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Srinivas Ramachandran

TitleAsst Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-BioChem&Molecular Genetics

    Collapse Biography 
    Collapse education and training
    University of North Carolina, Chapel Hill, NCPhD05/2011Biochemistry and Biophysics
    Fred Hutchinson Cancer Research Center, Seattle, WAPostdoctoral Training12/2017Chromatin Biology

    Collapse Overview 
    Collapse overview
    Regulation of genome access underlies growth, development, differentiation, and disease states including tumor initiation. Genome access is regulated by dynamic chromatin landscapes. We want to uncover fundamental mechanisms that shape chromatin landscapes by mapping chromatin structure at high temporal and spatial resolution using new experimental and/or computational methods. This research program in chromatin biology is at the intersection of genomics, biochemistry, and structural biology.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Fong N, Sheridan RM, Ramachandran S, Bentley DL. The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model. Mol Cell. 2022 10 06; 82(19):3632-3645.e4. PMID: 36206739.
      View in: PubMed
    2. Rao S, Han AL, Zukowski A, Kopin E, Sartorius CA, Kabos P, Ramachandran S. Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer. Sci Adv. 2022 08 26; 8(34):eabm4358. PMID: 36001652.
      View in: PubMed
    3. Rao S, Ramachandran S. A computational pipeline to visualize DNA-protein binding states using dSMF data. STAR Protoc. 2022 06 17; 3(2):101299. PMID: 35463472.
      View in: PubMed
    4. Rao S, Ahmad K, Ramachandran S. Cooperative binding between distant transcription factors is a hallmark of active enhancers. Mol Cell. 2021 04 15; 81(8):1651-1665.e4. PMID: 33705711.
      View in: PubMed
    5. Zukowski A, Rao S, Ramachandran S. Phenotypes from cell-free DNA. Open Biol. 2020 09; 10(9):200119. PMID: 32873154.
      View in: PubMed
    6. 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, Happoldt C, O'Conner B, Janknecht R, Li CY, Marrack P, Kappler J, Leach S, Zhang G. JMJD5 couples with CDK9 to release the paused RNA polymerase II. Proc Natl Acad Sci U S A. 2020 08 18; 117(33):19888-19895. PMID: 32747552.
      View in: PubMed
    7. Eniyan K, Rani J, Ramachandran S, Bhat R, Khan IA, Bajpai U. Screening of Antitubercular Compound Library Identifies Inhibitors of Mur Enzymes in Mycobacterium tuberculosis. SLAS Discov. 2020 01; 25(1):70-78. PMID: 31597510.
      View in: PubMed
    8. Jagannathan S, Ramachandran S, Rissland OS. Slow Down to Catch Up. Cell. 2019 08 08; 178(4):774-776. PMID: 31398334.
      View in: PubMed
    9. Alemasov NA, Ivanisenko NV, Taneja B, Taneja V, Ramachandran S, Ivanisenko VA. Improved regression model to predict an impact of SOD1 mutations on ALS patients survival time based on analysis of hydrogen bond stability. J Mol Graph Model. 2019 01; 86:247-255. PMID: 30414557.
      View in: PubMed
    10. Henikoff S, Ramachandran S. Pioneers Invade the Nucleosomal Landscape. Mol Cell. 2018 07 19; 71(2):193-194. PMID: 30028998.
      View in: PubMed
    11. Chereji RV, Ramachandran S, Bryson TD, Henikoff S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biol. 2018 02 09; 19(1):19. PMID: 29426353.
      View in: PubMed
    12. Ramachandran S, Henikoff S. MINCE-Seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing. Methods Mol Biol. 2018; 1832:159-168. PMID: 30073526.
      View in: PubMed
    13. Ramachandran S, Ahmad K, Henikoff S. Transcription and Remodeling Produce Asymmetrically Unwrapped Nucleosomal Intermediates. Mol Cell. 2017 12 21; 68(6):1038-1053.e4. PMID: 29225036.
      View in: PubMed
    14. 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 Factor TFIID. Mol Cell. 2017 Oct 05; 68(1):118-129.e5. PMID: 28918900.
      View in: PubMed
    15. Ramachandran S, Ahmad K, Henikoff S. Capitalizing on disaster: Establishing chromatin specificity behind the replication fork. Bioessays. 2017 04; 39(4). PMID: 28133760.
      View in: PubMed
    16. Chaudhuri R, Ramachandran S. Immunoinformatics as a Tool for New Antifungal Vaccines. Methods Mol Biol. 2017; 1625:31-43. PMID: 28584981.
      View in: PubMed
    17. Ramachandran S, Henikoff S. Transcriptional Regulators Compete with Nucleosomes Post-replication. Cell. 2016 Apr 21; 165(3):580-92. PMID: 27062929.
      View in: PubMed
    18. Ramachandran S, Henikoff S. Nucleosome dynamics during chromatin remodeling in vivo. Nucleus. 2016; 7(1):20-6. PMID: 26933790.
      View in: PubMed
    19. 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 Mol Biol. 2016; 1345:251-68. PMID: 26453217.
      View in: PubMed
    20. Ramachandran S, Henikoff S. Replicating Nucleosomes. Sci Adv. 2015 Aug 07; 1(7). PMID: 26269799.
      View in: PubMed
    21. Ramachandran S, Zentner GE, Henikoff S. Asymmetric nucleosomes flank promoters in the budding yeast genome. Genome Res. 2015 Mar; 25(3):381-90. PMID: 25491770.
      View in: PubMed
    22. 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. 2014 Apr 15; 3:e01861. PMID: 24737863.
      View in: PubMed
    23. Weber CM, Ramachandran S, Henikoff S. Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Mol Cell. 2014 Mar 06; 53(5):819-30. PMID: 24606920.
      View in: PubMed
    24. Chaudhuri R, Ramachandran S. Prediction of virulence factors using bioinformatics approaches. Methods Mol Biol. 2014; 1184:389-400. PMID: 25048137.
      View in: PubMed
    25. Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Familial Alzheimer's disease Osaka mutant (?E22) ?-barrels suggest an explanation for the different A?1-40/42 preferred conformational states observed by experiment. J Phys Chem B. 2013 Oct 03; 117(39):11518-29. PMID: 24000923.
      View in: PubMed
    26. Jang H, Connelly L, Arce FT, Ramachandran S, Lal R, Kagan BL, Nussinov R. Alzheimer's disease: which type of amyloid-preventing drug agents to employ? Phys Chem Chem Phys. 2013 Jun 21; 15(23):8868-77. PMID: 23450150.
      View in: PubMed
    27. Jang H, Connelly L, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Mechanisms for the Insertion of Toxic, Fibril-like ?-Amyloid Oligomers into the Membrane. J Chem Theory Comput. 2013 Jan 08; 9(1):822-833. PMID: 23316126.
      View in: PubMed
    28. Connelly L, Jang H, Arce FT, Ramachandran S, Kagan BL, Nussinov R, Lal R. Effects of point substitutions on the structure of toxic Alzheimer's ?-amyloid channels: atomic force microscopy and molecular dynamics simulations. Biochemistry. 2012 Apr 10; 51(14):3031-8. PMID: 22413858.
      View in: PubMed
    29. Zheng LY, Guo XS, He B, Sun LJ, Peng Y, Dong SS, Liu TF, Jiang S, Ramachandran S, Liu CM, Jing HC. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol. 2011 Nov 21; 12(11):R114. PMID: 22104744.
      View in: PubMed
    30. Wang J, Zhou J, Zhang B, Vanitha J, Ramachandran S, Jiang SY. Genome-wide expansion and expression divergence of the basic leucine zipper transcription factors in higher plants with an emphasis on sorghum. J Integr Plant Biol. 2011 Mar; 53(3):212-31. PMID: 21205183.
      View in: PubMed
    31. Jiang SY, Ramamoorthy R, Ramachandran S. Comparative transcriptional profiling and evolutionary analysis of the GRAM domain family in eukaryotes. Dev Biol. 2008 Feb 15; 314(2):418-32. PMID: 18201690.
      View in: PubMed
    32. Sharma VK, Kumar N, Brahmachari SK, Ramachandran S. Abundance of dinucleotide repeats and gene expression are inversely correlated: a role for gene function in addition to intron length. Physiol Genomics. 2007 Sep 19; 31(1):96-103. PMID: 17550993.
      View in: PubMed
    33. Ravi V, Ramachandran S, Thompson RW, Andersen JF, Neva FA. Characterization of a recombinant immunodiagnostic antigen (NIE) from Strongyloides stercoralis L3-stage larvae. Mol Biochem Parasitol. 2002 Nov-Dec; 125(1-2):73-81. PMID: 12467975.
      View in: PubMed
    34. Nandi T, B-Rao C, Ramachandran S. Comparative genomics using data mining tools. J Biosci. 2002 Feb; 27(1 Suppl 1):15-25. PMID: 11927774.
      View in: PubMed
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