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

doi:10.1007/978-3-642-14403-5_30

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

Biomedical Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

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 language	English (US)
Title of host publication	Parallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers
Pages	280-289
Number of pages	10
Edition	PART 2
DOIs	https://doi.org/10.1007/978-3-642-14403-5_30
State	Published - 2010
Event	8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009 - Wroclaw, Poland Duration: Sep 13 2009 → Sep 16 2009

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Number	PART 2
Volume	6068 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009
Country/Territory	Poland
City	Wroclaw
Period	9/13/09 → 9/16/09

ASJC Scopus subject areas

Theoretical Computer Science
General Computer Science

Access to Document

10.1007/978-3-642-14403-5_30

Cite this

Richardson, S. M., Olson, B. S., Dymond, J. S., Burns, R., Chandrasegaran, S., Boeke, J. D., Shehu, A., & Bader, J. S. (2010). Automated design of assemblable, modular, synthetic chromosomes. In Parallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers (PART 2 ed., pp. 280-289). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6068 LNCS, No. PART 2). https://doi.org/10.1007/978-3-642-14403-5_30

Automated design of assemblable, modular, synthetic chromosomes. / Richardson, Sarah M.; Olson, Brian S.; Dymond, Jessica S. et al.
Parallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers. PART 2. ed. 2010. p. 280-289 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6068 LNCS, No. PART 2).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Richardson, SM, Olson, BS, Dymond, JS, Burns, R, Chandrasegaran, S, Boeke, JD, Shehu, A & Bader, JS 2010, Automated design of assemblable, modular, synthetic chromosomes. in Parallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers. PART 2 edn, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), no. PART 2, vol. 6068 LNCS, pp. 280-289, 8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009, Wroclaw, Poland, 9/13/09. https://doi.org/10.1007/978-3-642-14403-5_30

Richardson SM, Olson BS, Dymond JS, Burns R, Chandrasegaran S, Boeke JD et al. Automated design of assemblable, modular, synthetic chromosomes. In Parallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers. PART 2 ed. 2010. p. 280-289. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2). doi: 10.1007/978-3-642-14403-5_30

Richardson, Sarah M. ; Olson, Brian S. ; Dymond, Jessica S. et al. / Automated design of assemblable, modular, synthetic chromosomes. Parallel Processing and Applied Mathematics - 8th International Conference, PPAM 2009, Revised Selected Papers. PART 2. ed. 2010. pp. 280-289 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2).

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Automated design of assemblable, modular, synthetic chromosomes

Abstract

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ASJC Scopus subject areas

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