Richard E. Green

Scholar: 2011

Awarded Institution
Assistant Professor
University of California, Santa Cruz
Department of Biomolecular Engineering


Research Interests

Insights from DNA Sequence Analysis

The biology and much of the history of an organism is written in its genome. Current technology provides an amazingly open foyer to extracting and understanding this information. My lab is focused on developing and applying technology to enable a full understanding of DNA sequence data at the scale it is now routinely produced.

My group is pursuing projects along several disparate lines. First, we are working on developing and evaluating assembly algorithms for next-generation sequencing. For many projects, the ability to generate sequence data is not limiting. Rather, accurate genome assembly or unbiased read mapping, more often stands between data generation and biological insight. We are currently working on de novo assembly algorithms and evaluation technology for genome assembly.

We are also assembling and analyzing the genomes of a handful of vertebrate species including the American alligator. Alligators, like most reptiles, do not carry out sex-determination via genetic means. That is, male and female alligators are genetically identical. Rather, temperature will specify male or female fate in alligators. To understand the molecular basis of this process, we are analyzing expressed sequence through embryonic development at male and female temperature. Further, by comparing the genome sequence of the alligator to other species for which the molecular basis of sex-determination is more completely understood, we hope to understand how this process evolves.

Ancient DNA presents a particularly vexing challenge for genome-scale analysis. Fragmentation and chemical damage occurs as bones age through tens of thousands of years. We are tackling this special challenge to unravel the important evolutionary changes that have occurred most recently in humans, since our split from Neanderthals, our closest extinct relatives.