Single Cell Data Analysis

I. scMultiOmics

I.1 Representative Integration Analysis

✅ 2024 Science - Single-cell genomics and regulatory networks for 388 human brains
✅ 2018 Science (machine learning model) - Comprehensive functional genomic resource and integrative model for the human brain

I.2 Others

✅ 2024 Nature - Single-cell multiplex chromatin and RNA interactions in ageing human brain
✅ 2023 Nature - Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes
✅ 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
2023 Nature - Epigenetic regulation during cancer transitions across 11 tumour types
2023 Nature Methods - SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
2022 Cell - Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution
2021 Cancer Cell - Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer
2021 Nature Genetics - Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease
2021 Nature Genetics - Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk
2021 Genome Biology - Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
2018 Science - Single-cell multiomics sequencing and analyses of human colorectal cancer

(1) Multi-Omics Data Integration Tools

2021 Brief Bioinfo - A comparative study of multi-omics integration tools

2017 PLoS computational biology - mixOmics: An R package for ‘omics feature selection and multiple data integration

(2) Bulk Multi-Omics Studies

✅ 2023 Immunity - Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection

✅ 2023 Nature Genetics - Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability

✅ 2021 Nature - Multi-omic machine learning predictor of breast cancer therapy response

2021 Cell - Integrated analysis of multimodal single-cell data

2021 Nature Commn - An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer

✅ 2020 Nature Medicine - Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer

II. scRNA

✅ 2023 Nature Genetics - Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution
✅ 2021 Science - The coding and long noncoding single-cell atlas of the developing human fetal striatum
2021 PNAS - Single-cell quantiﬁcation of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states
2020 Nature Cell Biol. - Differentiation of transplanted haematopoietic stem cells tracked by single-cell transcriptomic analysis

III. scRNA: Post-transcriptional Regulation

2024 Nature Commn - Interrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance
2024 Nature Commn - Divergent landscapes of A-to-I editing in postmortem and living human brain
2022 Nature Commn - Cellular and genetic drivers of RNA editing variation in the human brain

IV. scATAC-seq

✅ 2024 Immunity - Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells
2024 Nature Cell Biology - Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq
2024 Nature Cell Biology - A single-cell atlas of chromatin accessibility in mouse organogenesis