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*Equal contribution; Corresponding author; Bold – lab members
2021
- Mapping Transcription Factor-Nucleosome Dynamics from Plasma cfDNA. Biorxiv. 2021 April doi: 10.1101/2021.04.14.439883.
- Rao S, Ahmad K, Ramachandran S#. Cooperative Binding of Transcription Factors is a Hallmark of Active Enhancers. Molecular Cell 2021 Apr 15;81(8):1651-1665.e4. doi: 10.1016/j.molcel.2021.02.014. Epub 2021 Mar 1
Commentary by Abdulhay and Ramani
2020
- Zkowski A*, Rao S*, Ramachandran S#. Phenotypes from cell-free DNA. Open Biology 2020
- 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
2019
- 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
2018
- 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
2017
- Ramachandran S, Ahmad K, Henikoff, S. Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates. Molecular Cell 2017 Dec 21; 68(6):1038-1053. pubmed journal
Cover
Featured in “Meet the Author”
- Warfield L*, Ramachandran S*, Baptista T, Devys D, Tora L, Hahn S. Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factior TFIID. Molecular Cell 2017 Oct 5; 68:1-12 pubmed journal
Preview by Dylan Taatjes : The Continuing SAGA of TFIID and RNA Polymerase II Transcription - Ramachandran S, Ahmad K, Henikoff S. Capitalizing on disaster: establishing chromatin specificity behind the replication fork. Bioessays 2016 pubmed
2016
- Ramachandran, S., Henikoff, S. “Transcriptional regulators compete with nucleosomes post-replication”, Cell, 165(3):580-92 (2016) pubmed journal
Science Spotlight at Fred Hutchinson Cancer Research Center - Ramachandran S., and Henikoff, S. “Nucleosome dynamics during chromatin remodeling in vivo”, Nucleus 7(1):20-6 (2016) pubmed journal
2015
- 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
2014
- 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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