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COMPUTER-AIDED OPTIMIZATION OF DNA ARRAY DESIGN AND MANUFACTURING

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Design Automation Methods and Tools for Microfluidics-Based Biochips

Abstract

DNA probe arrays, or DNA chips, have emerged as a core genomic technology that enables cost-effective gene expression monitoring, mutation detection, single nucleotide polymorphism analysis and other genomic analyses. DNA chips are manufactured through a highly scalable process, called Very Large-Scale Immobilized Polymer Synthesis (VLSIPS), that combines photolithographic technologies adapted from the semiconductor industry with combinatorial chemistry. As the number and size of DNA array designs continues to grow, there is an imperative need for highly-scalable software tools with predictable solution quality to assist in the design and manufacturing process. In this chapter we review recent algorithmic and methodological advances forming the foundation for a new generation of DNA array design tools. A recurring motif behind these advances is exploiting the analogy between silicon chip design, pointing to the value of technology transfer between the 40-year old VLSI CAD field and the newer DNA array design field.

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Author information

Authors and Affiliations

  1. CSE and ECE Department, University of California at San Diego, La Jolla, CA, 92093-0114, USA

    Andrew B. Kahng

  2. CSE Department, University of Connecticut, 371 Fairfield Rd., Unit 2155, Storrs, CT, 06269-2155, USA

    Ion I. Măndoiu

  3. CSE Department, University of California at San Diego, La Jolla, CA, 92093-0114, USA

    Sherief Reda

  4. CSE Department, University of California at San Diego, La Jolla, CA, 92093-0114, USA

    Xu Xu

  5. CS Department, Georgia State University, University Plaza, Atlanta, Georgia, 30303, USA

    Alex Z. Zelikovsky

Authors
  1. Andrew B. Kahng
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  2. Ion I. Măndoiu
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  3. Sherief Reda
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  4. Xu Xu
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  5. Alex Z. Zelikovsky
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Editor information

Editors and Affiliations

  1. Duke University, Durham, NC, U.S.A.

    Krishnendu Chakrabarty

  2. Coventor Inc., Cambridge, MA, U.S.A.

    Jun Zeng

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Kahng, A.B., Măndoiu, I.I., Reda, S., Xu, X., Zelikovsky, A.Z. (2006). COMPUTER-AIDED OPTIMIZATION OF DNA ARRAY DESIGN AND MANUFACTURING. In: Chakrabarty, K., Zeng, J. (eds) Design Automation Methods and Tools for Microfluidics-Based Biochips. Springer, Dordrecht . https://doi.org/10.1007/1-4020-5123-9_10

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  • DOI: https://doi.org/10.1007/1-4020-5123-9_10

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-1-4020-5122-7

  • Online ISBN: 978-1-4020-5123-4

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