Vijay Ramani, PhD

Title(s)Assistant Professor, Biochemistry and Biophysics
SchoolSchool of Medicine
Address600 16th Street
San Francisco CA 94158
Phone415-734-2599
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Mol Cell. 2022 06 02; 82(11):2098-2112.e4. Hsieh LJ, Gourdet MA, Moore CM, Muñoz EN, Gamarra N, Ramani V, Narlikar GJ. PMID: 35597239; PMCID: PMC9351570.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    2. The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. PLoS Biol. 2021 10; 19(10):e3001085. Carroll PA, Freie BW, Cheng PF, Kasinathan S, Gu H, Hedrich T, Dowdle JA, Venkataramani V, Ramani V, Wu X, Raftery D, Shendure J, Ayer DE, Muller CH, Eisenman RN. PMID: 34669700; PMCID: PMC8528285.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    3. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Genome Biol. 2021 09 27; 22(1):279. Bonora G, Ramani V, Singh R, Fang H, Jackson DL, Srivatsan S, Qiu R, Lee C, Trapnell C, Shendure J, Duan Z, Deng X, Noble WS, Disteche CM. PMID: 34579774; PMCID: PMC8474932.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    4. At least two to tango: Choreographing chromatin through cooperative footprints. Mol Cell. 2021 04 15; 81(8):1591-1593. Abdulhay NJ, Ramani V. PMID: 33861946.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    5. Massively multiplex single-molecule oligonucleosome footprinting. Elife. 2020 12 02; 9. Abdulhay NJ, McNally CP, Hsieh LJ, Kasinathan S, Keith A, Estes LS, Karimzadeh M, Underwood JG, Goodarzi H, Narlikar GJ, Ramani V. PMID: 33263279; PMCID: PMC7735760.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    6. Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. PLoS Comput Biol. 2020 09; 16(9):e1008173. Kim HJ, Yardimci GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS. PMID: 32946435; PMCID: PMC7526900.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    7. Massively multiplex chemical transcriptomics at single-cell resolution. Science. 2020 01 03; 367(6473):45-51. Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers F, Shendure J, Trapnell C. PMID: 31806696; PMCID: PMC7289078.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    8. Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Methods. 2020 01 01; 170:61-68. Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z. PMID: 31536770; PMCID: PMC6949367.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    9. Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Nat Commun. 2019 04 04; 10(1):1538. Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE. PMID: 30948719; PMCID: PMC6449405.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    10. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Rep. 2019 02 26; 26(9):2465-2476.e4. Ramani V, Qiu R, Shendure J. PMID: 30811994; PMCID: PMC6582983.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    11. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science. 2018 09 28; 361(6409):1380-1385. Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J. PMID: 30166440; PMCID: PMC6571013.
      View in: PubMed   Mentions: 234     Fields:    Translation:HumansAnimalsCells
    12. Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. Nat Commun. 2018 04 13; 9(1):1445. Bonora G, Deng X, Fang H, Ramani V, Qiu R, Berletch JB, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche CM. PMID: 29654302; PMCID: PMC5899087.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    13. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science. 2017 08 18; 357(6352):661-667. Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J. PMID: 28818938; PMCID: PMC5894354.
      View in: PubMed   Mentions: 411     Fields:    Translation:HumansAnimalsCells
    14. Massively multiplex single-cell Hi-C. Nat Methods. 2017 03; 14(3):263-266. Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J. PMID: 28135255; PMCID: PMC5330809.
      View in: PubMed   Mentions: 196     Fields:    Translation:HumansCells
    15. Mapping 3D genome architecture through in situ DNase Hi-C. Nat Protoc. 2016 11; 11(11):2104-21. Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z. PMID: 27685100; PMCID: PMC5547819.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    16. Smash and DASH with Cas9. Genome Biol. 2016 Mar 05; 17:42. Ramani V, Shendure J. PMID: 26944856; PMCID: PMC4779193.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    17. Understanding Spatial Genome Organization: Methods and Insights. Genomics Proteomics Bioinformatics. 2016 Feb; 14(1):7-20. Ramani V, Shendure J, Duan Z. PMID: 26876719; PMCID: PMC4792841.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    18. Bipartite structure of the inactive mouse X chromosome. Genome Biol. 2015 Aug 07; 16:152. Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. PMID: 26248554; PMCID: PMC4539712.
      View in: PubMed   Mentions: 112     Fields:    Translation:HumansAnimalsCells
    19. High-throughput determination of RNA structure by proximity ligation. Nat Biotechnol. 2015 Sep; 33(9):980-4. Ramani V, Qiu R, Shendure J. PMID: 26237516; PMCID: PMC4564351.
      View in: PubMed   Mentions: 52     Fields:    Translation:Cells
    20. Can increasing the dose of radiation by HDR brachytherapy boost following pre operative chemoradiotherapy for advanced rectal cancer improve surgical outcomes? Colorectal Dis. 2010 Aug; 12 Suppl 2:30-6. Sun Myint A, Mukhopadhyay T, Ramani VS, Perkins K, Snee AJ, Jelley F, Wong H, Lee CD. PMID: 20618365.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
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