ArticleGenome biology2005
Explicit equilibrium modeling of transcription-factor binding and gene regulation.
Article in Genome biology, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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Who cites it
65 citing papers in PubMed.
- Evolutionary Simulations Reveal Role for Genomic Recombination in the Evolution of Gene Regulatory Network Complexity and Robustness.Genome biology and evolution · 2026Article
- Improving the generalization of protein expression models with mechanistic sequence information.Nucleic acids research · 2025Article
- Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode.Nucleic acids research · 2023Article
- Cooperative kinetics of ligand binding to linear polymers.Computational and structural biotechnology journal · 2022Article
- Fitting thermodynamic-based models: Incorporating parameter sensitivity improves the performance of an evolutionary algorithm.Mathematical biosciences · 2021Article
- Loop competition and extrusion model predicts CTCF interaction specificity.Nature communications · 2021Article
- Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features.Nature communications · 2020Article
- Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.Nature biotechnology · 2020Article
- A Comprehensive Drosophila melanogaster Transcription Factor Interactome.Cell reports · 2019Article
- Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli Are Altered with Age.Cell reports · 2018Article
- Article
- BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization.BMC bioinformatics · 2018Article
- Modulating Transcriptional Regulation of Plant Biomass Degrading Enzyme Networks for Rational Design of Industrial Fungal Strains.Frontiers in bioengineering and biotechnology · 2018Review
- Inherent limitations of probabilistic models for protein-DNA binding specificity.PLoS computational biology · 2017Article
- The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger.FEBS letters · 2017Article
- Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) · 2017Article
- Natural variation in non-coding regions underlying phenotypic diversity in budding yeast.Scientific reports · 2016Article
- A Systematic Ensemble Approach to Thermodynamic Modeling of Gene Expression from Sequence Data.Cell systems · 2015Article
- Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells.PloS one · 2015Article
- Transcription factor motif quality assessment requires systematic comparative analysis.F1000Research · 2015Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
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Abstract
We have developed a computational model that predicts the probability of transcription factor binding to any site in the genome. GOMER (generalizable occupancy model of expression regulation) calculates binding probabilities on the basis of position weight matrices, and incorporates the effects of cooperativity and competition by explicit calculation of coupled binding equilibria. GOMER can be used to test hypotheses regarding gene regulation that build upon this physically principled prediction of protein-DNA binding.
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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.