Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Srinivas Ramachandran

TitleAssistant 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.
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    1. Ahooyi TM, Stear B, Simmons JA, Metzger VT, Kumar P, Evangelista JE, Clarke DJB, Xie Z, Kim H, Jenkins SL, Maurya MR, Ramachandran S, Fahy E, Gillespie TH, Imam FT, Kokash N, Roth ME, Fullem R, Jevtic D, Mihajlovic A, Tiemeyer M, Bakker C, Schroeder AJ, Markowski J, Nedzel J, Hill DD, Terry J, Nemarich C, Boline J, Park PJ, Ardlie KG, Vora J, Mazumder R, Ranzinger R, de Bono B, Subramaniam S, Grethe JS, Yang JJ, Lambert CG, Resnick A, Milosavljevic A, Ma'ayan A, Silverstein JC, Taylor DM. The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data. bioRxiv. 2025 Oct 16. PMID: 40832351.
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    2. Tonsager AJ, Zukowski A, Radebaugh CA, Weirich A, Stargell LA, Ramachandran S. The histone chaperone Spn1 preserves chromatin protections at promoters and nucleosome positioning in open reading frames. G3 (Bethesda). 2025 Apr 17; 15(4). PMID: 39960479.
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    3. Trouth A, Ravichandran K, Gafken PR, Martire S, Boyle GE, Veronezi GMB, La V, Namciu SJ, Banaszynski LA, Sarthy JF, Ramachandran S. The length of the G1 phase is an essential determinant of H3K27me3 landscapes across diverse cell types. PLoS Biol. 2025 Apr; 23(4):e3003119. PMID: 40245079.
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    4. Han AL, Vinod Paul K, Rao S, Brechbuhl HM, Sartorius CA, Ramachandran S, Kabos P. Estradiol (E2) concentration shapes the chromatin binding landscape of estrogen receptor alpha. J Biol Chem. 2025 Jul; 301(7):108499. PMID: 40216250.
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    5. Clarke DJB, Evangelista JE, Xie Z, Marino GB, Byrd AI, Maurya MR, Srinivasan S, Yu K, Petrosyan V, Roth ME, Milinkov M, King CH, Vora JK, Keeney J, Nemarich C, Khan W, Lachmann A, Ahmed N, Agris A, Pan J, Ramachandran S, Fahy E, Esquivel E, Mihajlovic A, Jevtic B, Milinovic V, Kim S, McNeely P, Wang T, Wenger E, Brown MA, Sickler A, Zhu Y, Jenkins SL, Blood PD, Taylor DM, Resnick AC, Mazumder R, Milosavljevic A, Subramaniam S, Ma'ayan A. Playbook workflow builder: Interactive construction of bioinformatics workflows. PLoS Comput Biol. 2025 Apr; 21(4):e1012901. PMID: 40179105.
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    6. Tonsager AJ, Zukowski A, Radebaugh CA, Weirich A, Stargell LA, Ramachandran S. THE HISTONE CHAPERONE SPN1 PRESERVES CHROMATIN PROTECTIONS AT PROMOTERS AND NUCLEOSOME POSITIONING IN OPEN READING FRAMES. bioRxiv. 2025 Jan 09. PMID: 38559248.
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    7. Valdes P, Caldwell AB, Liu Q, Fitzgerald MQ, Ramachandran S, Karch CM, Galasko DR, Yuan SH, Wagner SL, Subramaniam S. Integrative multiomics reveals common endotypes across PSEN1, PSEN2, and APP mutations in familial Alzheimer's disease. Alzheimers Res Ther. 2025 Jan 04; 17(1):5. PMID: 39754192.
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    8. Brechbuhl HM, Han A, Paul KV, Nemkov T, Ramachandran S, Ward A, Jacobsen BM, Hansen K, Sartorius CA, D'Alessandro A, Kabos P. Metabolic Switch in Endocrine Resistant Estrogen Receptor Positive Breast Cancer. bioRxiv. 2024 Dec 29. PMID: 39763830.
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    9. Trouth A, Veronezi GMB, Ramachandran S. The impact of cell states on heterochromatin dynamics. Biochem J. 2024 11 06; 481(21):1519-1533. PMID: 39422321.
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    10. Peeters JGC, Silveria S, Ozdemir M, Ramachandran S, DuPage M. Hyperactivating EZH2 to augment H3K27me3 levels in regulatory T cells enhances immune suppression by driving early effector differentiation. Cell Rep. 2024 09 24; 43(9):114724. PMID: 39264807.
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    11. Veronezi GMB, Ramachandran S. Nucleation and spreading maintain Polycomb domains every cell cycle. Cell Rep. 2024 04 23; 43(4):114090. PMID: 38607915.
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    12. Ingersoll S, Trouth A, Luo X, Espinoza A, Wen J, Tucker J, Astatike K, Phiel CJ, Kutateladze TG, Wu TP, Ramachandran S, Ren X. Sparse CBX2 nucleates many Polycomb proteins to promote facultative heterochromatinization of Polycomb target genes. bioRxiv. 2024 Feb 05. PMID: 38370615.
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    13. Valdes P, Henry KW, Fitzgerald MQ, Muralidharan K, Caldwell AB, Ramachandran S, Goldstein LSB, Mobley WC, Galasko DR, Subramaniam S. Limitations of the human iPSC-derived neuron model for early-onset Alzheimer's disease. Mol Brain. 2023 11 03; 16(1):75. PMID: 37924159.
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    14. Caldwell AB, Anantharaman BG, Ramachandran S, Nguyen P, Liu Q, Trinh I, Galasko DR, Desplats PA, Wagner SL, Subramaniam S. Transcriptomic profiling of sporadic Alzheimer's disease patients. Mol Brain. 2022 10 12; 15(1):83. PMID: 36224601.
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    15. 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.
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    16. 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.
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    17. Azad P, Caldwell AB, Ramachandran S, Spann NJ, Akbari A, Villafuerte FC, Bermudez D, Zhao H, Poulsen O, Zhou D, Bafna V, Subramaniam S, Haddad GG. ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge's disease. Exp Mol Med. 2022 06; 54(6):777-787. PMID: 35672450.
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    18. 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.
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    19. Raghunandan S, Ramachandran S, Ke E, Miao Y, Lal R, Chen ZB, Subramaniam S. Heme Oxygenase-1 at the Nexus of Endothelial Cell Fate Decision Under Oxidative Stress. Front Cell Dev Biol. 2021; 9:702974. PMID: 34595164.
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    20. 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.
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    21. Vatsyayan A, Sharma P, Gupta S, Sandhu S, Venu SL, Sharma V, Badaoui B, Azedine K, Youssef S, Rajab A, Fayez A, Madinur S, Ranawat A, Pandhare K, Ramachandran S, Sivasubbu S, Scaria V. DALIA- a comprehensive resource of Disease Alleles in Arab population. PLoS One. 2021; 16(1):e0244567. PMID: 33439861.
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    22. Thakran S, Guin D, Singh P, Singh P, Kukal S, Rawat C, Yadav S, Kushwaha SS, Srivastava AK, Hasija Y, Saso L, Ramachandran S, Kukreti R. Genetic Landscape of Common Epilepsies: Advancing towards Precision in Treatment. Int J Mol Sci. 2020 Oct 21; 21(20). PMID: 33096746.
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    23. Zukowski A, Rao S, Ramachandran S. Phenotypes from cell-free DNA. Open Biol. 2020 09; 10(9):200119. PMID: 32873154.
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    24. 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.
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    25. Ban DK, Liu Y, Wang Z, Ramachandran S, Sarkar N, Shi Z, Liu W, Karkisaval AG, Martinez-Loran E, Zhang F, Glinsky G, Bandaru PR, Fan C, Lal R. Direct DNA Methylation Profiling with an Electric Biosensor. ACS Nano. 2020 06 23; 14(6):6743-6751. PMID: 32407064.
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    26. Jiang L, Ramamoorthy R, Ramachandran S, Kumar PP. Systems Metabolic Alteration in a Semi-Dwarf Rice Mutant Induced by OsCYP96B4 Gene Mutation. Int J Mol Sci. 2020 Mar 11; 21(6). PMID: 32168953.
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    27. 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.
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    28. Jagannathan S, Ramachandran S, Rissland OS. Slow Down to Catch Up. Cell. 2019 08 08; 178(4):774-776. PMID: 31398334.
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    29. Guo J, Ramachandran S, Zhong R, Lal R, Zhang F. Generating Cyan Fluorescence with De Novo Tripeptides: An In Vitro Mutation Study on the Role of Single Amino Acid Residues and Their Sequence. Chembiochem. 2019 09 16; 20(18):2324-2330. PMID: 31013385.
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    30. 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.
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    31. Henikoff S, Ramachandran S. Pioneers Invade the Nucleosomal Landscape. Mol Cell. 2018 07 19; 71(2):193-194. PMID: 30028998.
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    32. Alemasov NA, Ivanisenko NV, Ramachandran S, Ivanisenko VA. Correction to: selected articles from Belyaev Conference 2017: structural biology. BMC Struct Biol. 2018 03 21; 18(1):3. PMID: 29562896.
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    33. 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.
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    34. Alemasov NA, Ivanisenko NV, Ramachandran S, Ivanisenko VA. Molecular mechanisms underlying the impact of mutations in SOD1 on its conformational properties associated with amyotrophic lateral sclerosis as revealed with molecular modelling. BMC Struct Biol. 2018 02 05; 18(Suppl 1):1. PMID: 29431095.
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    35. Ramachandran S, Henikoff S. MINCE-Seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing. Methods Mol Biol. 2018; 1832:159-168. PMID: 30073526.
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    36. 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.
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    37. 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.
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    38. Ramachandran S, Ahmad K, Henikoff S. Capitalizing on disaster: Establishing chromatin specificity behind the replication fork. Bioessays. 2017 04; 39(4). PMID: 28133760.
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    39. Chaudhuri R, Ramachandran S. Immunoinformatics as a Tool for New Antifungal Vaccines. Methods Mol Biol. 2017; 1625:31-43. PMID: 28584981.
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    40. Feinstein HE, Benbow SJ, LaPointe NE, Patel N, Ramachandran S, Do TD, Gaylord MR, Huskey NE, Dressler N, Korff M, Quon B, Cantrell KL, Bowers MT, Lal R, Feinstein SC. Oligomerization of the microtubule-associated protein tau is mediated by its N-terminal sequences: implications for normal and pathological tau action. J Neurochem. 2016 06; 137(6):939-54. PMID: 26953146.
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    41. Ramachandran S, Henikoff S. Transcriptional Regulators Compete with Nucleosomes Post-replication. Cell. 2016 Apr 21; 165(3):580-92. PMID: 27062929.
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    42. Ramachandran S, Henikoff S. Nucleosome dynamics during chromatin remodeling in vivo. Nucleus. 2016; 7(1):20-6. PMID: 26933790.
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    43. 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. Sci Rep. 2016 Feb 22; 6:21285. PMID: 26899418.
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    44. 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.
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    45. Ramachandran S, Henikoff S. Replicating Nucleosomes. Sci Adv. 2015 Aug 07; 1(7). PMID: 26269799.
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    46. 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. 2015; 10(6):e0128711. PMID: 26035208.
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    47. 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.
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    48. Ye J, Qu J, Mao HZ, Ma ZG, Rahman NE, Bai C, Chen W, Jiang SY, Ramachandran S, Chua NH. Engineering geminivirus resistance in Jatropha curcus. Biotechnol Biofuels. 2014; 7(1):149. PMID: 25352912.
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    49. 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.
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    50. 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.
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    51. Chaudhuri R, Ramachandran S. Prediction of virulence factors using bioinformatics approaches. Methods Mol Biol. 2014; 1184:389-400. PMID: 25048137.
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    52. Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Familial Alzheimer's disease Osaka mutant (?E22) ß-barrels suggest an explanation for the different Aß1-40/42 preferred conformational states observed by experiment. J Phys Chem B. 2013 Oct 03; 117(39):11518-29. PMID: 24000923.
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    53. 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.
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    54. Jang H, Connelly L, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. Mechanisms for the Insertion of Toxic, Fibril-like ß-Amyloid Oligomers into the Membrane. J Chem Theory Comput. 2013 Jan 08; 9(1):822-833. PMID: 23316126.
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    55. 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 ß-amyloid channels: atomic force microscopy and molecular dynamics simulations. Biochemistry. 2012 Apr 10; 51(14):3031-8. PMID: 22413858.
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    56. 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.
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    57. 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.
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    58. 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.
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    59. 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.
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    60. La H, Li J, Ji Z, Cheng Y, Li X, Jiang S, Venkatesh PN, Ramachandran S. Genome-wide analysis of cyclin family in rice (Oryza Sativa L.). Mol Genet Genomics. 2006 Apr; 275(4):374-86. PMID: 16435118.
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    61. 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.
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    62. 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.
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