ArticleGenome biology2010
Genome-wide prediction of transcription factor binding sites using an integrated model.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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.
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Who cites it
71 citing papers in PubMed, 120 citations in OpenAlex.
- A Deep Learning Framework with Multi-perspective Feature Fusion for Transcription Factor Binding Site Prediction.Interdisciplinary sciences, computational life sciences · 2026Article
- BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning.Briefings in bioinformatics · 2024Article
- G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data.PLoS computational biology · 2023Article
- Fish-Ing for Enhancers in the Heart.International journal of molecular sciences · 2021Review
- An intriguing characteristic of enhancer-promoter interactions.BMC genomics · 2021Article
- A pitfall for machine learning methods aiming to predict across cell types.Genome biology · 2020Article
- Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types.Nucleic acids research · 2020Article
- A comprehensive review of computational prediction of genome-wide features.Briefings in bioinformatics · 2020Article
- MTTFsite: cross-cell type TF binding site prediction by using multi-task learning.Bioinformatics (Oxford, England) · 2019Article
- Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network.International journal of molecular sciences · 2019Article
- A neural network based model effectively predicts enhancers from clinical ATAC-seq samples.Scientific reports · 2018Article
- Cis-regulatory determinants of MyoD function.Nucleic acids research · 2018Article
- LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations.Nucleic acids research · 2018Article
- Noncoding Variants Functional Prioritization Methods Based on Predicted Regulatory Factor Binding Sites.Current genomics · 2017Review
- Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.Nucleic acids research · 2017Article
- Progress and challenges in bioinformatics approaches for enhancer identification.Briefings in bioinformatics · 2016Review
- A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions.Molecular systems biology · 2016Article
- The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs.Human molecular genetics · 2016Article
- Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges.Human heredity · 2016Review
- A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites.Bioinformatics (Oxford, England) · 2015Article
11 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 at 2 institutions in 2 countries.
Funding
Abstract
We present an integrated method called Chromia for the genome-wide identification of functional target loci of transcription factors. Designed to capture the characteristic patterns of transcription factor binding motif occurrences and the histone profiles associated with regulatory elements such as promoters and enhancers, Chromia significantly outperforms other methods in the identification of 13 transcription factor binding sites in mouse embryonic stem cells, evaluated by both binding (ChIP-seq) and functional (RNA interference knockdown) experiments.
Indexed as
Identifiers
What Socratic 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 Socratic graph.