Manuscripts describing BEDbase and geniml

Components of BEDbase and geniml have been published independently. Here, we showcase the tutorials organized by the manuscript that published them, so if you're reading a paper you can more easily find the relevant features. Find the citation of interest on the left to find links to tutorials published as part of each manuscript.

How to cite BEDbase and geniml

Thanks for citing us! If you use BEDbase, geniml, or their components in your research, here are papers you can cite.

If you use...	Please cite ...
region2vec embeddings	Gharavi et al. (2021) Bioinformatics
bedspace search and embeddings	Gharavi et al. (2024) Bioengineering
scEmbed single-cell embedding framework	LeRoy et al. (2023) bioRxiv
geniml region set evaluations	Zheng et al. (2023) bioRxiv
geniml hmm module	Rymuza et al. (2023) bioRxiv
bedbase database	Unpublished

Full citation information for manuscripts

Gharavi et al. (2024). Joint representation learning for retrieval and annotation of genomic interval sets
Bioengineering. DOI: 10.3390/bioengineering11030263

Zheng et al. (2023). Methods for evaluating unsupervised vector representations of genomic regions
bioRxiv. DOI: 10.1101/2023.08.28.555137

Xue et al. (2023). Opportunities and challenges in sharing and reusing genomic interval data
Frontiers in Genetics. DOI: 10.3389/fgene.2023.1155809

Rymuza et al. (2023). Methods for constructing and evaluating consensus genomic interval sets
bioRxiv. DOI: 10.1101/2023.08.03.551899

LeRoy et al. (2023). Fast clustering and cell-type annotation of scATACdata with pre-trained embeddings
bioRxiv. DOI: 10.1101/2023.08.01.551452

Gu et al. (2021). Bedshift: perturbation of genomic interval sets
Genome Biology. DOI: 10.1186/s13059-021-02440-w

Gharavi et al. (2021). Embeddings of genomic region sets capture rich biological associations in low dimensions
Bioinformatics. DOI: 10.1093/bioinformatics/btab439