ReviewNucleic acids research2013
Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.
Review in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- Unraveling the Enigma of Organismal Death: Insights, Implications, and Unexplored Frontiers.Physiology (Bethesda, Md.) · 2024Review
- ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation.BMC genomics · 2019Article
- VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens.Biomedical and environmental sciences : BES · 2018Article
- Comparison of statistical methods and the use of quality control samples for batch effect correction in human transcriptome data.PloS one · 2018Article
- Array Analysis Manager-An automated DNA microarray analysis tool simplifying microarray data filtering, bias recognition, normalization, and expression analysis.Engineering in life sciences · 2017Article
- Hamming Distance as a Concept in DNA Molecular Recognition.ACS omega · 2017Article
- Datasets used to discover the microbial signatures of oral dysbiosis, periodontitis and edentulism in humans.Data in brief · 2017Article
- Gene Meter: Accurate abundance calculations of gene expression.Communicative & integrative biology · 2017Article
- Tracing the dynamics of gene transcripts after organismal death.Open biology · 2017Article
- Thermodynamic framework to assess low abundance DNA mutation detection by hybridization.PloS one · 2017Article
- Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy.Beilstein journal of nanotechnology · 2016Article
- Information Limited Oligonucleotide Amplification Assay for Affinity-Based, Parallel Detection Studies.PloS one · 2016Article
- Surface vs. solution hybridization: effects of salt, temperature, and probe type.Chemical communications (Cambridge, England) · 2015Article
- Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism.BMC oral health · 2015Article
- The Impact of Photobleaching on Microarray Analysis.Biology · 2015Article
- Crowding-induced cooperativity in DNA surface hybridization.Scientific reports · 2015Article
- Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data.Microarrays (Basel, Switzerland) · 2014Article
- Estimating differential expression from multiple indicators.Nucleic acids research · 2014Article
- Single-stranded DNA catalyzes hybridization of PCR-products to microarray capture probes.PloS one · 2014Article
- A revised design for microarray experiments to account for experimental noise and uncertainty of probe response.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors.
Funding
Abstract
Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.
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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.