Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

• 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
• Donor-specific, but not sex-specific, signatures dominate cell-type classification in lung scRNA-seq data

  2026 Biochemistry and Biophysics Reports article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• FOXP1 is differentially active during development of murine vasopressin and oxytocin magnocellular neurons

  2026 iScience article Psychology Neuroendocrine regulation and behavior Open access

  0

  citations
• Integrative Learning of Disentangled Representations from Single-Cell RNA-Sequencing Datasets

  2026 Computational and Structural Biotechnology Journal article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  1

  citations
• SwarmMAP: swarm learning for decentralized cell type annotation in single cell sequencing data

  2026 npj Systems Biology and Applications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  1

  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 cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia

  2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  8

  citations
• Spatial Transcriptomics Reveals Injured Cells, Signature Genes, and Communication Patterns in the Cyst Microenvironment of Polycystic Kidney Disease

  2025 Journal of the American Society of Nephrology article Biochemistry, Genetics and Molecular Biology Genetic and Kidney Cyst Diseases Open access

  1

  citations
• FOXP1 differentially regulates the development of murine vasopressin and oxytocin magnocellular neurons

  2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Psychology Neuroendocrine regulation and behavior Open access

  0

  citations
• SwarmMAP: Swarm Learning for Decentralized Cell Type Annotation in Single Cell Sequencing Data

  2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  1

  citations
• scE(match): Privacy-Preserving Cluster Matching of Single-Cell Data

  2024 IEEE International Conference on Trust, Security and Privacy in Computing and Communications (TrustCom) conference-paper Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics

  2

  citations
• Spatial transcriptomic characterization of pathologic niches in IPF

  2024 Science Advances article Medicine Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis Open access cited by 1 patent

  106

  citations
• Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion

  2024 iScience article Medicine Cancer Immunotherapy and Biomarkers Open access

  16

  citations
• BERNN: Enhancing classification of Liquid Chromatography Mass Spectrometry data with batch effect removal neural networks

  2024 Nature Communications article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access cited by 1 patent

  24

  citations
• An integrated single‐cell RNA ‐seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptomic and functional types

  2024 Journal of Neuroendocrinology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  38

  citations
• Multimodal analysis unveils tumor microenvironment heterogeneity linked to immune activity and evasion

  2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Cancer Immunotherapy and Biomarkers Open access

  0

  citations
• Spatial Transcriptomic Characterization of Novel Pathologic Niches in IPF

  2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis Open access

  1

  citations
• Integrative learning of disentangled representations from single-cell RNA-sequencing datasets

  2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• An integrated single-cell RNA-seq atlas of the mouse hypothalamic paraventricular nucleus links transcriptional and functional types

  2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• Cell type matching across species using protein embeddings and transfer learning

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

  9

  citations

• A guide to the BRAIN Initiative Cell Census Network data ecosystem

  2023 PLoS Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  53

  citations

1 result