Srinivas Ramachandran - Publications

Affiliations: 
2012- Fred Hutchinson Cancer Research Center, Seattle, WA, United States 

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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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