ArticleGenome research2011
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 353 papers, 2 of them syntheses that pooled it.
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
353 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Improved linking of motifs to their TFs using domain information.Bioinformatics (Oxford, England) · 2020Pooled it
- A Review of Statistical Methods for Identifying Trait-Relevant Tissues and Cell Types.Frontiers in genetics · 2020Pooled it
- Type 1 interferon perturbates clonal competition by reshaping human blood development.Nature genetics · 2026Article
- Multi-tissue analyses of allele-specific chromatin accessibility nominate likely functional variants for type 2 diabetes.medRxiv : the preprint server for health sciences · 2026Article
- Predictive modeling of signal-responsive cis-elements in human red blood cell precursors.Nucleic acids research · 2026Article
- Modeling strategies forBioinformatics advances · 2026Article
- The Algorithm for Reversible Jump Inference of Motifs.bioRxiv : the preprint server for biology · 2025Article
- Multi-omics data-based modeling reveals tumorigenesis- and prognosis-associated genes with clinical potential in lung adenocarcinoma.BMC cancer · 2025Article
- HBMC bioinformatics · 2025Article
- BRD9 functions as an HIV-1 latency regulatory factor.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genomic analysis of progenitors in viral infection implicates glucocorticoids as suppressors of plasmacytoid dendritic cell generation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A genetically informed brain atlas for enhancing brain imaging genomics.Nature communications · 2025Article
- Functional characterization of eQTLs and asthma risk loci with scATAC-seq across immune cell types and contexts.American journal of human genetics · 2025Article
- KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome.Genome research · 2025Article
- ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants.bioRxiv : the preprint server for biology · 2025Article
- Overview and Prospects of DNA Sequence Visualization.International journal of molecular sciences · 2025Review
- The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes.BMC bioinformatics · 2024Article
- Article
- Coordination among frequent genetic variants imparts substance use susceptibility and pathogenesis.Frontiers in neuroscience · 2024Article
- XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2024Article
293 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
6 authors.
Funding
Abstract
Accurate functional annotation of regulatory elements is essential for understanding global gene regulation. Here, we report a genome-wide map of 827,000 transcription factor binding sites in human lymphoblastoid cell lines, which is comprised of sites corresponding to 239 position weight matrices of known transcription factor binding motifs, and 49 novel sequence motifs. To generate this map, we developed a probabilistic framework that integrates cell- or tissue-specific experimental data such as histone modifications and DNase I cleavage patterns with genomic information such as gene annotation and evolutionary conservation. Comparison to empirical ChIP-seq data suggests that our method is highly accurate yet has the advantage of targeting many factors in a single assay. We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell types or tissues under diverse conditions.
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.