ArticleBioinformatics (Oxford, England)2019
ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- Dynamic transcriptional and epigenetic changes define postnatal tendon growth.PLoS genetics · 2025Article
- A community effort to optimize sequence-based deep learning models of gene regulation.Nature biotechnology · 2025Article
- BIOMAPP::CHIP: large-scale motif analysis.BMC bioinformatics · 2024Article
- A weighted two-stage sequence alignment framework to identify motifs from ChIP-exo data.Patterns (New York, N.Y.) · 2024Article
- Article
- Evaluation and optimization of sequence-based gene regulatory deep learning models.bioRxiv : the preprint server for biology · 2024Article
- Identification of DNA motif pairs on paired sequences based on composite heterogeneous graph.Frontiers in genetics · 2024Article
- CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq.Briefings in bioinformatics · 2023Article
- A survey on algorithms to characterize transcription factor binding sites.Briefings in bioinformatics · 2023Review
- Article
- A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome.BMC genomics · 2022Article
- Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice.BMC biology · 2022Article
- PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes.Database : the journal of biological databases and curation · 2022Article
- STREME: accurate and versatile sequence motif discovery.Bioinformatics (Oxford, England) · 2021Article
- Fast and exact quantification of motif occurrences in biological sequences.BMC bioinformatics · 2021Article
- Accurate prediction ofNAR genomics and bioinformatics · 2021Article
- Deciphering epigenomic code for cell differentiation using deep learning.BMC genomics · 2019Article
- TFBSFootprinter: a multiomics tool for prediction of transcription factor binding sites in vertebrate species.TranscriptionArticle
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5 authors.
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Abstract
motivationThe availability of numerous ChIP-seq datasets for transcription factors (TF) has provided an unprecedented opportunity to identify all TF binding sites in genomes. However, the progress has been hindered by the lack of a highly efficient and accurate tool to find not only the target motifs, but also cooperative motifs in very big datasets.
resultsWe herein present an ultrafast and accurate motif-finding algorithm, ProSampler, based on a novel numeration method and Gibbs sampler. ProSampler runs orders of magnitude faster than the fastest existing tools while often more accurately identifying motifs of both the target TFs and cooperators. Thus, ProSampler can greatly facilitate the efforts to identify the entire cis-regulatory code in genomes. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available for download at https://github.com/zhengchangsulab/prosampler. It was implemented in C++ and supported on Linux, macOS and MS Windows platforms. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.
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