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Items: 1 to 20 of 256

1.

Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons.

Luo C, Lee QY, Wapinski O, Castanon R, Nery JR, Mall M, Kareta MS, Cullen SM, Goodell MA, Chang HY, Wernig M, Ecker JR.

Elife. 2019 Jan 15;8. pii: e40197. doi: 10.7554/eLife.40197.

PMID:
30644360
2.

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.

3.

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
4.

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.

5.

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.

6.

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
7.

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.

8.

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.

9.

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.

10.

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.

11.

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
12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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