Vijay Ramani is interested in the mechanisms that control how genes are turned on or off in our cells. He develops molecular techniques that make it possible to monitor gene activity at the level of single cells and single molecules. With these techniques, Ramani and his team study how changes in genome organization affect gene activity, or how the same gene may produce different RNA molecules under different conditions. In turn, the team hopes to parlay this information into a better understanding of the molecular steps that lead to disease or maintain the pluripotency of stem cells.
Areas of Expertise
Organs and tissues are made of heterogeneous collections of cells. Studying them in bulk preparations does not afford the resolution necessary to decipher the precise mechanisms underlying normal organ formation or disease progression.
Vijay Ramani has been at the forefront of a technological wave called single-cell genomics, which seeks to probe genome and cell function at the level of individual cells. He has developed a method based on DNA barcodes that allows scientists to analyze the genome and gene products of thousands of individual cells at once without having to physically separate the cells. With one version of this high-throughput approach, called SciHi-C, he produced maps of the genome’s 3D organization for more than 10,000 individual cells—100 times more than had been possible with previous approaches. Another adaptation of his single-cell technology is a drug-screening platform he calls SciPlex, with which he can evaluate the impact of thousands of drugs on gene activity in one experiment.
More recently, Ramani has become interested in probing gene activity at the single-molecule level. He is adapting existing sequencing technology to the high-throughput analysis of the diverse RNA molecules individual genes can produce in response to various stimuli.
Assistant Investigator, Gladstone Institutes
Assistant Professor, Department of Biochemistry and Biophysics, UC San Francisco
Vijay Ramani, PhD, is an assistant investigator at Gladstone Institutes and an assistant professor of biochemistry and biophysics at UC San Francisco (UCSF).
Prior to joining Gladstone, he was a Sandler Faculty Fellow at UCSF. Ramani holds a bachelor’s of science and engineering from Princeton University, and a PhD in genome sciences from the University of Washington, where he trained under Jay Shendure, MD, PhD.
His expertise is in genomic technology development, single-cell sequencing, gene regulation, chromatin structure, dosage compensation, and RNA biology. His current goals include single-cell and single-molecule technology development, with the aim to understand the impact of metabolism on pluripotency, cancer, and other diseases.
Ramani received a 2021 NIH Director’s New Innovator Award that supports high-risk, high-reward research. He was also selected as one of Forbes’ “30 under 30” in healthcare in 2020.
How did you get your start in science?
‟I had the great fortune to be surrounded by people who encouraged me to pursue a career in STEM. As a principal investigator, I'm excited to similarly encourage a new generation of scientists.”
Honors and Awards
2021 NIH Director’s New Innovator Award, National Institutes of Health
2020 “30 Under 30” in Healthcare, Forbes
2015 Graduate Research Fellowship Honorable Mention, National Science Foundation
2014 Genome Training Grant, National Human Genome Research Institute
2008 Semi-Finalist, Siemens-Westinghouse Competition
2008 Semi-Finalist, Intel Science Talent Search Competition
- A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Hsieh LJ, Gourdet MA, Moore CM, Muñoz EN, Gamarra N, Ramani V, Narlikar GJ. Mol Cell. 2022 06 02; 82(11):2098-2112.e4.
- The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. 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. PLoS Biol. 2021 10; 19(10):e3001085.
- Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. 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. Genome Biol. 2021 09 27; 22(1):279.
- At least two to tango: Choreographing chromatin through cooperative footprints. Abdulhay NJ, Ramani V. Mol Cell. 2021 04 15; 81(8):1591-1593.
- Massively multiplex single-molecule oligonucleosome footprinting. Abdulhay NJ, McNally CP, Hsieh LJ, Kasinathan S, Keith A, Estes LS, Karimzadeh M, Underwood JG, Goodarzi H, Narlikar GJ, Ramani V. Elife. 2020 12 02; 9.
- Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. Kim HJ, Yardimci GG, Bonora G, Ramani V, Liu J, Qiu R, Lee C, Hesson J, Ware CB, Shendure J, Duan Z, Noble WS. PLoS Comput Biol. 2020 09; 16(9):e1008173.
- Massively multiplex chemical transcriptomics at single-cell resolution. 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. Science. 2020 01 03; 367(6473):45-51.
- Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells. Ramani V, Deng X, Qiu R, Lee C, Disteche CM, Noble WS, Shendure J, Duan Z. Methods. 2020 01 01; 170:61-68.
- Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE. Nat Commun. 2019 04 04; 10(1):1538.
- High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Ramani V, Qiu R, Shendure J. Cell Rep. 2019 02 26; 26(9):2465-2476.e4.
- Joint profiling of chromatin accessibility and gene expression in thousands of single cells. 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. Science. 2018 09 28; 361(6409):1380-1385.
- Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. Bonora G, Deng X, Fang H, Ramani V, Qiu R, Berletch JB, Filippova GN, Duan Z, Shendure J, Noble WS, Disteche CM. Nat Commun. 2018 04 13; 9(1):1445.
- Comprehensive single-cell transcriptional profiling of a multicellular organism. 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. Science. 2017 08 18; 357(6352):661-667.
- Massively multiplex single-cell Hi-C. Ramani V, Deng X, Qiu R, Gunderson KL, Steemers FJ, Disteche CM, Noble WS, Duan Z, Shendure J. Nat Methods. 2017 03; 14(3):263-266.
- Mapping 3D genome architecture through in situ DNase Hi-C. Ramani V, Cusanovich DA, Hause RJ, Ma W, Qiu R, Deng X, Blau CA, Disteche CM, Noble WS, Shendure J, Duan Z. Nat Protoc. 2016 11; 11(11):2104-21.
- Smash and DASH with Cas9. Ramani V, Shendure J. Genome Biol. 2016 Mar 05; 17:42.
- Understanding Spatial Genome Organization: Methods and Insights. Ramani V, Shendure J, Duan Z. Genomics Proteomics Bioinformatics. 2016 Feb; 14(1):7-20.
- Bipartite structure of the inactive mouse X chromosome. Deng X, Ma W, Ramani V, Hill A, Yang F, Ay F, Berletch JB, Blau CA, Shendure J, Duan Z, Noble WS, Disteche CM. Genome Biol. 2015 Aug 07; 16:152.
- High-throughput determination of RNA structure by proximity ligation. Ramani V, Qiu R, Shendure J. Nat Biotechnol. 2015 Sep; 33(9):980-4.
- Can increasing the dose of radiation by HDR brachytherapy boost following pre operative chemoradiotherapy for advanced rectal cancer improve surgical outcomes? Sun Myint A, Mukhopadhyay T, Ramani VS, Perkins K, Snee AJ, Jelley F, Wong H, Lee CD. Colorectal Dis. 2010 Aug; 12 Suppl 2:30-6.