chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

• AtlasOT - The Fused Unbalanced Gromov-Wasserstein for Multimodal Integration of Disease Atlases

  2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• Multimodal single-cell analysis uncovers transcription factor networks underlying T-cell aging

  2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• PHLOWER leverages single-cell multimodal data to infer complex, multi-branching cell differentiation trajectories

  2025 Nature Methods article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  9

  citations
• The pioneer factor, ETV2, regulates networks to specify the embryonic endothelial lineage

  2025 Cardiovascular Research article Biochemistry, Genetics and Molecular Biology Developmental Biology and Gene Regulation Open access

  4

  citations
• PHLOWER - Single cell trajectory analysis using Hodge Decomposition

  2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• Epigenetic memory of coronavirus infection in innate immune cells and their progenitors

  2023 Cell article Immunology and Microbiology Immune responses and vaccinations Open access

  301

  citations
• Best practices for single-cell analysis across modalities

  2023 Nature Reviews Genetics review Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 7 patents

  1,043

  citations
• scMEGA: single-cell multi-omic enhancer-based gene regulatory network inference

  2023 Bioinformatics Advances article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access cited by 1 patent

  41

  citations
• scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

  2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  0

  citations
• Spatial multi-omic map of human myocardial infarction

  2022 Nature article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  764

  citations
• Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen

  2021 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  141

  citations
• Comparative cellular analysis of motor cortex in human, marmoset and mouse

  2021 Nature article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  882

  citations
• Microanatomy of the Human Atherosclerotic Plaque by Single-Cell Transcriptomics

  2020 Circulation Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access

  619

  citations
• Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

  2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  89

  citations

14 results