Journal article
MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs
BMC bioinformatics, Vol.10(1), pp.304-304
22 Sep 2009
PMCID: PMC2761410
PMID: 19772626
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing.
An efficient and scalable search method for finding near-optimal dual-channel microarray designs, based on a greedy hill-climbing optimization strategy, has been developed. It is empirically shown that this method can successfully and efficiently find near-optimal designs. Additionally, an improved interwoven loop design construction algorithm has been developed to provide an easily computable general class of near-optimal designs. Finally, in order to make the best results readily available to biologists, a continuously evolving catalog of near-optimal designs is provided.
A new search algorithm and database for near-optimal microarray designs have been developed. The search tool and the database are accessible via the World Wide Web at http://db.cse.ohio-state.edu/MicroarrayDesigner. Source code and binary distributions are available for academic use upon request.
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Details
- Title
- MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs
- Creators
- Ahmet Sacan - Computer Engineering Department, Middle East Technical University, Ankara, Turkey. ahmet@ceng.metu.edu.trNilgun FerhatosmanogluHakan Ferhatosmanoglu
- Publication Details
- BMC bioinformatics, Vol.10(1), pp.304-304
- Publisher
- Springer BMC; England
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Identifiers
- 991014877945204721
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- Domestic collaboration
- International collaboration
- Web of Science research areas
- Biochemical Research Methods
- Biotechnology & Applied Microbiology
- Mathematical & Computational Biology