Sarah Richardson

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Joint Genome Institute
Richardson, Sarah

Sarah M. Richardson received a B.S. degree in Biology from the University of Maryland in 2004 and a Ph.D. in Human Genetics from the Johns Hopkins University School of Medicine in 2011. Her research at Johns Hopkins with Joel Bader and Jef Boeke focused on algorithms for the design of synthetic nucleotide sequences.

Sarah joined the Lawrence Berkeley National Laboratory and the Department of Energy Joint Genome Institute in Walnut Creek, California in April 2012 as a Distinguished Postdoctoral Fellow in Genomics to work on massive scale synthetic biology projects in biogeochemistry and bioremediation.

Thu July 11 | 2:00 - 4:00 | Parallel Session
ABSTRACT: Tools for large scale synthetic design and assembly

The successful assembly of multikilobase pieces of DNA requires very careful top down design and planning. GeneDesign can manipulate restriction enzyme recognition sites, change codon usage, and smooth out repetitive regions to ease the design process. It can also direct simple, automatable assembly of synthetic constructs with a simple protocol that minimizes PCR and stages the parallel, stepwise assembly of up to 15kb pieces. This protocol has no special requirements for sequence, making it ideal for the assembly of large constructs on the plasmid scale. 

For constructs on the chromosome scale, there is BioStudio. BioStudio is a framework for the multi-scale design of synthetic genomes. It can modify nucleotide sequences automatically or manually at multiple resolutions, using the GeneDesign libraries where appropriate. It can use the excellent, open-source, and user-friendly GBrowse as a GUI.  It is currently able to select recognition sites for the physical assembly of designed sequence, identify and incorporate unique sequences for PCR identification of wildtype and synthetic sequence, edit existing genome features, and create and annotate user-created genome features.  BioStudio annotates all changes to the genome sequence for version control, allowing the “roll-back” of any modifications with lethal phenotypes.  When coupled with a modular design strategy, versioning allows genome synthesis to proceed with as little re-synthesis as possible.