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Items: 1 to 20 of 207

1.

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.

PMID:
29220033
2.

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

Huang SC, Ecker JR.

Wiley Interdiscip Rev Syst Biol Med. 2017 Nov 30. doi: 10.1002/wsbm.1411. [Epub ahead of print] Review.

PMID:
29194997
3.

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.

PMID:
29096072
4.

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.

5.

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.

PMID:
28798132
6.

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.

PMID:
28726847
7.

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.

8.

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.

PMID:
28432803
9.

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.

10.

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.

11.

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.

PMID:
28111153
12.

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.

PMID:
28106918
13.

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.

14.

JAZ2 controls stomata dynamics during bacterial invasion.

Gimenez-Ibanez S, Boter M, Ortigosa A, GarcĂ­a-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.

PMID:
28005270
15.

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.

PMID:
27859855
16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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