| Comprehensive single-cell transcriptional profiling of a multicellular organism J Cao, JS Packer, V Ramani, DA Cusanovich, C Huynh, R Daza, X Qiu, ... Science 357 (6352), 661-667, 2017 | 1454 | 2017 |
| Joint profiling of chromatin accessibility and gene expression in thousands of single cells J Cao, DA Cusanovich, V Ramani, D Aghamirzaie, HA Pliner, AJ Hill, ... Science 361 (6409), 1380-1385, 2018 | 864 | 2018 |
| Massively multiplex single-cell Hi-C V Ramani, X Deng, R Qiu, KL Gunderson, FJ Steemers, CM Disteche, ... Nature methods 14 (3), 263-266, 2017 | 596 | 2017 |
| Massively multiplex chemical transcriptomics at single-cell resolution SR Srivatsan, JL McFaline-Figueroa, V Ramani, L Saunders, J Cao, ... Science 367 (6473), 45-51, 2020 | 321 | 2020 |
| Bipartite structure of the inactive mouse X chromosome X Deng, W Ma, V Ramani, A Hill, F Yang, F Ay, JB Berletch, CA Blau, ... Genome biology 16, 1-21, 2015 | 247 | 2015 |
| Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory A Bertero, PA Fields, V Ramani, G Bonora, GG Yardimci, H Reinecke, ... Nature communications 10 (1), 1538, 2019 | 149 | 2019 |
| Mapping 3D genome architecture through in situ DNase Hi-C V Ramani, DA Cusanovich, RJ Hause, W Ma, R Qiu, X Deng, CA Blau, ... Nature protocols 11 (11), 2104-2121, 2016 | 127 | 2016 |
| High-throughput determination of RNA structure by proximity ligation V Ramani, R Qiu, J Shendure Nature biotechnology 33 (9), 980-984, 2015 | 119 | 2015 |
| Massively multiplex single-molecule oligonucleosome footprinting NJ Abdulhay, CP McNally, LJ Hsieh, S Kasinathan, A Keith, LS Estes, ... Elife 9, e59404, 2020 | 93 | 2020 |
| Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data HJ Kim, GG Yardımcı, G Bonora, V Ramani, J Liu, R Qiu, C Lee, J Hesson, ... PLoS computational biology 16 (9), e1008173, 2020 | 89 | 2020 |
| Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells V Ramani, X Deng, R Qiu, C Lee, CM Disteche, WS Noble, J Shendure, ... Methods 170, 61-68, 2020 | 80 | 2020 |
| Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome G Bonora, X Deng, H Fang, V Ramani, R Qiu, JB Berletch, GN Filippova, ... Nature communications 9 (1), 1445, 2018 | 80 | 2018 |
| Understanding spatial genome organization: methods and insights V Ramani, J Shendure, Z Duan Genomics, proteomics & bioinformatics 14 (1), 7-20, 2016 | 67 | 2016 |
| Unsupervised manifold alignment for single-cell multi-omics data R Singh, P Demetci, G Bonora, V Ramani, C Lee, H Fang, Z Duan, ... Proceedings of the 11th ACM International Conference on Bioinformatics …, 2020 | 63 | 2020 |
| High sensitivity profiling of chromatin structure by MNase-SSP V Ramani, R Qiu, J Shendure Cell reports 26 (9), 2465-2476. e4, 2019 | 38 | 2019 |
| A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function LJ Hsieh, MA Gourdet, CM Moore, EN Muñoz, N Gamarra, V Ramani, ... Molecular cell 82 (11), 2098-2112. e4, 2022 | 32 | 2022 |
| Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation G Bonora, V Ramani, R Singh, H Fang, DL Jackson, S Srivatsan, R Qiu, ... Genome Biology 22, 1-36, 2021 | 27 | 2021 |
| Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler NJ Abdulhay, LJ Hsieh, CP McNally, MS Ostrowski, CM Moore, ... Nature Structural & Molecular Biology 30 (10), 1571-1581, 2023 | 22* | 2023 |
| The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis PA Carroll, BW Freie, PF Cheng, S Kasinathan, H Gu, T Hedrich, ... PLoS biology 19 (10), e3001085, 2021 | 14* | 2021 |
| Direct transposition of native DNA for sensitive multimodal single-molecule sequencing AS Nanda, K Wu, I Irkliyenko, B Woo, MS Ostrowski, AS Clugston, ... Nature Genetics 56 (6), 1300-1309, 2024 | 10 | 2024 |