From Reading Genomes to Interpreting Genomes (to Rationally Engineering Genomes)

Friday, February 19, 2016 -
2:00pm to 3:00pm
Powell-Focht Bioengineering Hall
Prashant Mali

Assistant Professor
Department of Bioengineering
University of California, San Diego

From Reading Genomes to Interpreting Genomes (to Rationally Engineering Genomes)


Genomes encode the rules for most life forms. Differences in genomes underlie most organismal diversity, and aberrations in genomes underlie many disease states. With the rapid advances in DNA sequencing, our ability to read genomes has grown exponentially and we now have near-complete genomes of many organisms and a fairly comprehensive catalog of human germline and somatic variants. As we move next towards interpreting genomes, technologies to directly and precisely perturb genomic elements and combinations thereof will be a critical toolset towards obtaining the complete functional annotation of genomic elements and genetic variants at the cellular and whole organism levels. Resulting new found knowledge, especially in the human context, will pave the way for a deeper understanding of the genetic code, and will also power therapeutic interventions directed at both effecting cures as well as eventually also engineering disease resistance. In this regard, the recent advent of RNA-guided effectors derived from clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems have dramatically transformed our ability to engineer the genomes of diverse organisms. As unique factors capable of co-localizing RNA, DNA, and protein, tools and techniques based on these are paving the way for unprecedented control over cellular organization, regulation, and behavior. Here I will describe some of our ongoing work towards developing and scaling this genome engineering platform, as well as outline recent efforts into integrating tissue engineering technologies to enable better recapitulation and study of human biological systems.


Prashant Mali received a bachelor’s and master’s in Electrical Engineering from the Indian Institute of Technology Bombay, with a research focus on biomedical sensors; and a doctorate in Biomedical Engineering at the Johns Hopkins University, with a research focus on human pluripotent stem cell engineering. During his postdoctoral fellowship in the Department of Genetics at the Harvard Medical School, he pioneered the development of the CRISPR-Cas systems for eukaryotic genome engineering. For his graduate work he received the Siebel Scholar Award in 2011, and in 2014 he received the Burroughs Wellcome Career Award at the Scientific Interface. Mali joined the University of California, San Diego faculty in 2014 as an assistant professor in the Department of Bioengineering.