文献汇总

# 生物信息学

(Jean-Philippe Villemin, Laia Bassaganyas et al. Nucleic Acids Research,2023) Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR

(Haotian Cui et al. Nat Methods,2024) scGPT toward building a foundation model for single-cell multi-omics using generative AI

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    desc: <strong>(Jean-Philippe Villemin, Laia Bassaganyas et al.  Nucleic Acids Research,2023)</strong> Inferring ligand-receptor cellular networks from bulk and spatial transcriptomic datasets with BulkSignalR

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    desc: <strong>(Haotian Cui et al. Nat Methods,2024)</strong> scGPT toward building a foundation model for single-cell multi-omics using generative AI

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# 单细胞空间组

(Dries R, Chen J et al., Genome Res. 2021) Advances in spatial transcriptomic data analysis

(Li, B., Zhang, W., Guo, C. et al., Nat Methods ,2022) Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

(Yuan, Z., Pan, W., Zhao, X. et al., Nat Methods，2023) SODB facilitates comprehensive exploration of spatial omics data

(Chen, S., Zhu, B., Huang, S. et al., Nat Biotechnol，2023) Integration of spatial and single-cell data across modalities with weakly linked features

(Grabski, I.N., Street, K. & Irizarry, R.A., Nat Methods，2023) Significance analysis for clustering with single-cell RNA-sequencing data

(Yao, Z., van Velthoven, C.T.J., Kunst, M. et al., Nature，2023) A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

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    desc: <strong>(Dries R, Chen J et al., Genome Res. 2021)</strong> Advances in spatial transcriptomic data analysis

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    desc: <strong>(Li, B., Zhang, W., Guo, C. et al., Nat Methods ,2022)</strong> Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
    
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    desc: <strong>(Yuan, Z., Pan, W., Zhao, X. et al., Nat Methods，2023)</strong> SODB facilitates comprehensive exploration of spatial omics data

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    link: /pages/824737/
    name: ''
    desc: <strong>(Chen, S., Zhu, B., Huang, S. et al., Nat Biotechnol，2023)</strong> Integration of spatial and single-cell data across modalities with weakly linked features
 
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    desc: <strong>(Grabski, I.N., Street, K. & Irizarry, R.A., Nat Methods，2023)</strong> Significance analysis for clustering with single-cell RNA-sequencing data

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    link: /pages/58ba19/
    name: ''
    desc: <strong>(Yao, Z., van Velthoven, C.T.J., Kunst, M. et al., Nature，2023)</strong> A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

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# 免疫学相关

(Fei Tang,Jinhu Li,Lu Qi et al. Cell,2023) A pan-cancer single-cell panorama of human natural killer cells

(Cui, A., Huang, T., Li, S. et al. Nature,2023) Dictionary of immune responses to cytokines at single-cell resolution

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    desc: <strong>(Fei Tang,Jinhu Li,Lu Qi et al. Cell,2023)</strong> A pan-cancer single-cell panorama of human natural killer cells

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    link: /pages/c3a7f3/
    name: ''
    desc: <strong>(Cui, A., Huang, T., Li, S. et al. Nature,2023)</strong> Dictionary of immune responses to cytokines at single-cell resolution

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# scRNA-scATAC整合

(Schep, A., Wu, B., Buenrostro, J. et al. Nat Methods,2017) chromVAR inferring transcription-factor-associated accessibility from single-cell epigenomic data

(Lei Y, Cheng M et al. Nat Commun,2022) Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex

(Zhongli Xu, Xinjun Wang et al. iScience,2022) Integrative analysis of spatial transcriptome with single-cell transcriptome and single-cell epigenome in mouse lungs after immunization

(Deng, Y., Bartosovic, M., Ma, S. et al. Nature,2022) Spatial profiling of chromatin accessibility in mouse and human tissues

(Zhang, D., Deng, Y., Kukanja, P. et al. Nature,2023) Spatial epigenome-transcriptome co-profiling of mammalian tissues

(Zu, S., Li, Y.E., Wang, K. et al. Nature,2023) Single-cell analysis of chromatin accessibility in the adult mouse brain

(Terekhanova, N.V., Karpova, A., Liang, WW. et al. Nature,2023) Epigenetic regulation during cancer transitions across 11 tumour types

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    desc: <strong>(Schep, A., Wu, B., Buenrostro, J. et al. Nat Methods,2017)</strong> chromVAR inferring transcription-factor-associated accessibility from single-cell epigenomic data

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    desc: <strong>(Lei Y, Cheng M et al. Nat Commun,2022)</strong> Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex

  - img: https://www.cell.com/cms/attachment/c70e347b-3921-45c3-be57-e455c91976bc/gr1.jpg
    link: /pages/41e09e/
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    desc: <strong>(Zhongli Xu, Xinjun Wang et al. iScience,2022)</strong> Integrative analysis of spatial transcriptome with single-cell transcriptome and single-cell epigenome in mouse lungs after immunization

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    link: /pages/587589/
    name: ''
    desc: <strong>(Deng, Y., Bartosovic, M., Ma, S. et al. Nature,2022)</strong> Spatial profiling of chromatin accessibility in mouse and human tissues

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    link: /pages/9abd5e/
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    desc: <strong>(Zhang, D., Deng, Y., Kukanja, P. et al. Nature,2023)</strong> Spatial epigenome-transcriptome co-profiling of mammalian tissues

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    link: /pages/fa0e3f/
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    desc: <strong>(Zu, S., Li, Y.E., Wang, K. et al. Nature,2023)</strong> Single-cell analysis of chromatin accessibility in the adult mouse brain

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    link: /pages/17d203/
    name: ''
    desc: <strong>(Terekhanova, N.V., Karpova, A., Liang, WW. et al. Nature,2023)</strong> Epigenetic regulation during cancer transitions across 11 tumour types

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编辑

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