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References from SingPro 2.0: a proteomics-centric knowledge base for single-cell multimodal profiling. Local targets link to admitted publications; unresolved targets remain external evidence.
SingPro: a knowledge base providing single-cell proteomic data
10.1093/nar/gkad830 · 2024 · External reference
Computational methods for single-cell omics across modalities
10.1038/s41592-019-0692-4 · 2020 · External reference
Methods and applications for single-cell and spatial multi-omics
10.1038/s41576-023-00580-2 · 2023 · External reference
The technological landscape and applications of single-cell multi-omics
10.1038/s41580-023-00615-w · 2023 · External reference
Integrative spatial protein profiling with multi-omics
10.1038/s41592-024-02533-x · 2024 · External reference
Method of the year 2019: single-cell multimodal omics
2020 · External reference
A blood atlas of COVID-19 defines hallmarks of disease severity and specificity
10.1016/j.cell.2022.01.012 · 2022 · External reference
Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection
10.1038/s41590-023-01608-9 · 2023 · External reference
Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states
10.1038/s41590-021-01059-0 · 2021 · External reference
Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization
10.1038/s41593-020-00789-y · 2021 · External reference
An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors
10.1038/s41590-024-01782-4 · 2024 · External reference
Multi-omics resolves a sharp disease-state shift between mild and moderate COVID-19
10.1016/j.cell.2020.10.037 · 2020 · External reference
Entering the era of deep single-cell proteomics
10.1038/s41592-025-02620-7 · 2025 · External reference
Multimodal pooled perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion
10.1038/s41588-021-00779-1 · 2021 · External reference
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens
10.1038/s41588-021-00778-2 · 2021 · External reference
Towards multimodal foundation models in molecular cell biology
10.1038/s41586-025-08710-y · 2025 · External reference
The virtual cell
10.1038/s41592-025-02951-5 · 2025 · External reference
How to build the virtual cell with artificial intelligence: priorities and opportunities
10.1016/j.cell.2024.11.015 · 2024 · External reference
Single Cell Atlas: a single-cell multi-omics human cell encyclopedia
10.1186/s13059-024-03246-2 · 2024 · External reference
scMoresDB: a comprehensive database of single-cell multi-omics data for human respiratory system
10.1016/j.isci.2024.109567 · 2024 · External reference
scCancerExplorer: a comprehensive database for interactively exploring single-cell multi-omics data of human pan-cancer
10.1093/nar/gkae1100 · 2025 · External reference
SMARTdb: an integrated database for exploring single-cell multi-omics data of reproductive medicine
10.1093/gpbjnl/qzae005 · 2024 · External reference
scMMO-atlas: a single cell multimodal omics atlas and portal for exploring fine cell heterogeneity and cell dynamics
10.1093/nar/gkae821 · 2025 · External reference
scMOVIR: a single-cell multi-omics database for human viral infections and immune responses
10.1093/nar/gkaf1153 · 2026 · External reference
scImmOmics: a manually curated resource of single-cell multi-omics immune data
10.1093/nar/gkae985 · 2025 · External reference
SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution
10.1093/nar/gkad1018 · 2024 · External reference
Cell neighborhood topology directs rare cell population identification
10.1038/s41467-026-71180-x · 2026 · External reference
Comparative benchmarking of single-cell clustering algorithms for transcriptomic and proteomic data
10.1186/s13059-025-03719-y · 2025 · External reference
A pre-trained large generative model for translating single-cell transcriptomes to proteomes
10.1038/s41551-025-01528-z · 2025 · External reference
Intra-tumor heterogeneity-resistant gene signature predicts prognosis and immune infiltration in breast cancer
10.3389/fimmu.2025.1598858 · 2025 · External reference
A novel immune-related gene signature stratifies prognosis and characterizes the tumor immune microenvironment in head and neck squamous cell carcinoma
10.3389/fcell.2026.1756922 · 2026 · External reference
Simultaneous epitope and transcriptome measurement in single cells
10.1038/nmeth.4380 · 2017 · External reference
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells
10.1038/s41587-021-00927-2 · 2021 · External reference
Navigating the data processing for cytometry-based single-cell proteomics
10.1038/s41596-025-01257-2 · 2026 · External reference
The sequence read archive: a decade more of explosive growth
10.1093/nar/gkab1053 · 2022 · External reference
Dictionary learning for integrative, multimodal and scalable single-cell analysis
10.1038/s41587-023-01767-y · 2024 · External reference
Single-cell chromatin state analysis with Signac
10.1038/s41592-021-01282-5 · 2021 · External reference
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
10.1186/s13059-019-1874-1 · 2019 · External reference
Model-based analysis of ChIP-Seq (MACS)
10.1186/gb-2008-9-9-r137 · 2008 · External reference
Integrated analysis of multimodal single-cell data
10.1016/j.cell.2021.04.048 · 2021 · External reference
UMAP: uniform manifold approximation and projection
10.21105/joss.00861 · 2018 · External reference
Fast unfolding of communities in large networks
10.1088/1742-5468/2008/10/p10008 · 2008 · External reference
Type material in the NCBI taxonomy database
10.1093/nar/gku1127 · 2015 · External reference
Uberon, an integrative multi-species anatomy ontology
10.1186/gb-2012-13-1-r5 · 2012 · External reference
Icd-11
10.1016/s0140-6736(19)31205-x · 2019 · External reference
