ArticleApplied and environmental microbiology2006
Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications.
Article in Applied and environmental microbiology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities.mSystems · 2019Article
- Thermodynamically optimal whole-genome tiling microarray design and validation.BMC research notes · 2016Article
- Article
- The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities.The ISME journal · 2013Article
- Strain/species-specific probe design for microbial identification microarrays.Applied and environmental microbiology · 2013Article
- Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves.Journal of microbiological methods · 2012Article
- Use of functional gene arrays for elucidating in situ biodegradation.Frontiers in microbiology · 2012Article
- Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed.Applied and environmental microbiology · 2010Article
- Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain.Applied and environmental microbiology · 2010Article
- Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays.BMC bioinformatics · 2010Article
- Afforestation alters the composition of functional genes in soil and biogeochemical processes in South American grasslands.Applied and environmental microbiology · 2009Article
- Development and validation of a species-independent functional gene microarray that targets lactic acid bacteria.Applied and environmental microbiology · 2009Article
- sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters.BMC proceedings · 2009Article
- In silico microarray probe design for diagnosis of multiple pathogens.BMC genomics · 2008Article
- Design and analysis of mismatch probes for long oligonucleotide microarrays.BMC genomics · 2008Article
- Spatial scaling of functional gene diversity across various microbial taxa.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis.Applied and environmental microbiology · 2008Article
- A high-throughput pipeline for designing microarray-based pathogen diagnostic assays.BMC bioinformatics · 2008Article
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6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To optimize oligonucleotide probe design criteria, PCR products with different similarities to probes were hybridized to a functional gene microarray designed to detect homologous genes from different organisms. In contrast to more restrictive probe designs based on a single criterion, simultaneous consideration of the percent similarity (< or =90%), the length of identical sequence stretches (< or =20 bases), and the binding free energy (> or =-35 kcal mol(-1)) was found to be predictive of probe specificity.
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