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

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 languageEnglish (US)
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages280-289
Number of pages10
Volume6068 LNCS
EditionPART 2
DOIs
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)03029743
ISSN (Electronic)16113349

Other

Other8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009
CountryPoland
CityWroclaw
Period9/13/099/16/09

Fingerprint

Chromosomes
Chromosome
DNA
Yeast
Genes
Synthesis
Chemical Synthesis
Saccharomyces Cerevisiae
Dynamic programming
Dynamic Programming
Genome
Optimal Solution
Molecules
Entire
Optimization Problem
Gene
Experiment
Design
Experiments

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Richardson, S. M., Olson, B. S., Dymond, J. S., Burns, R., Chandrasegaran, S., Boeke, J. D., ... Bader, J. S. (2010). Automated design of assemblable, modular, synthetic chromosomes. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (PART 2 ed., Vol. 6068 LNCS, 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.; Burns, Randal; Chandrasegaran, Srinivasan; Boeke, Jef D.; Shehu, Amarda; Bader, Joel S.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6068 LNCS 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 proceedingConference 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 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PART 2 edn, vol. 6068 LNCS, 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 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PART 2 ed. Vol. 6068 LNCS. 2010. p. 280-289. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); PART 2). https://doi.org/10.1007/978-3-642-14403-5_30
Richardson, Sarah M. ; Olson, Brian S. ; Dymond, Jessica S. ; Burns, Randal ; Chandrasegaran, Srinivasan ; Boeke, Jef D. ; Shehu, Amarda ; Bader, Joel S. / Automated design of assemblable, modular, synthetic chromosomes. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6068 LNCS 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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