A curated list of awesome reproducible papers in single-cell omics.

The listed papers provide the code necessary for reproducing the figures or results.

• Guidelines for Single-Cell Analysis
• scRNA-seq
• scATAC-seq
• single-cell Proteomics
• scHi-C
• Spatial Transcriptome
• Multiomics

1. [2023 Nature Reviews Genetics]Best practices for single-cell analysis across modalities[paper][code]

1. [2024 Nature]Universal recording of immune cell interactions in vivo[paper][code]
2. [2024 Nature]Cellular communities reveal trajectories of brain ageing and Alzheimer’s disease[paper][code]
3. [2024 Nature]A single-cell time-lapse of mouse prenatal development from gastrula to birth[paper][code]
4. [2024 Cell]Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging[paper][code]
5. [2024 Nature Cell Biology]Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities[paper][code]
6. [2023 Nature Medicine]An integrated cell atlas of the lung in health and disease[paper][code]
7. [2023 Nature Communications]Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer[paper][code]
8. [2023 Cancer Cell]Tumor monocyte content predicts immunochemotherapy outcomes in esophageal adenocarcinoma[paper][code]
9. [2022 Molecular Neurodegeneration]Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer’s disease: review, recommendation, implementation and application[paper][code]
10. [2022 Nature Cancer]Breast cancer prevention by short-term inhibition of TGFβ signaling[paper][code]
11. [2022 Nature Cell Biology]Single-cell analysis of endometriosis reveals a coordinated transcriptional programme driving immunotolerance and angiogenesis across eutopic and ectopic tissues[paper][code]
12. [2022 Nature Neuroscience]Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain[paper][code]
13. [2021 Nature]Global absence and targeting of protective immune states in severe COVID-19[paper][code]
14. [2021 Science]Pan-cancer single-cell landscape of tumor-infiltrating T cells[paper][code]
15. [2021 Nature Communications]Single-cell transcriptomics captures features of human midbrain development and dopamine neuron diversity in brain organoids[paper][code]

1. [2024 Nature]Chromatin accessibility during human first-trimester neurodevelopment[paper][code]
2. [2024 Nature Cell Biology]A single-cell atlas of chromatin accessibility in mouse organogenesis[paper][code]
3. [2024 Cancer Discovery]Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers[paper][code]
4. [2023 Nature]Molecular features driving cellular complexity of human brain evolution[paper][code]
5. [2023 Nature]Single-cell analysis of chromatin accessibility in the adult mouse brain[paper][code]
6. [2023 Narure]Epigenetic regulation during cancer transitions across 11 tumour types[paper][code]
7. [2023 Nature]Organization of the human intestine at single-cell resolution[paper][code]
8. [2023 biorxiv]Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency[paper][code]
9. [2023 Nature Biotechnology]SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data[paper][code]
10. [2023 eLife]The single-cell chromatin accessibility landscape in mouse perinatal testis development[paper][code]
11. [2022 Nature Biotechnology]Variant to function mapping at single-cell resolution through network propagation[paper][code]
12. [2022 Nature Communications]Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions[paper][code]
13. [2021 Science]Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells[paper][code]
14. [2021 Nature Biotechnology]Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer[paper][code]
15. [2021 Nature Communications]High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer[paper][code]

1. Single Cell Proteomics Methods & Data[code]

1. Notes on single-cell Hi-C technologies, tools, and data[code]
2. [2023 Nature Communications]Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape[paper][code]

1. [2024 Nature Genetics]Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis[paper][code]
2. [2023 Science Advances]Single-cell and spatial transcriptome analysis reveals the cellular heterogeneity of liver metastatic colorectal cancer[paper][code]
3. [2023 Nature Genetics]CellCharter reveals spatial cell niches associated with tissue remodeling and cell plasticity[paper][code]
4. [2023 Cancer Research]Spatial Transcriptomics Depict Ligand–Receptor Cross-talk Heterogeneity at the Tumor-Stroma Interface in Long-Term Ovarian Cancer Survivors[paper][code]
5. [2022 Nature]Spatial genomics maps the structure, nature and evolution of cancer clones[paper][code]
6. [2022 Nature Methods]Squidpy: a scalable framework for spatial omics analysis[paper][code]
7. [2022 bioRxiv]Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma[paper][code]
8. [2021 Nature Neuroscience]Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex[paper][code]

1. [2024 Nature]Multimodal cell atlas of the ageing human skeletal muscle[paper][code]
2. [2024 Science]A blueprint for tumor-infiltrating B cells across human cancers[paper][code]
3. [2024 Nature Genetics]Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression[paper][code]
4. [2024 Nature Immunology]Age-related epithelial defects limit thymic function and regeneration[paper][code]
5. [2024 Nature Neuroscience]Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems[paper][code]
6. [2024 Developmental Cell]Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development[paper][code]
7. [2024 Nature Communications]Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma[paper][code]
8. [2023 Cell]Epigenomic dissection of Alzheimer’s disease pinpoints causal variants and reveals epigenome erosion[paper][code]
9. [2023 Nature Biotechnology]Multimodal spatiotemporal phenotyping of human retinal organoid development[paper][code]
10. [2023 Nature Genetics]Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes[paper][code]
11. [2023 Nature Genetics]Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases[paper][code]
12. [2023 Nature Communications]Deciphering early human pancreas development at the single-cell level[paper][code]
13. [2023 Nature Communications]Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis[paper][code]
14. [2022 Nature]Inferring and perturbing cell fate regulomes in human brain organoids[paper][code]
15. [2022 Nature Genetics]Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer[paper][code]
16. [2022 Nature Genetics]K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas[paper][code]
17. [2022 Nature Neuroscience]Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler[paper][code]
18. [2022 Cell Discovery]Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma[paper][code]
19. [2021 Molecular Cell]A multi-omic single-cell landscape of human gynecologic malignancies[paper][code]
20. [2019 Nature]Organoid single-cell genomic atlas uncovers human-specific features of brain development[paper])[code]
21. [2019 Nature Biotechnology]Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia[paper][code]