ReviewGenomics2015
Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences.
Review in Genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it, 76 citations in OpenAlex.
- Imputation of orofacial clefting data identifies novel risk loci and sheds light on the genetic background of cleft lip ± cleft palate and cleft palate only.Human molecular genetics · 2017Pooled it
- Review
- Applications of high-throughput reporter assays to gene regulation studies.Current opinion in structural biology · 2025Review
- Functional genomics in age-related macular degeneration: From genetic associations to understanding disease mechanisms.Experimental eye research · 2025Review
- HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.BMC genomics · 2024Article
- Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.ACS synthetic biology · 2024Article
- HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.bioRxiv : the preprint server for biology · 2024Article
- Engineering is evolution: a perspective on design processes to engineer biology.Nature communications · 2024Article
- From sequence to consequence: Deciphering the complex cisregulatory landscape.Journal of biosciences · 2024Article
- Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.Nature genetics · 2023Article
- Article
- A computational investigation of cis-gene regulation in evolution.Theory in biosciences = Theorie in den Biowissenschaften · 2023Article
- A scalable technology for measuring cell-type-specific activity of cis-regulatory sequences.Nature genetics · 2023Article
- Targeted mutagenesis and high-throughput screening of diversified gene and promoter libraries for isolating gain-of-function mutations.Frontiers in bioengineering and biotechnology · 2023Article
- Differentially Active and Conserved Neural Enhancers Define Two Forms of Adaptive Noncoding Evolution in Humans.Genome biology and evolution · 2022Article
- MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect.Genome biology · 2022Article
- Toward transcriptomics as a primary tool for rare disease investigation.Cold Spring Harbor molecular case studies · 2022Article
- Molecular and evolutionary processes generating variation in gene expression.Nature reviews. Genetics · 2021Review
- Detection of gene cis-regulatory element perturbations in single-cell transcriptomes.PLoS computational biology · 2021Article
- A Mutation in theG3 (Bethesda, Md.) · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Genome-scale methods have identified thousands of candidate cis-regulatory elements (CREs), but methods to directly assay the regulatory function of these elements on a comparably large scale have not been available. The inability to directly test and perturb the regulatory activity of large numbers of DNA sequences has hindered efforts to discover how cis-regulatory function is encoded in genomic sequence. Recently developed massively parallel reporter gene assays combine next generation sequencing with high-throughput oligonucleotide synthesis to offer the capacity to test and mutationally perturb thousands of specifically chosen or designed cis-regulatory sequences in a single experiment. These assays are the basis of recent studies that include large-scale functional validation of genomic CREs, exhaustive mutational analyses of individual regulatory sequences, and tests of large libraries of synthetic CREs. The results demonstrate how massively parallel reporter assays with libraries of designed sequences provide the statistical power required to address previously intractable questions about cis-regulatory function.
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.