ArticleNature communications2022
acorde unravels functionally interpretable networks of isoform co-usage from single cell data.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- Alternative splicing across the C. elegans nervous system.Nature communications · 2025Article
- Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids.Genome research · 2025Article
- MOSim: bulk and single-cell multilayer regulatory network simulator.Briefings in bioinformatics · 2025Article
- Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain.Nature neuroscience · 2024Article
- Quantifying transcriptome diversity: a review.Briefings in functional genomics · 2024Review
- Transcription factors and splice factors - interconnected regulators of stem cell differentiation.Current stem cell reports · 2023Article
- Analyzing alternative splicing in Alzheimer's disease postmortem brain: a cell-level perspective.Frontiers in molecular neuroscience · 2023Article
- Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease.Human molecular genetics · 2022Review
- ScisorWiz: visualizing differential isoform expression in single-cell long-read data.Bioinformatics (Oxford, England) · 2022Article
- acorde unravels functionally interpretable networks of isoform co-usage from single cell data.Nature communications · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Alternative splicing (AS) is a highly-regulated post-transcriptional mechanism known to modulate isoform expression within genes and contribute to cell-type identity. However, the extent to which alternative isoforms establish co-expression networks that may be relevant in cellular function has not been explored yet. Here, we present acorde, a pipeline that successfully leverages bulk long reads and single-cell data to confidently detect alternative isoform co-expression relationships. To achieve this, we develop and validate percentile correlations, an innovative approach that overcomes data sparsity and yields accurate co-expression estimates from single-cell data. Next, acorde uses correlations to cluster co-expressed isoforms into a network, unraveling cell type-specific alternative isoform usage patterns. By selecting same-gene isoforms between these clusters, we subsequently detect and characterize genes with co-differential isoform usage (coDIU) across cell types. Finally, we predict functional elements from long read-defined isoforms and provide insight into biological processes, motifs, and domains potentially controlled by the coordination of post-transcriptional regulation. The code for acorde is available at https://github.com/ConesaLab/acorde .
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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.