De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

• 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
• 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
• 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
• 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
• Fast model-free standardization and integration of single-cell transcriptomics data

  2023 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  0

  citations
• Epiblast inducers capture mouse trophectoderm stem cells in vitro and pattern blastoids for implantation in utero

  2022 Cell stem cell article Biochemistry, Genetics and Molecular Biology Pluripotent Stem Cells Research Open access

  50

  citations
• The rise of sparser single-cell RNAseq datasets; consequences and opportunities

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

  2

  citations
• Fast model-free standardization and integration of single-cell transcriptomics data

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

  0

  citations
• MACA: Marker-based automatic cell-type annotation for single cell expression data

  2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  2

  citations
• Prrx1b restricts fibrosis and promotes Nrg1-dependent cardiomyocyte proliferation during zebrafish heart regeneration

  2021 Development article Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access

  48

  citations
• DUX4 induces a homogeneous sequence of molecular changes, culminating in the activation of a stem-cell-like transcriptional network and induction of apoptosis in somatic cells

  2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Muscle Physiology and Disorders Open access

  1

  citations
• Computational Stem Cell Biology: Open Questions and Guiding Principles

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

  36

  citations
• Prrx1b directs pro-regenerative fibroblasts during zebrafish heart regeneration

  2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Congenital heart defects research Open access

  0

  citations
• Single-cell transcriptional diversity is a hallmark of developmental potential

  2020 Science article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 4 patents

  1,715

  citations

14 results