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*Equal contribution; #Corresponding author; Bold – lab members


  • Rao S, Ahmad K, Ramachandran S. Cooperative Binding of Transcription Factors is a Hallmark of Active Enhancers. Biorxiv 2020
  • Zukowski A*, Rao S*, Ramachandran S#. Phenotypes from cell-free DNA. Open Biology 2020 accepted
  • Liu H, Ramachandran S, Fong N, Phang T, Lee S, Parsa P, Liu X, Harmacek L, Danhorn T, Song T, Oh S, Zhang Q, Chen Z, Zhang Q, Tu T, Happoldt C, O’Conner B, Janknecht R, Li C, Marrack P, Kappler J, Leach S, Zhang G. JMJD5 couples with CDK9 to release the paused RNA polymerase II. Proceedings of the National Academy of Sciences of the USA 2020 Aug 3; 202005745


  • Yee WB, Delaney PM, Vanderzalm PJ, Ramachandran S#, Fehon, RG#. The CAF-1 Complex Couples Hippo Pathway Target Gene Expression and DNA Replication. Molecular Biology of the Cell 2019 Nov 1;30(23):2929-2942
  • Jagannathan S, Ramachandran S, Rissland O. Slow down to catch up. Cell 2019 Aug 8; 178(4):774-776


  • Chereji R*, Ramachandran S*, Bryson TD,  Henikoff, S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biology 2018 Feb 9; 19(1):19
  • Ramachandran S, and Henikoff S. MINCE-seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing. Methods in Molecular Biology 2018;1832:159-168
  • Henikoff S, and Ramachandran S. Pioneers invade the nucleosome landscape. Molecular Cell 2018 Jul 19;71(2):193-194




  • Ramachandran, S., Zentner G. E., Henikoff, S. “Asymmetric nucleosomes flank promoters in the budding yeast genome”, Genome Research, 25(3):381-90 (2015) pubmed     journal
  • Ramachandran, S., and Henikoff, S. “Replicating nucleosomes”, Science Advances 1, e1500587 (2015)  pubmed    journal


  • Henikoff, S, Ramachandran, S., Krassovsky K., Bryson, T. D., Brogaard, K., Widom, J., Wang, J-P. and Henikoff, J. G. “The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo”, eLife, e01861 (2014)  pubmed     journal
  • Weber, C. M., Ramachandran, S., Henikoff, S. “Nucleosomes are context-specific, H2A.Z modulated barriers to RNA polymerase”, Molecular Cell, 53(5):819-30 (2014) pubmed journal
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