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Epigenomics

Locus-specific editing of histone modifications at endogenous enhancers.

Mendenhall EM, Williamson KE, Reyon D, et al. Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol. 2013;31(12):1133-6. doi:10.1038/nbt.2701

Charting a dynamic DNA methylation landscape of the human genome.

Ziller MJ, Gu H, Müller F, et al. Charting a dynamic DNA methylation landscape of the human genome. Nature. 2013;500(7463):477-81. doi:10.1038/nature12433

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

Gifford CA, Ziller MJ, Gu H, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013;153(5):1149-63. doi:10.1016/j.cell.2013.04.037

Genome-wide chromatin state transitions associated with developmental and environmental cues.

Zhu J, Adli M, Zou JY, et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013;152(3):642-54. doi:10.1016/j.cell.2012.12.033

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling.

Boyle P, Clement K, Gu H, et al. Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol. 2012;13(10):R92. doi:10.1186/gb-2012-13-10-r92

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74. doi:10.1038/nature11247

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt S, Marinov G, Kundaje A, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome research. 2012;22(9):1813-31. doi:10.1101/gr.136184.111

Points of view: Data exploration.

Shoresh N, Wong B. Points of view: Data exploration. Nature methods. 2012;9(1):5.

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.

Brinkman A, Gu H, Bartels S, et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome research. 2012;22(6):1128-38. doi:10.1101/gr.133728.111

Mapping and analysis of chromatin state dynamics in nine human cell types.

Ernst J, Kheradpour P, Mikkelsen T, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011;473(7345):43-9. doi:10.1038/nature09906