ArticleCell systems2019
Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution.
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
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Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Coordinated neural progenitor adaptations contribute to primate neocortical downscaling.Science advances · 2026Article
- CellExLink: End-to-end cell-type recognition and normalization in biomedical text.PLoS computational biology · 2026Article
- The cell-type specific interaction based drug repurposing for psychiatric disorders.Translational psychiatry · 2026Article
- Protein foundation models: a comprehensive survey.Science China. Life sciences · 2026Review
- Immunotherapy drug target identification using machine learning and patient-derived tumour explant validation.Nature machine intelligence · 2026Article
- Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP.Genome research · 2025Article
- A cell type and state specific gene regulation network inference method for immune regulatory analysis.NPJ systems biology and applications · 2025Article
- Single-cell network biology enabling cell-type-resolved disease genetics.Genomics & informatics · 2025Review
- A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers.NPJ systems biology and applications · 2025Article
- HCNetlas: A reference database of human cell type-specific gene networks to aid disease genetic analyses.PLoS biology · 2025Article
- A computational Evo-Devo approach for elucidating the roles of PLETHORA transcription factors in regulating root development.PloS one · 2025Article
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- Prediction of immunotherapy response using mutations to cancer protein assemblies.Science advances · 2024Article
- Contextual AI models for single-cell protein biology.Nature methods · 2024Article
- Contextual AI models for single-cell protein biology.bioRxiv : the preprint server for biology · 2024Article
- GENIX enables comparative network analysis of single-cell RNA sequencing to reveal signatures of therapeutic interventions.Cell reports methods · 2024Article
- An atlas of cell-type-specific interactome networks across 44 human tumor types.Genome medicine · 2024Article
- Curation of causal interactions mediated by genes associated with autism accelerates the understanding of gene-phenotype relationships underlying neurodevelopmental disorders.Molecular psychiatry · 2024Article
- Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON.Nature communications · 2023Article
Corrections and comments
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3 authors.
Funding
Abstract
The human interactome is instrumental in the systems-level study of the cell and the contextualization of disease-associated gene perturbations. However, reference organismal interactomes do not capture the cell-type-specific context in which proteins and modules preferentially act. Here, we introduce SCINET, a computational framework that reconstructs an ensemble of cell-type-specific interactomes by integrating a global, context-independent reference interactome with a single-cell gene-expression profile. SCINET addresses technical challenges of single-cell data by robustly imputing, transforming, and normalizing the initially noisy and sparse expression of data. Inferred cell-level gene interaction probabilities and group-level interaction strengths define cell-type-specific interactomes. We use SCINET to reconstruct and analyze interactomes of the major human brain and immune cell types, revealing specificity and modularity of perturbations associated with neurodegenerative, neuropsychiatric, and autoimmune disorders. We report cell-type interactomes for brain and immune cell types, together with the SCINET package.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.