ArticleProceedings of the National Academy of Sciences of the United States of America2018
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 153 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
153 citing papers in PubMed.
- Single-allele chromatin tracing reveals cytokine-dependent super-enhancer repositioning in CD4Immunity · 2026Article
- Article
- Senescent cells cluster CTCF on nuclear speckles to instruct an alternative splicing program.Nature aging · 2026Article
- Exosome-Secreted Tropomyosin and Gigasin-6 Roles in Biomineralization Divergence Between Estuarine and Coastal Oysters.Marine biotechnology (New York, N.Y.) · 2026Article
- Phytochrome B sets condensate number through graded nucleator states and seeding-site efficacy.Nature communications · 2026Article
- Review
- Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.Molecular cell · 2026Article
- Accurate prediction of oligonucleotide probe hybridization efficiency via a transformer-based model.BMC genomics · 2026Article
- Ki-67 shapes the nucleolus by anchoring chromatin via its amphiphilic properties.The EMBO journal · 2026Article
- OligoN-Design: A Simple and Versatile Tool to Design Specific Probes and Primers From Large Heterogeneous Datasets.Molecular ecology resources · 2026Article
- Unique territorial and compartmental organization of chromosomes in the holocentric silkworm.The EMBO journal · 2026Article
- Heterogeneity between VIP and GRP neurons underlies AVP receptor signaling in the mouse suprachiasmatic nucleus.Communications biology · 2026Article
- Chromosome-specific painting provides insights into the karyotype evolutionary direction and trajectory in the genusHorticulture research · 2026Article
- The functional organization of chromosome territories in single nuclei during zygotic genome activation.Scientific reports · 2026Article
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships.Nature biomedical engineering · 2026Article
- Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation.Nature cell biology · 2026Article
- Nanoscale dynamics of enhancer-promoter interactions during exit from pluripotency.Nucleic acids research · 2025Article
- Transcription arrest induces formation of RNA granules in mitochondria.Life science alliance · 2025Article
- OligoY pipeline for full Y chromosome painting.Briefings in bioinformatics · 2025Article
93 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
8 authors.
Funding
Abstract
Oligonucleotide (oligo)-based FISH has emerged as an important tool for the study of chromosome organization and gene expression and has been empowered by the commercial availability of highly complex pools of oligos. However, a dedicated bioinformatic design utility has yet to be created specifically for the purpose of identifying optimal oligo FISH probe sequences on the genome-wide scale. Here, we introduce OligoMiner, a rapid and robust computational pipeline for the genome-scale design of oligo FISH probes that affords the scientist exact control over the parameters of each probe. Our streamlined method uses standard bioinformatic file formats, allowing users to seamlessly integrate new and existing utilities into the pipeline as desired, and introduces a method for evaluating the specificity of each probe molecule that connects simulated hybridization energetics to rapidly generated sequence alignments using supervised machine learning. We demonstrate the scalability of our approach by performing genome-scale probe discovery in numerous model organism genomes and showcase the performance of the resulting probes with diffraction-limited and single-molecule superresolution imaging of chromosomal and RNA targets. We anticipate that this pipeline will make the FISH probe design process much more accessible and will more broadly facilitate the design of pools of hybridization probes for a variety of applications.
Indexed as
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.