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Selected Publications

Ecker, J.R., Geschwind, D.H., Kriegstein, A.R., Ngai, J., Osten, P., Polioudakis, D., Regev, A., Sestan, N., Wickersham, I.R., Zeng, H. The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron, 2017 Nov 1;96(3):542-557. doi.10.1016/j.neuron. 2017.10.007. PMID:29096072.

Luo, C., Keown, C.L., Kurihara, L., Zhou, J., He, Y., Castanon, R., Lucero, J., Nery, J.R., Sandoval, J.P., Bui., B., Sejnowski, T.J., Harkins, T.T., Mukamel, E.A., Behrens, M.M., Ecker, J.R. Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex. Science, 2017 Aug 11;357(6351):600-604. doi. 10.1126/science.aan3351. PMID:28798132. PMCID: PMC5570439.

Trigg, S.A., Garza, R.M., MacWilliams, A., Nery, J.R., Bartlett, A., Castanon, R., Goubil, A., Feeney, J, O’Malley, R., Huang, S.C., Zhang, ZZ., Galli, M., Ecker, J.R. CrY2H-seq interactome screening. Prot Exchange. 2017 Jun 28. doi: 10.1038/protex.2017.058.

Trigg, S.A., Garza, R.M., MacWilliams, A., Nery, J.R., Bartlett, A., Castanon, R., Goubil, A., Feeney, J, O’Malley, R., Huang, S.C., Zhang, ZZ., Galli, M., Ecker, J.R. CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping. Nat Methods. 2017 Jun 26. doi: 10.1038/nmeth.4343. [Epub ahead of print] PMID:2865047.

Michael, T., Jupe, F., Bemm, F., Motley, S., Sandoval, J., Loudet, O., Weigel, D., Ecker, J.R. High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. bioRxiv, 2017 Jun 14. Doi:10.1101/149997.

Kawakatsu, T., Nery, J.R., Castanon, R., Ecker, J.R. Dynamic DNA methylation reconfiguration during seed development and germination. Genome Biology, 2017 Sep 15;18(1):171. doi: 10.1186/s13059-017-1251-x. PMID: 28911331.

Hsia, M., Malley, R.O., Cartwright, A., Nieu, R., Gordon, S., Kelly, S., Williams, T.G.,Wood, DF., Zhao, Y., Bragg, J., Jordan, M., Pauly,M., Ecker, J.R., Gu, Y., Vogel, J.P. Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection, Plant J, 2017 Apr 22. doi: 111/tpj.13582. [Epub ahead of print] PMID: 28432803.

Bartlett, A., O’Malley, R.D., Huang, S-s.C., Galli, M., Nery, J.R., Gallavotti, A., Ecker J.R. Mapping genome-wide transcription factor binding sites using DAP-seq. Nature Protocols, 2017 Aug;12(8):1659-1672. doi: 10.1038/nprot.2017.055. Epub 2017 Jul 20. PMID: 28726847.

He, Y., Gorkin, D.U., Dickel, D.E., Nery, J.R., Castanon, R., Lee, A.Y., Shen, Y., Visel, A., Pennacchio, L.A., Ren, B., Ecker, J.R. (2017) Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proc Natl Acad Sci U S A. 28;114(9):E1633-E1640. doi: 10.1073/pnas.1618353114.

Luo, C., Lancaster, M.A., Castanon, R., Nery, J.R., *Knoblich, J.A.,*Ecker, J.R. (2016) Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain, Cell Reports 17: 1-16. EndFragment

Song L., Huang SS., Wise A., Castanon R., Nery J.R., Chen H., Watanabe M., Thomas J., Bar-Joseph Z., Ecker JR. (2016) A transcription factor hierarchy defines an environmental stress response network. Science. 04 Nov 2016: Vol. 354, Issue 6312, p. 598. DOI: 10.1126/science.aag1550
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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. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature.2015 Jul 9;523(7559):212-6. PMCID: PMC4499021.

Luo C, Ecker JR. Epigenetics. Exceptional epigenetics in the brain. Science. 2015 Jun 5;348(6239):1094-5. NIHMSID752121.
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. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron. 2015 Jun 17;86(6):1369-84, PMCID: PMC4499463.

Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, Takahashi Y, Aizawa E, Kim NY, Lajara J, Guillen P, Campistol JM, Esteban CR, Ross PJ, Saghatelian A, Ren B, Ecker JR, Izpisua Belmonte JC. An alternative pluripotent state confers interspecies chimaeric competency. Nature. 2015 May 21;521(7552):316-21. [not NIH funded].

Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 2015 Feb 19;518(7539):350-4. PMCID: PMC4449149.

He Y, Ecker JR. Non-CG Methylation in the Human Genome. Annu Rev Genomics Hum Genet. 2015;16:55-77. NIHMSID752120.

Lister, R., Mukamel, E.A., Nery, J.R., Urich, M., Puddifoot, C.A., Johnson, N.D., Lucero, J., Huang, Y., Dwork, A.J., Schultz, M.D., Yu, M., Tonti-Filippini, J., Heyn, H., Hu, S., Wu, J.C., Rao, A., Esteller, M., He, C., Haghighi, F.G., Sejnowski, T.J., Behrens, M.M. and Ecker, JR. (2013) Global epigenomic reconfiguration during mammalian brain development. Science. 2013 Aug 9;341(6146):1237905. Epub 2013 Jul 4.

Chang, K.N., Zhong, S., Weirauch, M.T., Hon, G., Pelizzola, M., Li, H., Huang, S.S., Schmitz, R.J., Urich, M.A., Kuo, D., Nery, J.R., Qiao, H., Yang, A., Jamali, A., Chen, H., Ideker, T., Ren, B., Bar-Joseph, Z., Hughes, T.R. and Ecker, J.R. (2013) Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2013 Jun 11;2:e00675.

Schmitz, R.J., Schultz, M.D., Urich, M.A., Nery, J.R., Pelizzola, M., Libiger, O., Alix, A., McCosh, R.B., Chen, H., Schork, N.J. and Ecker, J.R.  (2013) Patterns of population epigenomic diversity.  Nature. Mar 14;495(7440):193-8. doi: 10.1038/nature11968. Epub 2013 Mar 6.

Ecker, J.R. (2013) Epigenetic trigger for tomato ripening. Nat Biotechnol. Feb. 7; 31(2):119-20.

O’Malley, R.C. and Ecker, J.R. (2012) Epiallelic Variation in Arabidopsis thaliana. Cold Spring Harb Symp Quant Biol. Dec. 5 [Epub ahead of print].

Vollmers, C., Schmitz, R.J., Nathanson, J., Yeo, G., Ecker, J.R. and Panda, S. (2012) Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metab. 16(6):833-45.

Schultz, M.D., Schmitz, R.J. and Ecker, J.R. (2012) ‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes. Trends Genet. 28(12):583-5.

Ecker, J.R., Bickmore, W.A., Barroso, I., Pritchard, J.K., Gilad, Y. and Segal, E. (2012) Genomics: ENCODE explained. Nature. 489(7414):52-5.

Wierzbicki, A.T., Cocklin, R., Mayampurath, A., Lister, R., Rowley, M.J., Gregory, B.D., Ecker, J.R., Tang, H. and Pikaard, C.S. (2012) Spatial and functional relationships among Pol V-associated loci, Pol IV-dependent siRNAs, and cytosine methylation in the Arabidopsis epigenome. Genes Dev. 26(16):1825-36.

Qiao, H., Shen, Z., Huang, S.S., Schmitz, R.J., Urich, M.A., Briggs, S.P. and Ecker, J.R. (2012) Processing and subcellular trafficking of ER-tethered EIN2 control response to ethylene gas. Science. 338(6105):390-3.

Dowen, R.H., Pelizzola, M., Schmitz, R.J., Lister, R., Dowen, J.M., Nery, J.R., Dixon, J.E. and Ecker, J.R. (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci USA. 109(32):E2183-91.

Peng, Q. and Ecker, J.R. (2012) Detection of allele-specific methylation through a generalized heterogeneous epigenome model. Bioinformatics. 28(12):i163-71.

Kurihara, Y., Schmitz, R.J., Nery, J.R., Schultz, M.D., Okubo-Kurihara, E., Morosawa, T., Tanaka, M., Toyoda, T., Seki, M. and Ecker, J.R. (2012) Surveillance of 3? Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis. G3. (Bethesda) 2(4):487-98.

Schmitz, R.J. and Ecker, J.R. (2012) Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends Plant Sci. 17(3):149-54.

Schmitz, R.J., Schultz, M.D., Lewsey, M.G., O’Malley, R.C., Urich, M.A., Libiger, O., Schork, N.J. and Ecker, J.R. (2012) Transgenerational epigenetic instability is a source of novel methylation variants. Science. 334(6054):369-73.

Lister R., Pelizzola M., Kida Y.S., Hawkins R.D., Nery J.R., Hon G., Antosiewicz-Bourget J., O’Malley R., Castanon R., Klugman S., Downes M., Yu R., Stewart R., Ren B., Thomson J.A., Evans R.M. and Ecker J.R. (2011) Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. Mar 3;471(7336):68-73. Epub 2011 Feb 2.

Lister, R., Pelizzola, M., Dowen, R.H, Hawkins, R.D., Hon, G., Tonti-Filippini, J., Nery, J.R., Lee, L., Ye, Z., Ngo, Q-M., Edsall, L., Antosiewicz-Bourget, J., Stewart, R., Ruotti, V., Millar, A.H., Thomson, J.A., Ren, B. and Ecker, J.R. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462:315-322. http://www.nature.com/nature/journal/vaop/ncurrent/index.html

Dowen, R.H., Engel, J.L., Shao F., Ecker, J.R. and Dixon, J.E. (2009) A family of bacterial cysteine protease type III effectors utilize acylation-dependent and independent strategies to localize to plasma membranes.J Biol Chem. 284(23):15867-79.

Lister, R. and Ecker, J.R. (2009) Finding the fifth base: Genome-wide sequencing of cytosine methylation.Genome Res. 19(6):959-66.

Hazen, S.P., Naef, F., Quisel, T., Gendron, J.M., Chen, H., Ecker, J.R., Borevitz, J.O. and Kay, S.A. (2009) Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol. 10:R17.

Qiao, H., Chang, K.N., Yazaki, J. and Ecker, J.R. (2009) Interplay between ethylene, ETP1/ETP2 F-box proteins, and degradation of EIN2 triggers ethylene responses in Arabidopsis. Genes Dev. 23:512-21.

Lister, R., Gregory, B.D. and Ecker, J.R. (2009) Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr Opin Plant Biol. 12:107-18.

Cusick, M.E., Yu, H., Smolyar, A., Venkatesan, K., Carvunis, A.R., Simonis, N., Rual, J.F., Borick, H., Braun, P., Dreze, M., Vandenhaute, J., Galli, M., Yazaki, J., Hill, D.E., Ecker, J.R., Roth, F.P. and Vidal, M. (2009) Literature-curated protein interaction datasets. Nat Methods. 61:39-46.

Liljegren, S.J., Leslie, M.E., Darnielle, L., Lewis, M.W., Taylor, S.M., Luo, R., Geldner, N., Chory, J., Randazzo, P.A., Yanofsky, M.F. and Ecker, J.R. (2009) Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein. Development. 136:1909-1918.

Full list of publications: http://www.ncbi.nlm.nih.gov/pubmed/?term=ecker+jr