Publications by authors named "Kristy Mualim"
Article Synopsis
- Genetic diversity is crucial for species' ability to adapt and is now a target for protection in the UN's Global Biodiversity Framework, but current predictive models to assess its loss are lacking.
- A study combining population genetics and genomic data showed that genetic diversity decreases slowly after habitat loss and will continue to decline for decades even with habitat protection.
- Predictions indicate a short-term genetic diversity loss of 13-22% and a long-term loss of 42-48% across 13,808 species, emphasizing that merely protecting existing habitats is not enough to maintain genetic health.
Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with the promoters of their target genes. However, genome-wide depletions of architectural proteins such as cohesin result in only limited changes in gene expression, despite a loss of contact domains and loops. Consequently, the role of cohesin and 3D contacts in enhancer function remains debated.
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- - This study identifies over 13 million interactions between transcriptional enhancers and their target genes across various cell types and tissues, which is crucial for understanding how gene regulation influences diseases.
- - Utilizing a new predictive model called ENCODE-rE2G, the researchers achieved high accuracy in predicting enhancer-gene interactions, supported by a robust dataset from CRISPR experiments and genetic mapping.
- - The findings highlight not only the role of enhancers and their contacts with promoters but also additional factors like promoter types and enhancer interactions that affect gene regulation, creating a detailed resource for future genetic research.
We present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al.
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- Genome-wide association studies (GWAS) have found many noncoding regions related to diseases, but translating these findings into functional insights is challenging due to insufficient maps of enhancers and target genes.
- The activity-by-contact (ABC) model was developed to predict enhancer-gene interactions and applied across 131 human cell types, linking over 5,000 GWAS signals to nearly 2,250 unique genes with implications for various diseases.
- Specifically for inflammatory bowel disease (IBD), ABC model identified risk variants in enhancers that regulate gene expression, offering a new understanding of disease mechanisms and providing a blueprint for future connections between genetic variants and their functions.