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Volume 41, Issue 5, May 2025
Original Paper
Sequence analysis
ProtNote: a multimodal method for protein–function annotation
Bioinformatics, Volume 41, Issue 5, May 2025, btaf170, https://doi.org/10.1093/bioinformatics/btaf170
De novo clustering of large long-read transcriptome datasets with isONclust3
Bioinformatics, Volume 41, Issue 5, May 2025, btaf207, https://doi.org/10.1093/bioinformatics/btaf207
EPIPDLF: a pretrained deep learning framework for predicting enhancer–promoter interactions
Bioinformatics, Volume 41, Issue 5, May 2025, btae716, https://doi.org/10.1093/bioinformatics/btae716
Structural bioinformatics
Finding antibodies in cryo-EM maps with CrAI
Bioinformatics, Volume 41, Issue 5, May 2025, btaf157, https://doi.org/10.1093/bioinformatics/btaf157
Gene expression
Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA
Bioinformatics, Volume 41, Issue 5, May 2025, btaf138, https://doi.org/10.1093/bioinformatics/btaf138
Systems biology
Topology-based metrics for finding the optimal sparsity in gene regulatory network inference
Bioinformatics, Volume 41, Issue 5, May 2025, btaf120, https://doi.org/10.1093/bioinformatics/btaf120
Applications Note
Sequence analysis
RabbitSketch: a high-performance sketching library for genome analysis
Bioinformatics, Volume 41, Issue 5, May 2025, btaf249, https://doi.org/10.1093/bioinformatics/btaf249
Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes
Bioinformatics, Volume 41, Issue 5, May 2025, btaf250, https://doi.org/10.1093/bioinformatics/btaf250
