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.

Disease Areas

Metabolic Diseases

Areas of Expertise

Developmental Biology
Single-Molecule Analysis
Stem Cells
Technology Development
Working in the Ramani lab

Lab Focus

Adapt long-read sequencing technology to determine the RNA output of individual genes in single cells.
Determine the impact of metabolism and epigenetic factors on a cell’s ability to turn into a stem cell or a cancer cell.
Understand how Myc, a protein that drives many types of cancers, simultaneously controls genome organization, gene expression, RNA splicing, and cell metabolism.

Research Impact

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.


Professional Titles

Assistant Investigator

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.”

Vijay Ramani, PhD

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



Vijay Ramani

Lab Members

Eliana Bondra, PhD
Bioinformatics Fellow
Zain Boxer
Student Intern
Shayla Caoile
Student Intern
Yousra Chouadra
Student Intern
Wendy Contreras Martinez
Student Intern
Aaron Corin
Graduate Student
Shelley Fernando
Student Intern
Joaquin Garcia
Student Intern
Nicole Harris
Student Intern
Iryna Irkliyenko
Iryna Irkliyenko, MS
Mythili Ketavarapu
Research Associate I
Brandy Mendoza
Student Intern
Camille Moore
Graduate Student
Scott Nanda
Graduate Student
Deniz Olgun
Visiting Researcher
Keerthi Renduchintala
Research Associate I
Hannah Richter, PhD
Bioinformatics Fellow
Sol Ulaszek
Student Intern
Sean Wang
Research Associate I
Marianne Weinans
Student Intern
Marty Yang, PhD
Bioinformatics Fellow
Marty Yang, PhD
Bioinformatics Fellow
Kaite Zhang
Graduate Student