ArticleGenome biology2022
TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 19 citations in OpenAlex.
- Decoding epithelial-mesenchymal transitions with multi-omics.Nature reviews. Genetics · 2026Review
- Decoding cell-cell communication in spatial transcriptomics: mechanistic insights, modeling constraints, and analytical caveats.Briefings in bioinformatics · 2026Review
- Synthetic developmental engineering of human liver organogenesis.Development (Cambridge, England) · 2026Review
- Single Cell RNA Sequencing in Colorectal Cancer Immunology: Recent Updates, Application, and Emerging Challenges.Current molecular medicine · 2026Review
- scACCorDiON: a clustering approach for explainable patient level cell-cell communication graph analysis.Bioinformatics (Oxford, England) · 2025Article
- Advances and challenges in cell-cell communication inference: a comprehensive review of tools, resources, and future directions.Briefings in bioinformatics · 2025Review
- New Insights and Implications of Cell-Cell Interactions in Developmental Biology.International journal of molecular sciences · 2025Review
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- The diversification of methods for studying cell-cell interactions and communication.Nature reviews. Genetics · 2024Review
- The spatially resolved transcriptome signatures of glomeruli in chronic kidney disease.JCI insight · 2024Article
- Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data.BMC bioinformatics · 2023Article
- The promising application of cell-cell interaction analysis in cancer from single-cell and spatial transcriptomics.Seminars in cancer biology · 2023Review
- Defining and identifying cell sub-crosstalk pairs for characterizing cell-cell communication patterns.Scientific reports · 2023Article
- Review
- RobustCCC: a robustness evaluation tool for cell-cell communication methods.Frontiers in genetics · 2023Article
- Adult tissue-specific stem cell interaction: novel technologies and research advances.Frontiers in cell and developmental biology · 2023Review
- Profiling intermediate cell states in high resolution.Cell reports methods · 2022Article
- TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data.Genome biology · 2022Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
A major advantage of single cell RNA-sequencing (scRNA-Seq) data is the ability to reconstruct continuous ordering and trajectories for cells. Here we present TraSig, a computational method for improving the inference of cell-cell interactions in scRNA-Seq studies that utilizes the dynamic information to identify significant ligand-receptor pairs with similar trajectories, which in turn are used to score interacting cell clusters. We applied TraSig to several scRNA-Seq datasets and obtained unique predictions that improve upon those identified by prior methods. Functional experiments validate the ability of TraSig to identify novel signaling interactions that impact vascular development in liver organoids.Software https://github.com/doraadong/TraSig .
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Registered trials
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.