ArticleGenome biology2019
CRUP: a comprehensive framework to predict condition-specific regulatory units.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- Modeling strategies forBioinformatics advances · 2026Article
- Structural variants in the 3D genome as drivers of disease.Nature reviews. Genetics · 2025Review
- Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.Nature genetics · 2025Article
- Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity.Nature structural & molecular biology · 2024Article
- Pig-eRNAdb: a comprehensive enhancer and eRNA dataset of pigs.Scientific data · 2024Article
- CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction.Bioinformatics (Oxford, England) · 2023Article
- Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes.Development (Cambridge, England) · 2023Article
- Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation.Nature communications · 2023Article
- Dynamic antagonism between key repressive pathways maintains the placental epigenome.Nature cell biology · 2023Article
- EBF1 primes B-lymphoid enhancers and limits the myeloid bias in murine multipotent progenitors.The Journal of experimental medicine · 2022Article
- Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes.Cell · 2022Article
- Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation.Molecular omics · 2022Article
- Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.Nucleic acids research · 2021Article
- Integrative analysis of epigenetics data identifies gene-specific regulatory elements.Nucleic acids research · 2021Article
- Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles.Briefings in bioinformatics · 2021Article
- ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.PLoS computational biology · 2021Article
- BAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genome.Genes & development · 2021Article
- DNA methylation and hydroxymethylation have distinct genome-wide profiles related to axonal regeneration.Epigenetics · 2021Article
- CRUP: a comprehensive framework to predict condition-specific regulatory units.Genome biology · 2019Article
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26 authors.
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Abstract
We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units. We thoroughly test and then apply CRUP to a rheumatoid arthritis model, identifying enhancer-gene pairs comprising known disease genes as well as new candidate genes.
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