ArticleNucleic acids research2018
Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
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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
36 citing papers in PubMed.
- Toward generalizable and interpretable AI in regulatory genomics.Nature genetics · 2026Review
- Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models.Nature communications · 2026Article
- Article
- ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes.Nucleic acids 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
- Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State.Hypertension (Dallas, Tex. : 1979) · 2024Article
- Functional Characterization of Accessible Chromatin in Common Wheat.International journal of molecular sciences · 2024Article
- The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis.Nature communications · 2024Article
- ZNF143 binds DNA and stimulates transcripstion initiation to activate and repress direct target genes.bioRxiv : the preprint server for biology · 2024Article
- Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.Epigenomes · 2024Review
- TRPS1 modulates chromatin accessibility to regulate estrogen receptor alpha (ER) binding and ER target gene expression in luminal breast cancer cells.PLoS genetics · 2024Article
- Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling.NAR genomics and bioinformatics · 2023Article
- The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis.bioRxiv : the preprint server for biology · 2023Article
- ATAC-seq exposes differences in chromatin accessibility leading to distinct leaf shapes in mulberry.Plant direct · 2022Article
- Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.Nature communications · 2022Article
- Chromatin accessibility profiling by ATAC-seq.Nature protocols · 2022Review
- Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data.Genome research · 2022Article
- Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification.NAR genomics and bioinformatics · 2021Article
- The ThioesteraseOmics : a journal of integrative biology · 2021Article
- Annotating the Insect Regulatory Genome.Insects · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Coupling molecular biology to high-throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases. SeqOutBias efficiently corrects DNase-seq, TACh-seq, ATAC-seq, MNase-seq and PRO-seq data. We show that seqOutBias correction facilitates identification of true molecular signatures resulting from transcription factors and RNA polymerase interacting with DNA.
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Registered trials
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