Vijay Ramani, Assistant Professor of Biophysics and Biochemistry, UCSF, and Institute of Data Science and Biotechnology at the Gladstone Institute
0:00 Long reads have become the baseline in genomics
8:18 Work on the structure of the chromatin fiber can’t be done with short reads
16:39 Sequencing post single cell revolution
20:09 New protocol developed for 1/100th of the sample size. What new applications does this open up?
30:20 Future of sequencing
34:48 The short read scale, scale, scale argument
38:26 What technology improvements would you like to see?
A new generation of biologists is pushing the limits of third-generation sequencing, furthering the technology's development and defining new applications to answer biology’s most pressing questions.
This is the express goal for the lab of Vijay Ramani, assistant professor at UCSF in the department of Biophysics and Biochemistry. Vijay also has an appointment in the Institute of Data Science and Biotechnology at the Gladstone Institute, and in 2019 he was named to the Forbes 30 under 30 rising stars in healthcare list.
Today Vijay shares his recent work to characterize the structure of the chromatin fiber which he says could not have been done on short read technology. Vijay uses epigenetic tagging to measure chromatin, a technology unique to 3rd generation sequencers.
One of the drawbacks to small molecule sequencers has been the large sample size needed. In a recent breakthrough, Vijay and his group published a preprint with a protocol for 1/100th the sample size. This opens up PacBio sequencers to a host of new applications, such as clinical and metagenomic work.
Vijay’s lab has been up and running for four years now. What does he see on the horizon for sequencing? What technology improvements does he desire? And what does he make of the short read scale, scale, scale argument?