VLSI cell placement techniques
ACM Computing Surveys (CSUR)
Scatter/Gather: a cluster-based approach to browsing large document collections
SIGIR '92 Proceedings of the 15th annual international ACM SIGIR conference on Research and development in information retrieval
Multi-way partitioning via spacefilling curves and dynamic programming
DAC '94 Proceedings of the 31st annual Design Automation Conference
Partitioning-based standard-cell global placement with an exact objective
Proceedings of the 1997 international symposium on Physical design
Optimal partitioners and end-case placers for standard-cell layout
ISPD '99 Proceedings of the 1999 international symposium on Physical design
Equireplicate Balanced Binary Codes for Oligo Arrays
SIAM Journal on Discrete Mathematics
Multilevel optimization for large-scale circuit placement
Proceedings of the 2000 IEEE/ACM international conference on Computer-aided design
Fidelity Probes for DNA Arrays
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Border Length Minimization in DNA Array Design
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Selecting Optimum DNA Oligos for Microarrays
BIBE '00 Proceedings of the 1st IEEE International Symposium on Bioinformatics and Biomedical Engineering
Rapid Large-Scale Oligonucleotide Selection for Microarrays
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
On the use of the linear assignment algorithm in module placement
DAC '81 Proceedings of the 18th Design Automation Conference
Evaluation of Placement Techniques for DNA Probe Array Layout
Proceedings of the 2003 IEEE/ACM international conference on Computer-aided design
On the border length minimization problem (BLMP) on a square array
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Improving the layout of oligonucleotide microarrays: pivot partitioning
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
A Novel Algorithm for Fast Synthesis of DNA Probes on Microarrays
ACM Journal on Emerging Technologies in Computing Systems (JETC)
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Design of DNA arrays for very large-scale immobilized polymer synthesis (VLSIPS) [8] seeks to minimize effects of unintended illumination during mask exposure steps. [9, 14] formulate this requirement as the Border Minimization Problem and give methods for placement (at array sites) and embedding (in the mask sequence) of probes in both synchronous and asynchronous regimes. These previous methods do not address several practical details of the application and, more critically, are not scalable to the O(108) probes contemplated for next-generation probe arrays. In this work, we make two main contributions:We give improved dynamic programming algorithms that perform probe embedding to minimize the number border conflicts while accounting for distance- and position-dependent border conflict weights, as well as the presence of polymorphic probes in the instance. We describe and experimentally validate the "engineering" of a scalable, high-quality asynchronous placement heuristic (which is moreover easily parallelizable) for DNA array design. Our heuristic is enabled by a novel approach for simultaneous re-placement and optimal re-embedding of an "independent set" of probes within a small window of the array..