diff --git a/docs/citations.md b/docs/citations.md index bfa974d..1047239 100644 --- a/docs/citations.md +++ b/docs/citations.md @@ -12,9 +12,9 @@ Thanks for citing us! If you use BEDbase, geniml, or their components in your re |---------------|-----------------| | `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* | +| `scEmbed` single-cell embedding framework | LeRoy et al. (2024) *NAR Genomics and Bioinformatics* | +| `geniml` region set evaluations | Zheng et al. (2024) *NAR Genomics and Bioinformatics* | +| `geniml hmm` module | Rymuza et al. (2024) *Nucleic Acis Research* | | `bedbase` database | Unpublished | @@ -22,15 +22,17 @@ Thanks for citing us! If you use BEDbase, geniml, or their components in your re
  • Gharavi et al. (2024). Joint representation learning for retrieval and annotation of genomic interval sets
    Bioengineering. DOI: 10.3390/bioengineering11030263
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  • Zheng et al. (2023). Methods for evaluating unsupervised vector representations of genomic regions -
    bioRxiv. DOI: 10.1101/2023.08.28.555137
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  • Zheng et al. (2024). Methods for evaluating unsupervised vector representations of genomic regions +
    Nucleic Acids Research Genomics and Bioinformatics. DOI: 10.1093/nargab/lqae086
  • Xue et al. (2023). Opportunities and challenges in sharing and reusing genomic interval data
    Frontiers in Genetics. DOI: 10.3389/fgene.2023.1155809
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  • Rymuza et al. (2023). Methods for constructing and evaluating consensus genomic interval sets -
    bioRxiv. DOI: 10.1101/2023.08.03.551899
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  • LeRoy et al. (2023). Fast clustering and cell-type annotation of scATACdata with pre-trained embeddings -
    bioRxiv. DOI: 10.1101/2023.08.01.551452
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  • Rymuza et al. (2024). Methods for constructing and evaluating consensus genomic interval sets +
    Nucleic Acids Research. DOI: 10.1093/nar/gkae685
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  • LeRoy et al. (2024). Fast clustering and cell-type annotation of scATACdata with pre-trained embeddings +
    Nucleic Acids Research Genomics and Bioinformatics. DOI: 10.1093/nargab/lqae073
  • 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
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    Bioinformatics. DOI: 10.1093/bioinformatics/btab439 + +