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bedbase database Unpublished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

Full citation information for manuscripts

N. J. LeRoy et al., “Fast clustering and cell-type annotation of scATACdata with pre-trained embeddings,” bioRxiv, 2023, doi: 10.1101/2023.08.01.551452.

J. Rymuza et al., “Methods for constructing and evaluating consensus genomic interval sets,” bioRxiv, 2023, doi: 10.1101/2023.08.03.551899.

E. Gharavi, N. J. LeRoy, G. Zheng, A. Zhang, D. E. Brown, and N. C. Sheffield, “Joint representation learning for retrieval and annotation of genomic interval sets,” bioRxiv, 2023, doi: 10.1101/2023.08.21.554131.

G. Zheng et al., “Methods for evaluating unsupervised vector representations of genomic regions,” bioRxiv, 2023, doi: 10.1101/2023.08.03.551899.

B. Xue, O. Khoroshevskyi, R. A. Gomez, and N. C. Sheffield, “Opportunities and challenges in sharing and reusing genomic interval data,” Frontiers in Genetics, vol. 14, 2023-03, doi: 10.3389/fgene.2023.1155809.

E. Gharavi et al., “Embeddings of genomic region sets capture rich biological associations in low dimensions,” Bioinformatics, 2021-03, doi: 10.1093/bioinformatics/btab439.