[HTML][HTML] Joint representation learning for retrieval and annotation of genomic interval sets

E Gharavi, NJ LeRoy, G Zheng, A Zhang, DE Brown… - Bioengineering, 2024 - mdpi.com
As available genomic interval data increase in scale, we require fast systems to search
them. A common approach is simple string matching to compare a search term to metadata …

[HTML][HTML] Methods for constructing and evaluating consensus genomic interval sets

J Rymuza, Y Sun, G Zheng, NJ LeRoy… - Nucleic Acids …, 2024 - academic.oup.com
The amount of genomic region data continues to increase. Integrating across diverse
genomic region sets requires consensus regions, which enable comparing regions across …

[PDF][PDF] Methods for evaluating unsupervised vector representations of genomic regions

G Zheng, J Rymuza, E Gharavi… - NAR Genomics and …, 2024 - academic.oup.com
Abstract Representation learning models have become a mainstay of modern genomics.
These models are trained to yield vector representations, or embeddings, of various …