| Year |
Citation |
Score |
| 2022 |
Ahmad K, Henikoff S, Ramachandran S. Managing the Steady State Chromatin Landscape by Nucleosome Dynamics. Annual Review of Biochemistry. PMID 35303789 DOI: 10.1146/annurev-biochem-032620-104508 |
0.654 |
|
| 2021 |
Rao S, Ahmad K, Ramachandran S. Cooperative binding between distant transcription factors is a hallmark of active enhancers. Molecular Cell. PMID 33705711 DOI: 10.1016/j.molcel.2021.02.014 |
0.496 |
|
| 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 TH, et al. JMJD5 couples with CDK9 to release the paused RNA polymerase II. Proceedings of the National Academy of Sciences of the United States of America. PMID 32747552 DOI: 10.1073/Pnas.2005745117 |
0.323 |
|
| 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. mbcE19070387. PMID 31553691 DOI: 10.1091/Mbc.E19-07-0387 |
0.332 |
|
| 2018 |
Ramachandran S, Henikoff S. MINCE-Seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing. Methods in Molecular Biology (Clifton, N.J.). 1832: 159-168. PMID 30073526 DOI: 10.1007/978-1-4939-8663-7_8 |
0.542 |
|
| 2018 |
Henikoff S, Ramachandran S. Pioneers Invade the Nucleosomal Landscape. Molecular Cell. 71: 193-194. PMID 30028998 DOI: 10.1016/J.Molcel.2018.07.004 |
0.476 |
|
| 2018 |
Chereji RV, Ramachandran S, Bryson TD, Henikoff S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biology. 19: 19. PMID 29426353 DOI: 10.1186/S13059-018-1398-0 |
0.563 |
|
| 2017 |
Ramachandran S, Ahmad K, Henikoff S. Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates. Molecular Cell. PMID 29225036 DOI: 10.1016/J.Molcel.2017.11.015 |
0.673 |
|
| 2017 |
Dronamraju R, Ramachandran S, Jha DK, Adams AT, DiFiore JV, Parra MA, Dokholyan NV, Strahl BD. Redundant Functions for Nap1 and Chz1 in H2A.Z Deposition. Scientific Reports. 7: 10791. PMID 28883625 DOI: 10.1038/S41598-017-11003-8 |
0.528 |
|
| 2017 |
Ramachandran S, Ahmad K, Henikoff S. Capitalizing on disaster: Establishing chromatin specificity behind the replication fork. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. PMID 28133760 DOI: 10.1002/Bies.201600150 |
0.661 |
|
| 2017 |
Campbell SL, Thompson PM, Ramachandran S, Case L, Dokholyan N, Tolbert C, Waterman CM. Role of PIP2-Dependent Membrane Interactions in Vinculin Activation, Motility and Force Transmission Biophysical Journal. 112: 479a. DOI: 10.1016/J.Bpj.2016.11.2594 |
0.533 |
|
| 2016 |
Thompson PM, Ramachandran S, Case LB, Tolbert CE, Tandon A, Pershad M, Dokholyan NV, Waterman CM, Campbell SL. A Structural Model for Vinculin Insertion into PIP2-Containing Membranes and the Effect of Insertion on Vinculin Activation and Localization. Structure (London, England : 1993). PMID 28089450 DOI: 10.1016/J.Str.2016.12.002 |
0.51 |
|
| 2016 |
Ramachandran S, Henikoff S. Transcriptional Regulators Compete with Nucleosomes Post-replication. Cell. PMID 27062929 DOI: 10.1016/J.Cell.2016.02.062 |
0.565 |
|
| 2016 |
Ramachandran S, Henikoff S. Nucleosome dynamics during chromatin remodeling in vivo. Nucleus (Austin, Tex.). 1-7. PMID 26933790 DOI: 10.1080/19491034.2016.1149666 |
0.583 |
|
| 2016 |
Henikoff S, Weber CM, Teves SS, Ramachandran S. Abstract IA09: Nucleosome barriers to transcription Cancer Research. 76. DOI: 10.1158/1538-7445.Chromepi15-Ia09 |
0.756 |
|
| 2015 |
Ramachandran S, Henikoff S. Replicating Nucleosomes. Science Advances. 1. PMID 26269799 DOI: 10.1126/sciadv.1500587 |
0.475 |
|
| 2015 |
Wang L, Xie L, Ramachandran S, Lee Y, Yan Z, Zhou L, Krajewski K, Liu F, Zhu C, Chen DJ, Strahl BD, Jin J, Dokholyan NV, Chen X. Non-canonical Bromodomain within DNA-PKcs Promotes DNA Damage Response and Radioresistance through Recognizing an IR-Induced Acetyl-Lysine on H2AX. Chemistry & Biology. PMID 26119999 DOI: 10.1016/J.Chembiol.2015.05.014 |
0.537 |
|
| 2015 |
Ramachandran S, Zentner GE, Henikoff S. Asymmetric nucleosomes flank promoters in the budding yeast genome. Genome Research. 25: 381-90. PMID 25491770 DOI: 10.1101/Gr.182618.114 |
0.742 |
|
| 2015 |
Thompson PM, Lee HT, Kim L, Ramachandran S, Tandon A, Mendez-Giraldez R, Alushin GM, Dokholyan NV, Campbell SL. New Models for Regulation of Vinculin by Actin and Phospholipids Biophysical Journal. 108: 508a-509a. DOI: 10.1016/J.Bpj.2014.11.2784 |
0.505 |
|
| 2014 |
Shirvanyants D, Ramachandran S, Mei Y, Xu L, Meissner G, Dokholyan NV. Pore dynamics and conductance of RyR1 transmembrane domain. Biophysical Journal. 106: 2375-84. PMID 24896116 DOI: 10.1016/J.Bpj.2014.04.023 |
0.538 |
|
| 2014 |
Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang JP, Henikoff JG. The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. Elife. 3: e01861. PMID 24737863 DOI: 10.7554/Elife.01861 |
0.752 |
|
| 2014 |
Redler RL, Shirvanyants D, Dagliyan O, Ding F, Kim DN, Kota P, Proctor EA, Ramachandran S, Tandon A, Dokholyan NV. Computational approaches to understanding protein aggregation in neurodegeneration. Journal of Molecular Cell Biology. 6: 104-15. PMID 24620031 DOI: 10.1093/Jmcb/Mju007 |
0.714 |
|
| 2014 |
Weber CM, Ramachandran S, Henikoff S. Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Molecular Cell. 53: 819-30. PMID 24606920 DOI: 10.1016/J.Molcel.2014.02.014 |
0.535 |
|
| 2014 |
Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang J, Henikoff JG. Author response: The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo Elife. DOI: 10.7554/Elife.01861.026 |
0.728 |
|
| 2013 |
Ramachandran S, Chakraborty A, Xu L, Mei Y, Samsó M, Dokholyan NV, Meissner G. Structural determinants of skeletal muscle ryanodine receptor gating. The Journal of Biological Chemistry. 288: 6154-65. PMID 23319589 DOI: 10.1074/Jbc.M112.433789 |
0.522 |
|
| 2013 |
Ramachandran S, Ding F, Weeks KM, Dokholyan NV. Statistical analysis of SHAPE-directed RNA secondary structure modeling. Biochemistry. 52: 596-9. PMID 23286327 DOI: 10.1021/Bi300756S |
0.569 |
|
| 2012 |
Ramachandran S, Temple B, Alexandrova AN, Chaney SG, Dokholyan NV. Recognition of platinum-DNA adducts by HMGB1a. Biochemistry. 51: 7608-17. PMID 22950413 DOI: 10.1021/Bi3008577 |
0.55 |
|
| 2012 |
Shirvanyants D, Ding F, Tsao D, Ramachandran S, Dokholyan NV. Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. The Journal of Physical Chemistry. B. 116: 8375-82. PMID 22280505 DOI: 10.1021/Jp2114576 |
0.702 |
|
| 2012 |
Gyimesi G, Ramachandran S, Kota P, Dokholyan NV, Sarkadi B, Hegedűs T. Corrigendum to “ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions” [Biochim. Biophys. Acta 1808 (2011) 2954–2964] Biochimica Et Biophysica Acta (Bba) - Biomembranes. 1818: 1435. DOI: 10.1016/J.Bbamem.2012.01.004 |
0.674 |
|
| 2011 |
Bhattacharyya D, Ramachandran S, Sharma S, Pathmasiri W, King CL, Baskerville-Abraham I, Boysen G, Swenberg JA, Campbell SL, Dokholyan NV, Chaney SG. Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG) cross-links. Plos One. 6: e23582. PMID 21853154 DOI: 10.1371/Journal.Pone.0023582 |
0.651 |
|
| 2011 |
Gyimesi G, Ramachandran S, Kota P, Dokholyan NV, Sarkadi B, Hegedus T. ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions. Biochimica Et Biophysica Acta. 1808: 2954-64. PMID 21840296 DOI: 10.1016/J.Bbamem.2011.07.038 |
0.711 |
|
| 2011 |
Kota P, Ding F, Ramachandran S, Dokholyan NV. Gaia: automated quality assessment of protein structure models. Bioinformatics (Oxford, England). 27: 2209-15. PMID 21700672 DOI: 10.1093/Bioinformatics/Btr374 |
0.732 |
|
| 2011 |
Ramachandran S, Vogel L, Strahl BD, Dokholyan NV. Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation. Plos Computational Biology. 7: e1001042. PMID 21253558 DOI: 10.1371/Journal.Pcbi.1001042 |
0.516 |
|
| 2011 |
Ramachandran S, Kota P, Ding F, Dokholyan NV. Automated minimization of steric clashes in protein structures. Proteins. 79: 261-70. PMID 21058396 DOI: 10.1002/Prot.22879 |
0.735 |
|
| 2009 |
Ramachandran S, Serohijos AW, Xu L, Meissner G, Dokholyan NV. A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1). Plos Computational Biology. 5: e1000367. PMID 19390614 DOI: 10.1371/Journal.Pcbi.1000367 |
0.726 |
|
| 2009 |
Ramachandran S, Temple BR, Chaney SG, Dokholyan NV. Structural basis for the sequence-dependent effects of platinum-DNA adducts. Nucleic Acids Research. 37: 2434-48. PMID 19255091 DOI: 10.1093/Nar/Gkp029 |
0.56 |
|
| 2009 |
Jayanth N, Ramachandran S, Puranik M. Solution structure of the DNA damage lesion 8-oxoguanosine from ultraviolet resonance Raman spectroscopy. The Journal of Physical Chemistry. A. 113: 1459-71. PMID 19191520 DOI: 10.1021/Jp8071519 |
0.325 |
|
| 2009 |
Meissner G, Pasek DA, Yamaguchi N, Ramachandran S, Dokholyan NV, Tripathy A. Thermodynamics of calmodulin binding to cardiac and skeletal muscle ryanodine receptor ion channels. Proteins. 74: 207-11. PMID 18618700 DOI: 10.1002/Prot.22148 |
0.479 |
|
| 2009 |
Ramachandran S, Serohijos AW, Xu L, Meissner G, Dokholyan NV. Ryanodine Receptor Pore Structure and Function Biophysical Journal. 96: 107a. DOI: 10.1016/J.Bpj.2008.12.462 |
0.73 |
|
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