ArticleNature communications2021
Learning a genome-wide score of human-mouse conservation at the functional genomics level.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Harnessing Deep Learning Models for Guide RNA Optimization and Off-Target Prediction in CRISPR Systems.Biotechnology journal · 2026Review
- Deep learning of 777 K bulk transcriptomes reveals human-mouse gene conservation beyond DNA sequence similarity.Communications biology · 2026Article
- Learning a pairwise epigenomic and transcription factor binding association score across the human genome.Bioinformatics (Oxford, England) · 2026Article
- EnhancerMatcher: comparing cell-type-specific enhancer activity of DNA sequences using deep convolutional neural networks and explainable AI.NAR genomics and bioinformatics · 2025Article
- Mechanisms of Globin Gene Regulation in Mammals.Annual review of genetics · 2025Review
- Targeting eRNA-Producing Super-Enhancers Regulates TNFα Expression and Mitigates Chronic Inflammation in Mice and Patient-Derived Immune Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The Inhibition of Bromodomain and Extraterminal Domain (BET) Proteins Protects Against Microglia-Mediated Neuronal Loss In Vitro.Biomolecules · 2025Article
- Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.Genome research · 2024Article
- PlantFUNCO: Integrative Functional Genomics Database Reveals Clues into Duplicates Divergence Evolution.Molecular biology and evolution · 2024Article
- Genetic effects of sequence-conserved enhancer-like elements on human complex traits.Genome biology · 2024Article
- Learning functional conservation between human and pig to decipher evolutionary mechanisms underlying gene expression and complex traits.Cell genomics · 2023Article
- Universal chromatin state annotation of the mouse genome.Genome biology · 2023Article
- AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver.Bioinformatics (Oxford, England) · 2023Article
- A mammalian methylation array for profiling methylation levels at conserved sequences.Nature communications · 2022Article
- Intravenous AAV9 administration results in safe and widespread distribution of transgene in the brain of mini-pig.Frontiers in cell and developmental biology · 2022Article
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Authors and funding
2 authors.
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Abstract
Identifying genomic regions with functional genomic properties that are conserved between human and mouse is an important challenge in the context of mouse model studies. To address this, we develop a method to learn a score of evidence of conservation at the functional genomics level by integrating information from a compendium of epigenomic, transcription factor binding, and transcriptomic data from human and mouse. The method, Learning Evidence of Conservation from Integrated Functional genomic annotations (LECIF), trains neural networks to generate this score for the human and mouse genomes. The resulting LECIF score highlights human and mouse regions with shared functional genomic properties and captures correspondence of biologically similar human and mouse annotations. Analysis with independent datasets shows the score also highlights loci associated with similar phenotypes in both species. LECIF will be a resource for mouse model studies by identifying loci whose functional genomic properties are likely conserved.
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