| Visualizing DNA folding and RNA in embryos at single-cell resolution LJ Mateo, SE Murphy, A Hafner, IS Cinquini, CA Walker, AN Boettiger Nature 568 (7750), 49-54, 2019 | 394 | 2019 |
| Advances in chromatin imaging at kilobase-scale resolution A Boettiger, S Murphy Trends in Genetics 36 (4), 273-287, 2020 | 105 | 2020 |
| Cross-talk between lysine-modifying enzymes controls site-specific DNA amplifications S Mishra, C Van Rechem, S Pal, TL Clarke, D Chakraborty, SD Mahan, ... Cell 174 (4), 803-817. e16, 2018 | 59 | 2018 |
| Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation K Kraft, KE Yost, SE Murphy, A Magg, Y Long, MR Corces, JM Granja, ... Proceedings of the National Academy of Sciences 119 (22), e2201883119, 2022 | 55 | 2022 |
| Loop stacking organizes genome folding from TADs to chromosomes A Hafner, M Park, SE Berger, SE Murphy, EP Nora, AN Boettiger Molecular cell 83 (9), 1377-1392. e6, 2023 | 44 | 2023 |
| Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer–promoter contact AR Rajpurkar, LJ Mateo, SE Murphy, AN Boettiger Nature communications 12 (1), 3423, 2021 | 19 | 2021 |
| Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement ZH Gray, D Chakraborty, RR Duttweiler, GD Alekbaeva, SE Murphy, ... Cell 186 (21), 4528-4545. e18, 2023 | 9 | 2023 |
| The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes C Van Rechem, F Ji, S Mishra, D Chakraborty, SE Murphy, ME Dillingham, ... Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1863 (10), 194624, 2020 | 9 | 2020 |
| Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition SE Murphy, AN Boettiger Nature genetics 56 (3), 493-504, 2024 | 6 | 2024 |
| Polycomb repression of Hox genes involves spatial feedback but not domain compaction or demixing S Murphy, AN Boettiger bioRxiv, 2022.10. 14.512199, 2022 | 5 | 2022 |
| Enhancer activation from transposable elements in extrachromosomal DNA K Kraft, SE Murphy, MG Jones, Q Shi, A Bhargava-Shah, C Luong, ... bioRxiv, 2024 | | 2024 |
| Encoding Memory in 3d: How Polycomb-Mediated Genome Folding Facilitates Epigenetic Memory Through Dynamic Chromatin Architecture SE Murphy Stanford University, 2023 | | 2023 |
| Physics-Based Modeling of Chromosomal Organization Impacted By Multiple Epigenetic Factors J Wakim, S Murphy, A Boettiger, A Spakowitz 2022 AIChE Annual Meeting, 2022 | | 2022 |
| Epigenetics Impacts Copy Number Heterogeneity and Drug Resistant Gene Selection JR Whetstine, JC Black, S Mishra, B Sexton, C Van Rechem, S Murphy The FASEB Journal 30, 802.10-802.10, 2016 | | 2016 |
