Selected Papers
01. How do cells remember their identity?
- Nucleation and spreading maintain Polycomb domains every cell cycle
Veronezi & Ramachandran, Cell Reports, 2024 - The length of the G1 phase is an essential determinant of H3K27me3 landscapes across diverse cell types
Trouth et al., PLOS Biology, 2025 - Self-clustering of three CBX2 molecules drives PRC2 to promote facultative heterochromatinization of Polycomb target genes
Ingersoll et al., Molecular Cell, 2026 - The impact of cell states on heterochromatin dynamics
Trouth, Veronezi & Ramachandran, Biochemical Journal, 2024
02. How do TFs compete with nucleosomes?
- Managing the Steady State Chromatin Landscape by Nucleosome Dynamics
Ahmad, Henikoff & Ramachandran, Annual Review of Biochemistry, 2022 - Cooperative binding between distant transcription factors is a hallmark of active enhancers
Rao, Ahmad & Ramachandran, Molecular Cell, 2021 - Rotational settings quantize nucleosome movement by chromatin regulators
La, Trouth, Ramani & Ramachandran, Cell Reports, 2026
03. Where proteins bind in the genome
- Phenotypes from cell-free DNA
Zukowski, Rao & Ramachandran, Open Biology, 2020 - Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer
Rao et al., Science Advances, 2022 - Cell-Free DNA-Based Methods to Map Chromatin
Eramo, Weirich & Ramachandran, Methods in Molecular Biology (Cancer Epigenetics), 2026 - Fragmentation patterns of human telomeric chromatin in plasma cfDNA
Buck et al., Nature Communications, 2026
