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Vijay Ramani - Publications

Affiliations: 
University of California, San Francisco, San Francisco, CA 
Area:
molecular biology, genetics, genomics, biochemistry
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19 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 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. The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. Plos Biology. 19: e3001085. PMID 34669700 DOI: 10.1371/journal.pbio.3001085  0.453
2021 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. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Genome Biology. 22: 279. PMID 34579774 DOI: 10.1186/s13059-021-02432-w  0.606
2020 Singh R, Demetci P, Bonora G, Ramani V, Lee C, Fang H, Duan Z, Deng X, Shendure J, Disteche C, Noble WS. Unsupervised manifold alignment for single-cell multi-omics data. Acm-Bcb ... ... : the ... Acm Conference On Bioinformatics, Computational Biology and Biomedicine. Acm Conference On Bioinformatics, Computational Biology and Biomedicine. 2020: 1-10. PMID 33954299 DOI: 10.1145/3388440.3412410  0.58
2020 Kim HJ, Yardımcı GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS. Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. Plos Computational Biology. 16: e1008173. PMID 32946435 DOI: 10.1371/Journal.Pcbi.1008173  0.63
2019 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. Massively multiplex chemical transcriptomics at single cell resolution. Science (New York, N.Y.). PMID 31806696 DOI: 10.1126/Science.Aax6234  0.717
2019 Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z. Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Methods (San Diego, Calif.). PMID 31536770 DOI: 10.1016/J.Ymeth.2019.09.012  0.652
2019 Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE. Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Nature Communications. 10: 1538. PMID 30948719 DOI: 10.1038/S41467-019-09483-5  0.595
2019 Ramani V, Qiu R, Shendure J. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Reports. 26: 2465-2476.e4. PMID 30811994 DOI: 10.1016/J.Celrep.2019.02.007  0.564
2018 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. Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science (New York, N.Y.). PMID 30166440 DOI: 10.1126/Science.Aau0730  0.678
2018 Bonora G, Deng X, Fang H, Ramani V, Qiu R, Berletch JB, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche CM. Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. Nature Communications. 9: 1445. PMID 29654302 DOI: 10.1038/S41467-018-03694-Y  0.546
2017 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. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science (New York, N.Y.). 357: 661-667. PMID 28818938 DOI: 10.1126/Science.Aam8940  0.673
2017 Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J. Massively multiplex single-cell Hi-C. Nature Methods. PMID 28135255 DOI: 10.1038/Nmeth.4155  0.65
2017 Ramani V, Duan Z, Shendure J. Massively multiplex single-cell Hi-C by combinatorial indexing Protocol Exchange. DOI: 10.1038/Protex.2017.005  0.589
2016 Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z. Mapping 3D genome architecture through in situ DNase Hi-C. Nature Protocols. 11: 2104-2121. PMID 27685100 DOI: 10.1038/Nprot.2016.126  0.707
2016 Ramani V, Shendure J. Smash and DASH with Cas9. Genome Biology. 17: 42. PMID 26944856 DOI: 10.1186/S13059-016-0905-4  0.503
2016 Ramani V, Shendure J, Duan Z. Understanding Spatial Genome Organization: Methods and Insights. Genomics, Proteomics & Bioinformatics. PMID 26876719 DOI: 10.1016/J.Gpb.2016.01.002  0.516
2015 Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. Bipartite structure of the inactive mouse X chromosome. Genome Biology. 16: 152. PMID 26248554 DOI: 10.1186/S13059-015-0728-8  0.545
2015 Ramani V, Qiu R, Shendure J. High-throughput determination of RNA structure by proximity ligation. Nature Biotechnology. 33: 980-4. PMID 26237516 DOI: 10.1038/Nbt.3289  0.542
2015 Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. Bipartite structure of the inactive mouse X chromosome Genome Biology. 16. DOI: 10.1186/s13059-015-0728-8  0.393
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