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BEDbase

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

Section titled “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 embeddingsGharavi et al. (2021) Bioinformatics
bedspace search and embeddingsGharavi et al. (2024) Bioengineering
scEmbed single-cell embedding frameworkLeRoy et al. (2024) NAR Genomics and Bioinformatics
geniml region set evaluationsZheng et al. (2024) NAR Genomics and Bioinformatics
geniml hmm moduleRymuza et al. (2024) Nucleic Acis Research
bedbase databaseUnpublished
tokenizers moduleLeRoy et al. (2025) arXiv
atacformer foundation modelLeRoy et al. (2025) bioRxiv

Full citation information for manuscripts

Section titled “Full citation information for manuscripts”

  • LeRoy et al. (2025). Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data. bioRxiv. 10.1101/2025.11.03.685753

  • LeRoy et al. (2025). Fast, memory-efficient genomic interval tokenizers for modern machine learning. arXiv. 10.48550/arXiv.2511.01555

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

  • Zheng et al. (2024). Methods for evaluating unsupervised vector representations of genomic regions. Nucleic Acids Research Genomics and Bioinformatics. 10.1093/nargab/lqae086

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

  • Rymuza et al. (2024). Methods for constructing and evaluating consensus genomic interval sets. Nucleic Acids Research. 10.1093/nar/gkae685

  • LeRoy et al. (2024). Fast clustering and cell-type annotation of scATAC data with pre-trained embeddings. Nucleic Acids Research Genomics and Bioinformatics. 10.1093/nargab/lqae073

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

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