ArticleBiology direct2007
nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays.
Article in Biology direct, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 1 of them a synthesis that pooled it.
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
61 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Integration of the naive pluripotency gene network with the response to GSK3 inhibition by Tcf7l1-driven enhancer decommissioning.Stem cell reports · 2026Article
- Text mining reveals the increasing importance of genomic approaches in crop research and breeding.Molecular breeding : new strategies in plant improvement · 2025Review
- Article
- HPVTIMER: A shiny web application for tumor immune estimation in human papillomavirus-associated cancers.iMeta · 2023Article
- Blood RNA transcripts reveal similar and differential alterations in fundamental cellular processes in Alzheimer's disease and other neurodegenerative diseases.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2023Article
- Blood Transcript Biomarkers Selected by Machine Learning Algorithm Classify Neurodegenerative Diseases including Alzheimer's Disease.Biomolecules · 2022Article
- Rapid ovarian transcript changes during the onset of premature ovarian insufficiency.Reproduction & fertility · 2022Article
- Pathogen-induced inflammation is attenuated by the iminosugar MON-DNJ via modulation of the unfolded protein response.Immunology · 2021Article
- Elevated Choline Kinase α-Mediated Choline Metabolism Supports the Prolonged Survival of TRAF3-Deficient B Lymphocytes.Journal of immunology (Baltimore, Md. : 1950) · 2020Article
- Probing seco-steroid inhibition of the hedgehog signaling pathway.Molecular and cellular biochemistry · 2019Article
- Gene Coexpression Networks in Whole Blood Implicate Multiple Interrelated Molecular Pathways in Obesity in People with Asthma.Obesity (Silver Spring, Md.) · 2018Article
- The GPR120 agonist TUG-891 promotes metabolic health by stimulating mitochondrial respiration in brown fat.EMBO molecular medicine · 2018Article
- Each pregnancy linearly changes immune gene expression in the blood of healthy women compared with breast cancer patients.Clinical epidemiology · 2018Article
- An unbiased in vivo functional genomics screening approach in mice identifies novel tumor cell-based regulators of immune rejection.Cancer immunology, immunotherapy : CII · 2017Article
- Partial exhaustion of CD8 T cells and clinical response to teplizumab in new-onset type 1 diabetes.Science immunology · 2016Article
- A new statistical method for curve group analysis of longitudinal gene expression data illustrated for breast cancer in the NOWAC postgenome cohort as a proof of principle.BMC medical research methodology · 2016Article
- A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal.BMC genomics · 2015Article
- A gene expression-based comparison of cell adhesion to extracellular matrix and RGD-terminated monolayers.Biomaterials · 2015Article
- Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe.
resultsWe have devised a unique, non-degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide across manufacturers. We have named the encoded representation 'nuID', for nucleotide universal identifier. Inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, the encoding algorithm uniquely and non-degenerately transforms the sequence itself into a compact identifier (a lossless compression). In addition, we added a redundancy check (checksum) to validate the integrity of the identifier. These two steps, encoding plus checksum, result in an nuID, which is a unique, non-degenerate, permanent, robust and efficient representation of the probe sequence. For commercial applications that require the sequence identity to be confidential, we have an encryption schema for nuID. We demonstrate the utility of nuIDs for the annotation of Illumina microarrays, and we believe it has universal applicability as a source-independent naming convention for oligomers. REVIEWERS: This article was reviewed by Itai Yanai, Rong Chen (nominated by Mark Gerstein), and Gregory Schuler (nominated by David Lipman).
Identifiers
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.