Benchmarking atlas-level data integration in single-cell genomics

• The Human Pancreas Cell Atlas defines a healthy reference framework for disease contextualization and translational benchmarking

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

  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
• 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
• In situ multi-modal characterization of pancreatic cancer reveals tumor cell identity as a defining factor of the surrounding microenvironment

  2026 Cell Reports article Medicine Pancreatic and Hepatic Oncology Research Open access

  8

  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
• Tackling vaccine hyporesponsiveness through global collaboration, diverse population studies, and data integration

  2025 The Lancet Microbe article Immunology and Microbiology Immune responses and vaccinations Open access

  4

  citations
• Mass cytometry data integration methods reveal rural-urban gradient of immune profiles across geography

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

  1

  citations
• PILOT-GM-VAE: patient-level analysis of single-cell disease atlas with optimal transport of Gaussian mixture variational autoencoders

  2025 Briefings in Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• PILOT-GM-VAE: Patient-Level Analysis of single cell Disease Atlas with Optimal Transport of Gaussian Mixture Variational Autoencoders

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

  0

  citations
• Encompassing view of spatial and single-cell RNA sequencing renews the role of the microvasculature in human atherosclerosis

  2024 Nature Cardiovascular Research article Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access

  67

  citations
• scDecorr - Feature decorrelation representation learning with domain adaptation enables self-supervised alignment of multiple single-cell experiments

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

  0

  citations
• Encompassing view of spatial and single-cell RNA-seq renews the role of the microvasculature in human atherosclerosis

  2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Atherosclerosis and Cardiovascular Diseases Open access

  5

  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
• 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
• MASIv2 enables standardization and integration of multi-modal single-cell and spatial omics data with one general framework

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

  1

  citations
• A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery

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

  38

  citations
• MASI enables fast model-free standardization and integration of single-cell transcriptomics data

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

  4

  citations
• Multi-omic analyses in immune cell development with lessons learned from T cell development

  2023 Frontiers in Cell and Developmental Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  9

  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
• Community-driven ELIXIR activities in single-cell omics

  2022 F1000Research article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  11

  citations

• Eleven grand challenges in single-cell data science

  2020 Genome biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 2 patents

  1,504

  citations

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