ArticleBMC bioinformatics2009
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 17 citations in OpenAlex.
- Protocol for identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data.STAR protocols · 2026Article
- BayesPI-FLY: a Bayesian neural network approach for inferring feature weighted TF-DNA interaction.Briefings in bioinformatics · 2026Article
- SMUG1 DNA glycosylase modulates reward behaviour through regulation of olfactory receptor gene expression.Nucleic acids research · 2025Article
- Identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data.iScience · 2023Article
- abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis.BMC bioinformatics · 2022Article
- Anticipating response function in gene regulatory networks.Journal of the Royal Society, Interface · 2021Article
- IGAP-integrative genome analysis pipeline reveals new gene regulatory model associated with nonspecific TF-DNA binding affinity.Computational and structural biotechnology journal · 2020Article
- BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts.Frontiers in genetics · 2019Article
- Article
- Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma.Scientific reports · 2017Article
- BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations.Nucleic acids research · 2015Article
- Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation.BMC genomics · 2015Article
- Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence.BMC bioinformatics · 2014Article
- Computational study of associations between histone modification and protein-DNA binding in yeast genome by integrating diverse information.BMC genomics · 2011Article
- Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions.PloS one · 2011Article
- The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data.BMC bioinformatics · 2010Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe have incorporated Bayesian model regularization with biophysical modeling of protein-DNA interactions, and of genome-wide nucleosome positioning to study protein-DNA interactions, using a high-throughput dataset. The newly developed method (BayesPI) includes the estimation of a transcription factor (TF) binding energy matrices, the computation of binding affinity of a TF target site and the corresponding chemical potential.
resultsThe method was successfully tested on synthetic ChIP-chip datasets, real yeast ChIP-chip experiments. Subsequently, it was used to estimate condition-specific and species-specific protein-DNA interaction for several yeast TFs.
conclusionThe results revealed that the modification of the protein binding parameters and the variation of the individual nucleotide affinity in either recognition or flanking sequences occurred under different stresses and in different species. The findings suggest that such modifications may be adaptive and play roles in the formation of the environment-specific binding patterns of yeast TFs and in the divergence of TF binding sites across the related yeast species.
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