CREU 2014-15

Department of Computer Science


Algorithms and Tools for Synthetic Gene Design

The emerging field of synthetic biology moves beyond conventional genetic manipulation towards the redesign and construction of novel genes and genomes that do not originate in nature. With enormous advances in large scale DNA synthesis and sequencing we are now in a position to design large-scale experiments with synthetic genes to quantitatively characterize biological components and bridge the gap of knowledge between sequence and function. Our project aims to create efficient algorithms and computational tools for the rational engineering of protein-coding DNA sequences for acquisition of new attributes. Our ultimate goal is for these algorithms and tools to be used to rationally construct large numbers of synthetic designs, with varied but well controlled optimization objectives, enabling researchers to delineate which sequence features contribute the most to properties such as expression and stability of molecules.

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J.R. Villari
(class of 2016)

Joie Murphy
(class of 2017)

Kate Evans
(class of 2017)


Dimitris Papamichail


Funding is provided by the Computer Research Association’s Committee on the Status of Women in Computing Research (CRA-W) and the Coalition to Diversify Computing (CDC), with support from the National Science Foundation (NSF).