Key Publications:

Kraft K*, Murphy SE*, Matthew JG*, …Boettiger, AN, Howard CY, Enhancer activation from transposable elements in extrachromosomal DNA. bioRxiv 2024.09.04.611262; doi: https://doi.org/10.1101/2024.09.04.611262

Murphy SE, Boettiger AN. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. Nat Genet. 2024 Feb 15. doi: 10.1038/s41588-024-01661-6. Epub ahead of print. PMID: 38361032.

Hafner, A., Park, M., Berger, S., Murphy, S.E., Nora, E., Boettiger, A.N., (2023) Loop stacking organizes genome folding from TADs to chromosomes. Molecular Cell, doi.org/10.1016/j.molcel.2023.04.008.

Kraft, K*., Yost, K.E*., Murphy, S.E., Magg, A., Long, Y.,...Chang, H.Y. (2022)Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation. PNAS, 119 (22) e2201883119

Rajpurkar A.R., Mateo L.J., Murphy S.E, Boettiger AN. (2021)Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer–promoter contact. Nat Commun 12, 3423.

Mateo, L.J., Murphy, S.E., Hafner, A.; Cinquini, I., Walker, C.,  and Boettiger, A. (2019)Visualizing DNA folding and transcription in embryogenesis at single-cell resolution. Nature, 568, pp. 49-54

Reviews:

Boettiger, A.N., Murphy, S.E., (2020) Advances in chromatin imaging at kilobase-scale resolution. Trends in Genetics. Online: 29 January 2020.