3):437-444. doi: 10.1016/j.cub.2016.12.016. Epub 2017 Jan 19.

20.

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.

Hossain MS, Kawakatsu T, Kim KD, Zhang N, Nguyen CT, Khan SM, Batek JM, Joshi T, Schmutz J, Grimwood J, Schmitz RJ, Xu D, Jackson SA, Ecker JR, Stacey G.

New Phytol. 2017 Apr;214(2):808-819. doi: 10.1111/nph.14421. Epub 2017 Jan 20.

21.

Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain.

Luo C, Lancaster MA, Castanon R, Nery JR, Knoblich JA, Ecker JR.

Cell Rep. 2016 Dec 20;17(12):3369-3384. doi: 10.1016/j.celrep.2016.12.001.

22.

JAZ2 controls stomata dynamics during bacterial invasion.

Gimenez-Ibanez S, Boter M, Ortigosa A, García-Casado G, Chini A, Lewsey MG, Ecker JR, Ntoukakis V, Solano R.

New Phytol. 2017 Feb;213(3):1378-1392. doi: 10.1111/nph.14354. Epub 2016 Dec 22.

23.

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.

24.

Functional Human Oocytes Generated by Transfer of Polar Body Genomes.

Ma H, O'Neil RC, Marti Gutierrez N, Hariharan M, Zhang ZZ, He Y, Cinnioglu C, Kayali R, Kang E, Lee Y, Hayama T, Koski A, Nery J, Castanon R, Tippner-Hedges R, Ahmed R, Van Dyken C, Li Y, Olson S, Battaglia D, Lee DM, Wu DH, Amato P, Wolf DP, Ecker JR, Mitalipov S.

Cell Stem Cell. 2017 Jan 5;20(1):112-119. doi: 10.1016/j.stem.2016.10.001. Epub 2016 Nov 10.

25.

A transcription factor hierarchy defines an environmental stress response network.

Song L, Huang SC, Wise A, Castanon R, Nery JR, Chen H, Watanabe M, Thomas J, Bar-Joseph Z, Ecker JR.

Science. 2016 Nov 4;354(6312). pii: aag1550.

26.

Phased diploid genome assembly with single-molecule real-time sequencing.

Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC.

Nat Methods. 2016 Dec;13(12):1050-1054. doi: 10.1038/nmeth.4035. Epub 2016 Oct 17.

27.

EIN2-dependent regulation of acetylation of histone H3K14 and non-canonical histone H3K23 in ethylene signalling.

Zhang F, Qi B, Wang L, Zhao B, Rode S, Riggan ND, Ecker JR, Qiao H.

Nat Commun. 2016 Oct 3;7:13018. doi: 10.1038/ncomms13018.

28.

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR.

Cell. 2016 Sep 8;166(6):1598. doi: 10.1016/j.cell.2016.08.063. Epub 2016 Sep 8. No abstract available.

29.

Integration of omic networks in a developmental atlas of maize.

Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP.

Science. 2016 Aug 19;353(6301):814-8. doi: 10.1126/science.aag1125.

30.

Molecular Criteria for Defining the Naive Human Pluripotent State.

Theunissen TW, Friedli M, He Y, Planet E, O'Neil RC, Markoulaki S, Pontis J, Wang H, Iouranova A, Imbeault M, Duc J, Cohen MA, Wert KJ, Castanon R, Zhang Z, Huang Y, Nery JR, Drotar J, Lungjangwa T, Trono D, Ecker JR, Jaenisch R.

Cell Stem Cell. 2016 Oct 6;19(4):502-515. doi: 10.1016/j.stem.2016.06.011. Epub 2016 Jul 14.

31.

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O'Neil R, O'Malley RC, Quarless DX; 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR.

Cell. 2016 Jul 14;166(2):492-505. doi: 10.1016/j.cell.2016.06.044.

32.

An ABA-increased interaction of the PYL6 ABA receptor with MYC2 Transcription Factor: A putative link of ABA and JA signaling.

Aleman F, Yazaki J, Lee M, Takahashi Y, Kim AY, Li Z, Kinoshita T, Ecker JR, Schroeder JI.

Sci Rep. 2016 Jun 30;6:28941. doi: 10.1038/srep28941.

33.

Mapping transcription factor interactome networks using HaloTag protein arrays.

Yazaki J, Galli M, Kim AY, Nito K, Aleman F, Chang KN, Carvunis AR, Quan R, Nguyen H, Song L, Alvarez JM, Huang SS, Chen H, Ramachandran N, Altmann S, Gutiérrez RA, Hill DE, Schroeder JI, Chory J, LaBaer J, Vidal M, Braun P, Ecker JR.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4238-47. doi: 10.1073/pnas.1603229113. Epub 2016 Jun 29.

34.

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.

35.

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR.

Cell. 2016 May 19;165(5):1280-1292. doi: 10.1016/j.cell.2016.04.038. Erratum in: Cell. 2016 Sep 8;166(6):1598.

36.

The Arabidopsis Auxin Receptor F-Box Proteins AFB4 and AFB5 Are Required for Response to the Synthetic Auxin Picloram.

Prigge MJ, Greenham K, Zhang Y, Santner A, Castillejo C, Mutka AM, O'Malley RC, Ecker JR, Kunkel BN, Estelle M.

G3 (Bethesda). 2016 May 3;6(5):1383-90. doi: 10.1534/g3.115.025585.

37.

A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants.

Bergelson J, Buckler ES, Ecker JR, Nordborg M, Weigel D.

Plant Cell. 2016 Mar;28(3):606-9. doi: 10.1105/tpc.15.00502. Epub 2016 Mar 8. No abstract available.

38.

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.

39.

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.

40.

Mobile small RNAs regulate genome-wide DNA methylation.

Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR.

Proc Natl Acad Sci U S A. 2016 Feb 9;113(6):E801-10. doi: 10.1073/pnas.1515072113. Epub 2016 Jan 19.

41.

Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns.

Sanchez-Mut JV, Heyn H, Vidal E, Moran S, Sayols S, Delgado-Morales R, Schultz MD, Ansoleaga B, Garcia-Esparcia P, Pons-Espinal M, de Lagran MM, Dopazo J, Rabano A, Avila J, Dierssen M, Lott I, Ferrer I, Ecker JR, Esteller M.

Transl Psychiatry. 2016 Jan 19;6:e718. doi: 10.1038/tp.2015.214.

42.

Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light.

Pedmale UV, Huang SC, Zander M, Cole BJ, Hetzel J, Ljung K, Reis PAB, Sridevi P, Nito K, Nery JR, Ecker JR, Chory J.

Cell. 2016 Jan 14;164(1-2):233-245. doi: 10.1016/j.cell.2015.12.018. Epub 2015 Dec 24.

43.

Profiling of transcription factor binding events by chromatin immunoprecipitation sequencing (ChIP-seq).

Song L, Koga Y, Ecker JR.

Curr Protoc Plant Biol. 2016;1(2):293-306. doi: 10.1002/cppb.20014. Epub 2016 Jun 10.

44.

Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation.

Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, Ren B, Sejnowski TJ, Wang W, Ecker JR.

Nature. 2016 Feb 11;530(7589):242. doi: 10.1038/nature16179. Epub 2015 Nov 25. No abstract available.

PMID:
26605523
45.

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.

46.

Correction: DNA Topoisomerase 1α Promotes Transcriptional Silencing of Transposable Elements through DNA Methylation and Histone Lysine 9 Dimethylation in Arabidopsis.

Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella PA, Li S, Weigel D, Pontes O, Ecker JR, Chen X.

PLoS Genet. 2015 Sep 17;11(9):e1005452. doi: 10.1371/journal.pgen.1005452. eCollection 2015 Sep. No abstract available.

47.

Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis.

Nagel DH, Doherty CJ, Pruneda-Paz JL, Schmitz RJ, Ecker JR, Kay SA.

Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):E4802-10. doi: 10.1073/pnas.1513609112. Epub 2015 Aug 10.

48.

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.

49.

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.

50.

Non-CG Methylation in the Human Genome.

He Y, Ecker JR.

Annu Rev Genomics Hum Genet. 2015;16:55-77. doi: 10.1146/annurev-genom-090413-025437. Epub 2015 Jun 4. Review.

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