Deciphering cell–cell interactions and communication from gene expression

• Pathway-centric visualization of cell-cell communication in single-cell transcriptomics data

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

  0

  citations
• GraphComm predicts cell cell communication using a graph based deep learning method in single cell RNA sequencing data

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

  6

  citations
• Advances and challenges in cell–cell communication inference: a comprehensive review of tools, resources, and future directions

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

  39

  citations
• scACCorDiON: a clustering approach for explainable patient level cell–cell communication graph analysis

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

  3

  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
• scACCorDiON: A clustering approach for explainable patient level cell cell communication graph analysis

  2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics 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
• Cardiovascular complications of diabetes: role of non-coding RNAs in the crosstalk between immune and cardiovascular systems

  2023 Cardiovascular Diabetology article Biochemistry, Genetics and Molecular Biology MicroRNA in disease regulation Open access

  32

  citations
• GraphComm: A Graph-based Deep Learning Method to Predict Cell-Cell Communication in single-cell RNAseq data

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

  13

  citations
• The evolving tumor microenvironment: From cancer initiation to metastatic outgrowth

  2023 Cancer Cell article Medicine Cancer Cells and Metastasis Open access cited by 3 patents

  3,982

  citations
• Multiomic Spatial Mapping of Myocardial Infarction and Implications for Personalized Therapy

  2022 Arteriosclerosis Thrombosis and Vascular Biology article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  22

  citations
• Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

  2022 Nature Communications article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access cited by 1 patent

  670

  citations
• How a cell decides its own fate: a single-cell view of molecular mechanisms and dynamics of cell-type specification

  2021 Biochemical Society Transactions article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  7

  citations
• Cell-cell Communication Inference from Single-cell RNA-Seq Data: a Comparison of Methods and Resources

  2021 Research Square preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access

  3

  citations
• Ligand–Receptor Interactions Elucidate Sex-Specific Pathways in the Trajectory From Primordial Germ Cells to Gonia During Human Development

  2021 Frontiers in Cell and Developmental Biology article Biochemistry, Genetics and Molecular Biology Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities Open access cited by 1 patent

  23

  citations
• Comparison of Resources and Methods to infer Cell-Cell Communication from Single-cell RNA Data

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

  23

  citations
• CrossTalkeR: analysis and visualization of ligand–receptorne tworks

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

  58

  citations
• Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis

  2021 Molecular Systems Biology article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access

  406

  citations
• CrossTalkeR: Analysis and Visualisation of Ligand Receptor Networks

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

  9

  citations

19 results

• 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

1 result