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Selected Publications

Cell Cell Cell Cell Genes Journal of Virology Nature PLOS Biomedical Computation Cell JCB Genes Discover Science Time Nature

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.

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. 

Recent Publications - Pubmed database