ArticleGenome biology2007
Determining promoter location based on DNA structure first-principles calculations.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- Structural Features of DNA in TATA-Containing and TATA-Less Core Promoters of RNA Polymerase II Differ.International journal of molecular sciences · 2026Article
- An ensemble deep learning framework for multi-class LncRNA subcellular localization with innovative encoding strategy.BMC biology · 2025Article
- Characterization of Single-Cell Cis-regulatory Elements Informs Implications for Cell Differentiation.Genome biology and evolution · 2024Article
- Assessing the reliability of point mutation as data augmentation for deep learning with genomic data.BMC bioinformatics · 2024Article
- Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network.PLoS computational biology · 2023Article
- Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs.International journal of molecular sciences · 2023Article
- Promoter evolution of mammalian gene duplicates.BMC biology · 2023Article
- Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change.International journal of molecular sciences · 2023Review
- Large-scale integration of DNA methylation and gene expression array platforms identifies bothEpigenetics · 2022Article
- Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters.International journal of molecular sciences · 2022Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- Article
- Current Analytical Strategies in Studying Chromatin-Associated-Proteome (Chromatome).Molecules (Basel, Switzerland) · 2021Review
- Computational Method for Classification of Avian Influenza A Virus Using DNA Sequence Information and Physicochemical Properties.Frontiers in genetics · 2021Article
- A Mini-review of the Computational Methods Used in Identifying RNA 5-Methylcytosine Sites.Current genomics · 2020Review
- RNAm5CPred: Prediction of RNA 5-Methylcytosine Sites Based on Three Different Kinds of Nucleotide Composition.Molecular therapy. Nucleic acids · 2019Article
- Integration of methylation QTL and enhancer-target gene maps with schizophrenia GWAS summary results identifies novel genes.Bioinformatics (Oxford, England) · 2019Article
- iProEP: A Computational Predictor for Predicting Promoter.Molecular therapy. Nucleic acids · 2019Article
- Toward a Universal Structural and Energetic Model for Prokaryotic Promoters.Biophysical journal · 2018Article
- M6APred-EL: A Sequence-Based Predictor for Identifying N6-methyladenosine Sites Using Ensemble Learning.Molecular therapy. Nucleic acids · 2018Article
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
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A new method for the prediction of promoter regions based on atomic molecular dynamics simulations of small oligonucleotides has been developed. The method works independently of gene structure conservation and orthology and of the presence of detectable sequence features. Results obtained with our method confirm the existence of a hidden physical code that modulates genome expression.
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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.