Automated design of assemblable, modular, synthetic chromosomes

Sarah M. Richardson, Brian S. Olson, Jessica S. Dymond, Randal Burns, Srinivasan Chandrasegaran, Jef D. Boeke, Amarda Shehu, Joel S. Bader

Research output: Chapter in Book/Report/Conference proceedingConference contribution


The goal of the Saccharomyces cerevisiae v2.0 project is the complete synthesis of a re-designed genome for baker's yeast. The resulting organism will permit systematic studies of eukaryotic chromosome structure that have been impossible to explore with traditional gene-at-a-time experiments. The efficiency of chemical synthesis of DNA does not yet permit direct synthesis of an entire chromosome, although it is now feasible to synthesize multi-kilobase pieces of DNA that can be combined into larger molecules. Designing a chromosome-sized sequence that can be assembled from smaller pieces has to date been accomplished by biological experts in a laborious and error-prone fashion. Here we pose DNA design as an optimization problem and obtain optimal solutions with a parallelizable dynamic programming algorithm.

Original languageEnglish (US)
Title of host publicationParallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers
Number of pages10
EditionPART 2
StatePublished - 2010
Event8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009 - Wroclaw, Poland
Duration: Sep 13 2009Sep 16 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
NumberPART 2
Volume6068 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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