ArticleNucleic acids research2009
Model-based probe set optimization for high-performance microarrays.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- The Gpr1-regulated Sur7 family protein Sfp2 is required for hyphal growth and cell wall stability in the mycoparasite Trichoderma atroviride.Scientific reports · 2018Article
- Experiences with workflows for automating data-intensive bioinformatics.Biology direct · 2015Article
- Phylloxera (Daktulosphaira vitifoliae Fitch) alters the carbohydrate metabolism in root galls to allowing the compatible interaction with grapevine (Vitis ssp.) roots.Plant science : an international journal of experimental plant biology · 2015Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- Article
- The LO-BaFL method and ALS microarray expression analysis.BMC bioinformatics · 2012Article
- Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.Bioinformatics (Oxford, England) · 2011Article
- The impact of quantitative optimization of hybridization conditions on gene expression analysis.BMC bioinformatics · 2011Article
- Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida.PloS one · 2010Article
- Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization.Nucleic acids research · 2010Article
- Hybridization thermodynamics of NimbleGen microarrays.BMC bioinformatics · 2010Article
- PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification.Nucleic acids research · 2010Article
- Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays.BMC genomics · 2008Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A major challenge in microarray design is the selection of highly specific oligonucleotide probes for all targeted genes of interest, while maintaining thermodynamic uniformity at the hybridization temperature. We introduce a novel microarray design framework (Thermodynamic Model-based Oligo Design Optimizer, TherMODO) that for the first time incorporates a number of advanced modelling features: (i) A model of position-dependent labelling effects that is quantitatively derived from experiment. (ii) Multi-state thermodynamic hybridization models of probe binding behaviour, including potential cross-hybridization reactions. (iii) A fast calibrated sequence-similarity-based heuristic for cross-hybridization prediction supporting large-scale designs. (iv) A novel compound score formulation for the integrated assessment of multiple probe design objectives. In contrast to a greedy search for probes meeting parameter thresholds, this approach permits an optimization at the probe set level and facilitates the selection of highly specific probe candidates while maintaining probe set uniformity. (v) Lastly, a flexible target grouping structure allows easy adaptation of the pipeline to a variety of microarray application scenarios. The algorithm and features are discussed and demonstrated on actual design runs. Source code is available on request.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.