ReviewBriefings in bioinformatics2023
A survey on algorithms to characterize transcription factor binding sites.
Review in Briefings in bioinformatics, 2023. 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.
- Non-Coding Negative Regulatory Features in Livestock Genomes: Functional Annotation and Causal Validation.Animals : an open access journal from MDPI · 2026Review
- AdipocyteCells · 2026Article
- Engineering genetic elements for microbial protein expression systems: Advances, challenges, applications, and prospects.Synthetic and systems biotechnology · 2026Review
- GAMMA: gap-aware motif mining under incomplete labeling with applications to MHC motifs.Bioinformatics (Oxford, England) · 2026Article
- Motif-based models accurately predict cell type-specific distal regulatory elements.Nature communications · 2025Article
- Inferring binding specificities of human transcription factors with the wisdom of crowds.bioRxiv : the preprint server for biology · 2025Article
- Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.Communications biology · 2025Article
- QTFPred: robust high-performance quantum machine learning modeling that predicts main and cooperative transcription factor bindings with base resolution.Briefings in bioinformatics · 2025Article
- Benchmarking transcription factor binding site prediction models: a comparative analysis on synthetic and biological data.Briefings in bioinformatics · 2025Article
- Benchmarking tools for transcription factor prioritization.Computational and structural biotechnology journal · 2024Article
- Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.bioRxiv : the preprint server for biology · 2024Article
- A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data.Briefings in bioinformatics · 2024Review
- Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function.BMC genomics · 2024Article
- Transcription factor ATMIN facilitates chemoresistance in nasopharyngeal carcinoma.Cell death & disease · 2024Article
- BestCRM: An Exhaustive Search for Optimal Cis-Regulatory Modules in Promoters Accelerated by the Multidimensional Hash Function.International journal of molecular sciences · 2024Article
- Comparative analysis of models in predicting the effects of SNPs on TF-DNA binding using large-scale in vitro and in vivo data.Briefings in bioinformatics · 2024Article
- HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors.Nucleic acids research · 2024Article
- Bioinformatics tools for the sequence complexity estimates.Biophysical reviews · 2023Review
- TFBSFootprinter: a multiomics tool for prediction of transcription factor binding sites in vertebrate species.TranscriptionArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Transcription factors (TFs) are key regulatory proteins that control the transcriptional rate of cells by binding short DNA sequences called transcription factor binding sites (TFBS) or motifs. Identifying and characterizing TFBS is fundamental to understanding the regulatory mechanisms governing the transcriptional state of cells. During the last decades, several experimental methods have been developed to recover DNA sequences containing TFBS. In parallel, computational methods have been proposed to discover and identify TFBS motifs based on these DNA sequences. This is one of the most widely investigated problems in bioinformatics and is referred to as the motif discovery problem. In this manuscript, we review classical and novel experimental and computational methods developed to discover and characterize TFBS motifs in DNA sequences, highlighting their advantages and drawbacks. We also discuss open challenges and future perspectives that could fill the remaining gaps in the field.
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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.