ArticleGenome research2008
Generic eukaryotic core promoter prediction using structural features of DNA.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
- Characterization of archaeal promoters using explainable and web-based CNN model.BMC genomics · 2025Article
- Review
- Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function.International journal of molecular sciences · 2024Article
- Utilizing biological experimental data and molecular dynamics for the classification of mutational hotspots through machine learning.Bioinformatics advances · 2024Article
- Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters.International journal of molecular sciences · 2022Article
- PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest.Interdisciplinary sciences, computational life sciences · 2022Article
- Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle.BMC genomics · 2022Article
- A successful hybrid deep learning model aiming at promoter identification.BMC bioinformatics · 2022Article
- Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice.Scientific reports · 2022Article
- Leveraging omic features with F3UTER enables identification of unannotated 3'UTRs for synaptic genes.Nature communications · 2022Article
- Engineered Sleeping Beauty transposase redirects transposon integration away from genes.Nucleic acids research · 2022Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- Article
- ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.PLoS computational biology · 2021Article
- Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks.Briefings in bioinformatics · 2021Article
- DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs.Nucleic acids research · 2021Article
- Multiple plasmid origin-of-transfer regions might aid the spread of antimicrobial resistance to human pathogens.MicrobiologyOpen · 2020Article
- Promoter Architecture and Promoter Engineering inMetabolites · 2020Review
- Cloning and promoter analysis of palladin 90-kDa, 140-kDa, and 200-kDa isoforms involved in skeletal muscle cell maturation.BMC research notes · 2020Article
- RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum.Database : the journal of biological databases and curation · 2020Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite many recent efforts, in silico identification of promoter regions is still in its infancy. However, the accurate identification and delineation of promoter regions is important for several reasons, such as improving genome annotation and devising experiments to study and understand transcriptional regulation. Current methods to identify the core region of promoters require large amounts of high-quality training data and often behave like black box models that output predictions that are difficult to interpret. Here, we present a novel approach for predicting promoters in whole-genome sequences by using large-scale structural properties of DNA. Our technique requires no training, is applicable to many eukaryotic genomes, and performs extremely well in comparison with the best available promoter prediction programs. Moreover, it is fast, simple in design, and has no size constraints, and the results are easily interpretable. We compared our approach with 14 current state-of-the-art implementations using human gene and transcription start site data and analyzed the ENCODE region in more detail. We also validated our method on 12 additional eukaryotic genomes, including vertebrates, invertebrates, plants, fungi, and protists.
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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.