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The Applications of General Expression Transformer
The applications of general expression transformer – an interpretable foundation model for human transcriptional regulation based on genome sequence and chromatin accessibility data
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An Interpretable Foundation Model for Predicting Transcriptional Regulation
General expression transformer or “GET” represents an interpretable foundation model for transcriptional regulation that can predict gene expression using chromatin accessibility data and sequence information from human cells
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Our Understanding of the Retina Just Got a Multi-Omic Overhaul
How Do Non-Coding Risk Variants and Cis-Regulatory Elements Contribute to Retinal Disease-associated Vision Loss? The growing global incidence of retinal diseases and the associated loss…
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Studying the Epigenetics of Tissue Development at Single-cell Resolution
Embracing the Potential of Integrated Single-cell Epigenetic and Transcriptomic Analyses Due to the importance of histone modifications in regulating the tightly controlled programs of gene…
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Contact Maps Define Developmental Roles of Regulatory Elements
The Mystery of Cis-Regulatory Elements Function during Mouse Fetal Development: What Genes are Involved? Analyzing layers of epigenetic regulation such as chromatin accessibility and histone…
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Single-cell Chromatin Conformations mapped by Droplet Hi-C (#2)
In the third in this series of blogs, we reported on the description of Droplet Hi-C by researchers from the laboratory of Bing Ren (University of…
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Mechanisms of β Cell Stress Responses revealed by Paired-Tag
A focus on β Cells in Type 2 Diabetes Pancreatic islet β cell dysfunction represents a core cause of most forms of diabetes. In type-1…
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Droplet Hi-C reveals cell-type-specific chromatin conformation
The Importance of Chromatin Organization to Normal Development and Tumorigenesis In the first and second in this series of blogs, we described the evaluation of…
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scDNAm and sc3C Analyses Describe the Developing Human Brain (Part 2)
Single-cell Joint Epigenetic Analyses in the Developing Brain In the first of this series of blogs, we described how Heffel et al. evaluated chromatin conformation…
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scDNAm and sc3C Analyses Describe the Developing Human Brain (Part 1)
Epigenetic Dynamism and Diversity in the Developing Human Brain The development of the human brain involves dynamic alterations at multiple epigenetic levels in the diverse…
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Paired-Tag Reveals Aberrant Activation States in AD Excitatory Neurons
Applying “Paired-Tag” (parallel analysis of individual cells for RNA expression and DNA from targeted tagmentation by sequencing) for joint epigenetic and gene expression profiling at single-cell…
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Paired-Tag: The Droplet Frontier
Improving Joint Single-cell Analysis with Droplet Paired-Tag Applying “Paired-Tag” (parallel analysis of individual cells for RNA expression and DNA from targeted tagmentation by sequencing) for joint…
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The Power of Paired-Tag: Part 2
Applications of Transcriptome/Epigenome Joint Profiling The first in a series of articles from Epigenome Technologies described “Paired-Tag” (parallel analysis of individual cells for RNA expression and…
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The Power of Paired-Tag: Part 1
Single-Cell Joint Profiling of Histone Modifications and Gene Expression The Importance of Joint Single-cell Analysis The identification of gene regulatory elements through the combination of…
