Missing papers

[ttgump]

Hi, I found the list missed some recent papers:

[Multimodal Integration] [2022 Nature Biotechnology] Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

[Gene Regulatory Network] [2022 Nature Machine Intelligence] Inferring transcription factor regulatory networks from single-cell ATAC-seq data based on graph neural networks

[Spatial Domain] [2022 Genome Research] A model-based constrained deep learning clustering approach for spatially resolved single-cell data

I also recommend to add a new category [Dimensionality Reduction and Visualization], it might be related to [Representation Learning], here are some papers:

[2018 Nature Communications] Interpretable dimensionality reduction of single cell transcriptome data with deep generative models

[2021 Nature Communications] Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces

[2023 Genome Research] Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning

[JiayuanDing100]

Hi,

Thanks for your recommended papers!

I have added all of them. Thanks a lot!

[berlingyan]

I also find one paper: [2023 Briefings in Bioinformatics ]SC-AIR-BERT: a pre-trained single-cell model for predicting the antigenbinding specificity of the adaptive immune receptor