Merge remote-tracking branch 'origin/master'

docs/citations.md

@@ -12,25 +12,27 @@ 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 | `bedbase` database | Unpublished |
 
 
 ## Full citation information for manuscripts 
 
 <li><b>Gharavi et al. (2024). </b><i>Joint representation learning for retrieval and annotation of genomic interval sets</i> 
 <br><i>Bioengineering</i>.  <span class="doi">DOI: <a href="http://dx.doi.org/10.3390/bioengineering11030263">10.3390/bioengineering11030263</a></span></li>
-<li><b>Zheng et al. (2023). </b><i>Methods for evaluating unsupervised vector representations of genomic regions</i> 
-<br><i>bioRxiv</i>.  <span class="doi">DOI: <a href="http://dx.doi.org/10.1101/2023.08.28.555137">10.1101/2023.08.28.555137</a></span></li>
+<li><b>Zheng et al. (2024). </b><i>Methods for evaluating unsupervised vector representations of genomic regions</i> 
+<br><i>Nucleic Acids Research Genomics and Bioinformatics</i>.  <span class="doi">DOI: <a href="https://doi.org/10.1093/nargab/lqae086">10.1093/nargab/lqae086</a></span></li>
 <li><b>Xue et al. (2023). </b><i>Opportunities and challenges in sharing and reusing genomic interval data</i> 
 <br><i>Frontiers in Genetics</i>.  <span class="doi">DOI: <a href="http://dx.doi.org/10.3389/fgene.2023.1155809">10.3389/fgene.2023.1155809</a></span></li>
-<li><b>Rymuza et al. (2023). </b><i>Methods for constructing and evaluating consensus genomic interval sets</i> 
-<br><i>bioRxiv</i>.  <span class="doi">DOI: <a href="http://dx.doi.org/10.1101/2023.08.03.551899">10.1101/2023.08.03.551899</a></span></li>
-<li><b>LeRoy et al. (2023). </b><i>Fast clustering and cell-type annotation of scATACdata with pre-trained embeddings</i> 
-<br><i>bioRxiv</i>.  <span class="doi">DOI: <a href="http://dx.doi.org/10.1101/2023.08.01.551452">10.1101/2023.08.01.551452</a></span></li>
+<li><b>Rymuza et al. (2024). </b><i>Methods for constructing and evaluating consensus genomic interval sets</i> 
+<br><i>Nucleic Acids Research</i>.  <span class="doi">DOI: <a href="https://doi.org/10.1093/nar/gkae685">10.1093/nar/gkae685</a></span></li>
+<li><b>LeRoy et al. (2024). </b><i>Fast clustering and cell-type annotation of scATACdata with pre-trained embeddings</i> 
+<br><i>Nucleic Acids Research Genomics and Bioinformatics</i>.  <span class="doi">DOI: <a href="http://dx.doi.org/10.1093/nargab/lqae073">10.1093/nargab/lqae073</a></span></li>
 <li><b>Gu et al. (2021). </b><i>Bedshift: perturbation of genomic interval sets</i> 
 <br><i>Genome Biology</i>.  <span class="doi">DOI: <a href="http://dx.doi.org/10.1186/s13059-021-02440-w">10.1186/s13059-021-02440-w</a></span></li>
 <li><b>Gharavi et al. (2021). </b><i>Embeddings of genomic region sets capture rich biological associations in low dimensions</i> 
-<br><i>Bioinformatics</i>.  <span class="doi">DOI: <a href="http://dx.doi.org/10.1093/bioinformatics/btab439">10.1093/bioinformatics/btab439</a></span></li>
+<br><i>Bioinformatics</i>.  <span class="doi">DOI: <a href="http://dx.doi.org/10.1093/bioinformatics/btab439">10.1093/bioinformatics/btab439</a></span></li>
+
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