ArticlePloS one2014
A new exhaustive method and strategy for finding motifs in ChIP-enriched regions.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Naïve pluripotency and genomic stability are coordinated in embryonic stem cells by a novel pluripotency regulator ZFP998.Nucleic acids research · 2026Article
- Revisiting motif finding: do bi-objective metaheuristics surpass single-objective metaheuristics?BMC bioinformatics · 2025Article
- G-protein-coupled receptor ADGRG1 drives a protective microglial state in Alzheimer's disease through MYC activation.Neuron · 2025Article
- CHD7 and SOX2 act in a common gene regulatory network during mammalian semicircular canal and cochlear development.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks.International journal of molecular sciences · 2024Article
- MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2023Article
- Genome-wide mapping of G-quadruplex structures with CUT&Tag.Nucleic acids research · 2022Article
- A survey on deep learning in DNA/RNA motif mining.Briefings in bioinformatics · 2021Article
- A Clustering Approach for Motif Discovery in ChIP-Seq Dataset.Entropy (Basel, Switzerland) · 2019Article
- MODSIDE: a motif discovery pipeline and similarity detector.BMC genomics · 2018Article
- SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets.BMC bioinformatics · 2018Article
- Insights from resolving protein-DNA interactions at near base-pair resolution.Briefings in functional genomics · 2018Review
- Performance evaluation for MOTIFSIM.Biological procedures online · 2018Article
- Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production.Frontiers in bioengineering and biotechnology · 2018Review
- Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells.Frontiers in genetics · 2016Review
- An Entropy-Based Position Projection Algorithm for Motif Discovery.BioMed research international · 2016Article
- PairMotifChIP: A Fast Algorithm for Discovery of Patterns Conserved in Large ChIP-seq Data Sets.BioMed research international · 2016Article
- A Fast Cluster Motif Finding Algorithm for ChIP-Seq Data Sets.BioMed research international · 2015Article
- Review of Different Sequence Motif Finding Algorithms.Avicenna journal of medical biotechnologyReview
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with next-generation parallel sequencing, allows for the genome-wide identification of protein-DNA interactions. This technology poses new challenges for the development of novel motif-finding algorithms and methods for determining exact protein-DNA binding sites from ChIP-enriched sequencing data. State-of-the-art heuristic, exhaustive search algorithms have limited application for the identification of short (l, d) motifs (l ≤ 10, d ≤ 2) contained in ChIP-enriched regions. In this work we have developed a more powerful exhaustive method (FMotif) for finding long (l, d) motifs in DNA sequences. In conjunction with our method, we have adopted a simple ChIP-enriched sampling strategy for finding these motifs in large-scale ChIP-enriched regions. Empirical studies on synthetic samples and applications using several ChIP data sets including 16 TF (transcription factor) ChIP-seq data sets and five TF ChIP-exo data sets have demonstrated that our proposed method is capable of finding these motifs with high efficiency and accuracy. The source code for FMotif is available at http://211.71.76.45/FMotif/.
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