ArticleNucleic acids research2010
chipD: a web tool to design oligonucleotide probes for high-density tiling arrays.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Accurate prediction of oligonucleotide probe hybridization efficiency via a transformer-based model.BMC genomics · 2026Article
- Dual RNA-seq in filarial nematodes andFrontiers in microbiology · 2024Article
- The Pathway-Specific Regulator ClaR of Streptomyces clavuligerus Has a Global Effect on the Expression of Genes for Secondary Metabolism and Differentiation.Applied and environmental microbiology · 2015Article
- Comparative genomics of Saccharomyces cerevisiae natural isolates for bioenergy production.Genome biology and evolution · 2014Article
- DksA guards elongating RNA polymerase against ribosome-stalling-induced arrest.Molecular cell · 2014Article
- Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses.Applied and environmental microbiology · 2013Article
- Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909).PloS one · 2013Article
- Rho and NusG suppress pervasive antisense transcription in Escherichia coli.Genes & development · 2012Article
- Conservation of thiol-oxidative stress responses regulated by SigR orthologues in actinomycetes.Molecular microbiology · 2012Article
- Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria.BMC genomics · 2012Article
- Comparative genomics of xylose-fermenting fungi for enhanced biofuel production.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
chipD is a web server that facilitates design of DNA oligonucleotide probes for high-density tiling arrays, which can be used in a number of genomic applications such as ChIP-chip or gene-expression profiling. The server implements a probe selection algorithm that takes as an input, in addition to the target sequences, a set of parameters that allow probe design to be tailored to specific applications, protocols or the array manufacturer's requirements. The algorithm optimizes probes to meet three objectives: (i) probes should be specific; (ii) probes should have similar thermodynamic properties; and (iii) the target sequence coverage should be homogeneous and avoid significant gaps. The output provides in a text format, the list of probe sequences with their genomic locations, targeted strands and hybridization characteristics. chipD has been used successfully to design tiling arrays for bacteria and yeast. chipD is available at http://chipd.uwbacter.org/.
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What OpenQuestion holds
Registered trials
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.