ArticleBiophysical reports2023
Length biases in single-cell RNA sequencing of pre-mRNA.
Article in Biophysical reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Coordinated dysregulation of modular gene activity in human neuropathologies.bioRxiv : the preprint server for biology · 2026Article
- The evolution of gene regulation in mammalian cerebellum development.Science (New York, N.Y.) · 2026Article
- Paradigms, innovations, and biological applications of RNA velocity: a comprehensive review.Briefings in bioinformatics · 2025Review
- Accurate quantification of nascent and mature RNAs from single-cell and single-nucleus RNA-seq.Nucleic acids research · 2025Article
- Trajectory inference from single-cell genomics data with a process time model.PLoS computational biology · 2025Article
- Stochastic Modeling of Biophysical Responses to Perturbation.bioRxiv : the preprint server for biology · 2024Article
- Dissection and integration of bursty transcriptional dynamics for complex systems.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A dynamical perspective: moving towards mechanism in single-cell transcriptomics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Single-nucleus RNA velocity reveals critical synaptic and cell-cycle dysregulations in neuropathologically confirmed Alzheimer's disease.Scientific reports · 2024Article
- Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments.Genome research · 2024Article
- Review
- Biophysically Interpretable Inference of Cell Types from Multimodal Sequencing Data.bioRxiv : the preprint server for biology · 2023Article
- Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems.bioRxiv : the preprint server for biology · 2023Article
- Studying stochastic systems biology of the cell with single-cell genomics data.bioRxiv : the preprint server for biology · 2023Article
- Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data.bioRxiv : the preprint server for biology · 2023Article
- Gene length is a pivotal feature to explain disparities in transcript capture between single transcriptome techniques.Frontiers in bioinformatics · 2023Article
- Signal and noise in metabarcoding data.PloS one · 2023Article
- Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments.Nature communications · 2022Article
- RNA velocity unraveled.PLoS computational biology · 2022Article
- Modeling bursty transcription and splicing with the chemical master equation.Biophysical journal · 2022Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell RNA sequencing data can be modeled using Markov chains to yield genome-wide insights into transcriptional physics. However, quantitative inference with such data requires careful assessment of noise sources. We find that long pre-mRNA transcripts are over-represented in sequencing data. To explain this trend, we propose a length-based model of capture bias, which may produce false-positive observations. We solve this model and use it to find concordant parameter trends as well as systematic, mechanistically interpretable technical and biological differences in paired data sets.
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Registered trials
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