| Year |
Citation |
Score |
| 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 |
0.64 |
|
| 2020 |
Zukowski A, Rao S, Ramachandran S. Phenotypes from cell-free DNA. Open Biology. 10: 200119. PMID 32873154 DOI: 10.1098/rsob.200119 |
0.56 |
|
| 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 |
0.64 |
|
| 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 |
0.64 |
|
| 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 |
0.64 |
|
| 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 |
0.64 |
|
| 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 |
1 |
|
| 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 |
0.64 |
|
| 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 |
1 |
|
| 2016 |
Puniya BL, Kulshreshtha D, Mittal I, Mobeen A, Ramachandran S. Corrigendum: Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis. Scientific Reports. 6: 24916. PMID 27129109 DOI: 10.1038/srep24916 |
0.32 |
|
| 2016 |
Ramachandran S, Henikoff S. Transcriptional Regulators Compete with Nucleosomes Post-replication. Cell. PMID 27062929 DOI: 10.1016/j.cell.2016.02.062 |
1 |
|
| 2016 |
Puniya BL, Kulshreshtha D, Mittal I, Mobeen A, Ramachandran S. Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis. Scientific Reports. 6: 23440. PMID 27000948 DOI: 10.1038/srep23440 |
0.32 |
|
| 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 |
1 |
|
| 2016 |
Ahirwar R, Nahar S, Aggarwal S, Ramachandran S, Maiti S, Nahar P. In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer-alike molecules. Scientific Reports. 6: 21285. PMID 26899418 DOI: 10.1038/srep21285 |
0.32 |
|
| 2016 |
Jang H, Arce FT, Lee J, Gillman AL, Ramachandran S, Kagan BL, Lal R, Nussinov R. Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels. Methods in Molecular Biology (Clifton, N.J.). 1345: 251-68. PMID 26453217 DOI: 10.1007/978-1-4939-2978-8_16 |
0.32 |
|
| 2015 |
Rani J, Shah AB, Ramachandran S. pubmed.mineR: An R package with text-mining algorithms to analyse PubMed abstracts. Journal of Biosciences. 40: 671-82. PMID 26564970 DOI: 10.1007/s12038-015-9552-2 |
0.32 |
|
| 2015 |
Adamczyk L, Adkins JK, Agakishiev G, Aggarwal MM, Ahammed Z, Alekseev I, Alford J, Anson CD, Aparin A, Arkhipkin D, Aschenauer EC, Averichev GS, Banerjee A, Beavis DR, Bellwied R, ... ... Ramachandran S, et al. Precision Measurement of the Longitudinal Double-Spin Asymmetry for Inclusive Jet Production in Polarized Proton Collisions at sqrt[s]=200 GeV. Physical Review Letters. 115: 092002. PMID 26371644 |
1 |
|
| 2015 |
Ramachandran S, Henikoff S. Replicating Nucleosomes. Science Advances. 1. PMID 26269799 DOI: 10.1126/sciadv.1500587 |
0.64 |
|
| 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 |
1 |
|
| 2015 |
Jalali S, Kohli S, Latka C, Bhatia S, Vellarikal SK, Sivasubbu S, Scaria V, Ramachandran S. Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach. Plos One. 10: e0128711. PMID 26035208 DOI: 10.1371/journal.pone.0128711 |
0.32 |
|
| 2015 |
Adamczyk L, Adkins JK, Agakishiev G, Aggarwal MM, Ahammed Z, Alekseev I, Alford J, Anson CD, Aparin A, Arkhipkin D, Aschenauer EC, Averichev GS, Banerjee A, Beavis DR, Bellwied R, ... ... Ramachandran S, et al. ΛΛ Correlation function in Au+Au collisions at √[S(NN)]=200 GeV. Physical Review Letters. 114: 022301. PMID 25635541 |
1 |
|
| 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 |
1 |
|
| 2015 |
Yan L, Gregg P, Karimi E, Rubano A, Marrucci L, Boyd R, Ramachandran S. Q-plate enabled spectrally diverse orbital-angular-momentum conversion for stimulated emission depletion microscopy Optica. 2: 900-903. DOI: 10.1364/OPTICA.2.000900 |
0.36 |
|
| 2015 |
Gregg P, Kristensen P, Ramachandran S. Conservation of orbital angular momentum in air-core optical fibers Optica. 2: 267-270. DOI: 10.1364/OPTICA.2.000267 |
0.36 |
|
| 2015 |
Demas J, Steinvurzel P, Tai B, Rishøj L, Chen Y, Ramachandran S. Intermodal nonlinear mixing with Bessel beams in optical fiber Optica. 2: 14-17. DOI: 10.1364/OPTICA.2.000014 |
0.36 |
|
| 2015 |
Ramachandran S. Low cross-talk fibers using OAM Photonic Networks and Devices, Networks 2015. 204p. DOI: 10.1364/NETWORKS.2015.NeS2D.3 |
0.36 |
|
| 2015 |
Yan L, Karimi E, Gregg P, Boyd R, Ramachandran S. Single-aperture STED illumination using a q-plate and fiber Cleo: Science and Innovations, Cleo-Si 2015. 2267. DOI: 10.1364/CLEO_SI.2015.STu1L.5 |
0.36 |
|
| 2015 |
Willner AE, Huang H, Yan Y, Ren Y, Ahmed N, Xie G, Bao C, Li L, Cao Y, Zhao Z, Wang J, Lavery MPJ, Tur M, Ramachandran S, Molisch AF, et al. Optical communications using orbital angular momentum beams Advances in Optics and Photonics. 7: 66-106. DOI: 10.1364/AOP.7.000066 |
0.36 |
|
| 2015 |
Shcherbina AY, Sundermeyer MA, Kunze E, D'Asaro E, Badin G, Birch D, Brunner-Suzuki AMEG, Callies J, Kuebel Cervantes BT, Claret M, Concannon B, Early J, Ferrari R, Goodman L, Harcourt RR, ... ... Ramachandran S, et al. The latmix summer campaign : Submesoscale stirring in the upper ocean Bulletin of the American Meteorological Society. 96: 1257-1279. DOI: 10.1175/BAMS-D-14-00015.1 |
0.6 |
|
| 2015 |
Gregg P, Mirhosseini M, Rubano A, Marrucci L, Karimi E, Boyd R, Ramachandran S. Q-plates for switchable excitation of fiber OAM modes Conference On Lasers and Electro-Optics Europe - Technical Digest. 2015. |
0.36 |
|
| 2015 |
Rishoj L, Jones M, Demas J, Prabhakar G, Yan L, Hawkins T, Ballato J, Ramachandran S. Large mode area guidance in a simple fiber structure Conference On Lasers and Electro-Optics Europe - Technical Digest. 2015. |
0.36 |
|
| 2015 |
Demas J, Rishoj L, Ramachandran S. Input and output coupling in higher order mode fibers Conference On Lasers and Electro-Optics Europe - Technical Digest. 2015. |
0.36 |
|
| 2015 |
Kang Q, Gregg P, Jung Y, Lim EL, Alam SU, Ramachandran S, Richardson DJ. Amplification of 12 OAM States in an air-core EDF Optical Fiber Communication Conference, Ofc 2015. |
0.36 |
|
| 2015 |
Kang Q, Gregg P, Jung Y, Lim EL, Alam SU, Ramachandran S, Richardson DJ. Amplification of 12 OAM States in an air-core EDF Optical Fiber Communication Conference, Ofc 2015. |
0.36 |
|
| 2015 |
Ramachandran S. Optical vortices in fiber Proceedings of Frontiers in Optics 2015, Fio 2015. |
0.36 |
|
| 2014 |
Demas J, Ramachandran S. Sub-second mode measurement of fibers using C2 imaging. Optics Express. 22: 23043-56. PMID 25321775 |
0.36 |
|
| 2014 |
Adamczyk L, Adkins JK, Agakishiev G, Aggarwal MM, Ahammed Z, Alekseev I, Alford J, Anson CD, Aparin A, Arkhipkin D, Aschenauer EC, Averichev GS, Balewski J, Banerjee A, Beavis DR, ... ... Ramachandran S, et al. Measurement of longitudinal spin asymmetries for weak boson production in polarized proton-proton collisions at RHIC. Physical Review Letters. 113: 072301. PMID 25170701 DOI: 10.1103/PhysRevLett.113.072301 |
0.76 |
|
| 2014 |
Adamczyk L, Adkins JK, Agakishiev G, Aggarwal MM, Ahammed Z, Alekseev I, Alford J, Anson CD, Aparin A, Arkhipkin D, Aschenauer EC, Averichev GS, Banerjee A, Beavis DR, Bellwied R, ... ... Ramachandran S, et al. Beam-energy dependence of charge separation along the magnetic field in Au+Au collisions at RHIC. Physical Review Letters. 113: 052302. PMID 25126911 |
1 |
|
| 2014 |
Adamczyk L, Adkins JK, Agakishiev G, Aggarwal MM, Ahammed Z, Alekseev I, Alford J, Anson CD, Aparin A, Arkhipkin D, Aschenauer EC, Averichev GS, Banerjee A, Barnovska Z, Beavis DR, ... ... Ramachandran S, et al. Dielectron mass spectra from Au+Au collisions at √[s(NN)]=200 GeV. Physical Review Letters. 113: 022301. PMID 25062167 |
1 |
|
| 2014 |
Chaudhuri R, Ramachandran S. Prediction of virulence factors using bioinformatics approaches. Methods in Molecular Biology (Clifton, N.J.). 1184: 389-400. PMID 25048137 DOI: 10.1007/978-1-4939-1115-8_22 |
0.32 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 2012 |
King CL, Ramachandran S, Chaney SG, Collins L, Swenberg JA, DeKrafft KE, Lin W, Cicurel L, Barbier M. Debio 0507 primarily forms diaminocyclohexane-Pt-d(GpG) and -d(ApG) DNA adducts in HCT116 cells. Cancer Chemotherapy and Pharmacology. 69: 665-77. PMID 21968950 DOI: 10.1007/s00280-011-1744-3 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 2011 |
Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (London, England : 1993). 19: 1108-26. PMID 21827947 DOI: 10.1016/j.str.2011.05.012 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
|
| 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 |
1 |
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