A Python library for probabilistic analysis of single-cell omics data

• Single-cell characterization of human periodontal ligament (PDL) cells reveals uniformly mesenchymal populations in matched maxilla and mandible pairs from four donors

  2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Periodontal Regeneration and Treatments Open access

  0

  citations
• Evaluating exon skipping in the central nervous system in Duchenne muscular dystrophy using spatial transcriptomics

  2026 iScience article Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access

  0

  citations
• Single-cell integration and multi-modal profiling reveals phenotypes and spatial organization of neutrophils in colorectal cancer

  2026 Cancer Cell article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  33

  citations
• A unified rodent atlas reveals the cellular complexity and evolutionary divergence of the dorsal vagal complex

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

  1

  citations
• A unified rodent atlas reveals the cellular complexity and evolutionary divergence of the dorsal vagal complex

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

  0

  citations
• A unified rodent atlas reveals the cellular complexity and evolutionary divergence of the dorsal vagal complex

  2025 eLife preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  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
• A unified rodent atlas reveals the cellular complexity and evolutionary divergence of the dorsal vagal complex

  2025 eLife preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  5

  citations
• A unified rodent atlas reveals the cellular complexity and evolutionary divergence of the dorsal vagal complex

  2025 eLife preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  1

  citations
• RORγt-expressing dendritic cells are functionally versatile and evolutionarily conserved antigen-presenting cells

  2025 Proceedings of the National Academy of Sciences article Immunology and Microbiology Immunotherapy and Immune Responses Open access

  44

  citations
• Cross-species analyses reveal RORγt-expressing dendritic cells are a lineage of antigen presenting cells conserved across tissues

  2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Immunotherapy and Immune Responses Open access cited by 3 patents

  5

  citations
• An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics

  2023 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  12

  citations
• Single-cell reference mapping to construct and extend cell-type hierarchies

  2023 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  43

  citations
• The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

  2023 Genome biology article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access

  56

  citations
• Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models

  2023 Nature Biotechnology article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  109

  citations
• miR449 Protects Airway Regeneration by Controlling AURKA/HDAC6-Mediated Ciliary Disassembly

  2022 International Journal of Molecular Sciences article Biochemistry, Genetics and Molecular Biology MicroRNA in disease regulation Open access

  7

  citations
• Single-cell reference mapping to construct and extend cell-type hierarchies

  2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  7

  citations
• SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis

  2021 Cell article Medicine COVID-19 Clinical Research Studies Open access cited by 5 patents

  523

  citations

18 results