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References from Single-cell and long-read sequencing to enhance modelling of splicing and cell-fate determination. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/s41576-020-00292-x
10.1038/s41576-020-00292-x · External reference
10.1038/s41467-023-36116-9
10.1038/s41467-023-36116-9 · External reference
10.1038/nmeth.1315
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Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes
10.1186/s12864-021-08261-2 · 2022 · External reference
Short-read and long-read full-length transcriptome of mouse neural stem cells across neurodevelopmental stages
10.1038/s41597-022-01165-0 · 2022 · External reference
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files
10.1093/bioinformatics/bty841 · 2019 · External reference
10.1038/s41587-021-01108-x
10.1038/s41587-021-01108-x · External reference
DNA sequencing from single polymerase molecules
10.1126/science.1162986 · 2009 · External reference
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The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
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Unresolved reference
External reference
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The blooming of long-read sequencing reforms biomedical research
10.1186/s13059-022-02604-2 · 2022 · External reference
LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing
10.1186/s12864-020-07207-4 · 2020 · External reference
JAFFAL: detecting fusion genes with long-read transcriptome sequencing
10.1186/s13059-021-02588-5 · 2022 · External reference
Real-time selective sequencing using nanopore technology
10.1038/nmeth.3930 · 2016 · External reference
Nanocall: an open source basecaller for Oxford Nanopore sequencing data
10.1093/bioinformatics/btw569 · 2016 · External reference
DeepNano: deep recurrent neural networks for base calling in MinION nanopore reads
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Analysis of recombinational switching at the antigenic variation locus of the Lyme spirochete using a novel PacBio sequencing pipeline
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10.1093/bioinformatics/bty654 · 2018 · External reference
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Detecting DNA cytosine methylation using nanopore sequencing
10.1038/nmeth.4184 · 2017 · External reference
10.1038/nmeth.4189
10.1038/nmeth.4189 · External reference
DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning
10.1093/bioinformatics/btz276 · 2019 · External reference
10.1038/s41467-019-11713-9
10.1038/s41467-019-11713-9 · External reference
Decoding the epitranscriptional landscape from native RNA sequences
2020 · External reference
Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
10.1186/s13059-020-02241-7 · 2021 · External reference
DRUMMER-Rapid detection of RNA modifications through comparative nanopore sequencing
10.1093/bioinformatics/btac274 · 2022 · External reference
Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon
10.1038/s41467-018-06910-x · 2018 · External reference
IsoTV: processing and visualizing functional features of translated transcript isoforms
10.1093/bioinformatics/btab103 · 2021 · External reference
NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing
10.1093/bioinformatics/btac359 · 2022 · External reference
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10.1186/s13059-021-02399-8
10.1186/s13059-021-02399-8 · External reference
Determination of isoform-specific RNA structure with nanopore long reads
10.1038/s41587-020-0712-z · 2021 · External reference
Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing
10.1016/j.celrep.2021.110022 · 2021 · External reference
10.1126/sciadv.abg6711
10.1126/sciadv.abg6711 · External reference
10.1101/2022.07.22.501076
10.1101/2022.07.22.501076 · External reference
10.1038/s41576-018-0003-4
10.1038/s41576-018-0003-4 · External reference
Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data
10.1016/j.tig.2021.09.001 · 2022 · External reference
Long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data
10.1093/gigascience/giab003 · 2021 · External reference
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10.1038/nrm.2017.27
10.1038/nrm.2017.27 · External reference
tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
10.1186/s13059-020-02028-w · 2020 · External reference
Accurate isoform discovery with IsoQuant using long reads
10.1038/s41587-022-01565-y · 2023 · External reference
10.1016/j.cell.2021.04.012
10.1016/j.cell.2021.04.012 · External reference
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10.1038/s41467-019-11049-4
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Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq
10.1038/s41587-021-00965-w · 2021 · External reference
Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
10.1186/s13059-021-02505-w · 2021 · External reference
10.1126/science.aab1601
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10.1038/s41587-019-0147-6
10.1038/s41587-019-0147-6 · External reference
scNanoATAC-seq: a long-read single-cell ATAC sequencing method to detect chromatin accessibility and genetic variants simultaneously within an individual cell
10.1038/s41422-022-00730-x · 2023 · External reference
10.1186/s13059-021-02525-6
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10.1016/j.bpj.2022.02.004
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ScisorWiz: visualizing differential isoform expression in single-cell long-read data
10.1093/bioinformatics/btac340 · 2022 · External reference
10.1186/s13059-020-1926-6
10.1186/s13059-020-1926-6 · External reference
Unresolved reference
External reference
Using single-cell genomics to understand developmental processes and cell fate decisions
10.15252/msb.20178046 · 2018 · External reference
ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis
10.1186/s13059-015-0805-z · 2015 · External reference
10.1093/bioinformatics/bty533
10.1093/bioinformatics/bty533 · External reference
Visualizing data using t-SNE
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10.1038/nbt.4314
10.1038/nbt.4314 · External reference
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10.1038/s41467-018-04696-6 · External reference
10.1038/s41576-020-0223-2
10.1038/s41576-020-0223-2 · External reference
Accuracy, robustness and scalability of dimensionality reduction methods for single-cell RNA-seq analysis
10.1186/s13059-019-1898-6 · 2019 · External reference
10.15252/msb.20188746
10.15252/msb.20188746 · External reference
Dynamical systems model of RNA velocity improves inference of single-cell trajectory, pseudo-time and gene regulation
10.1016/j.jmb.2022.167606 · 2022 · External reference
10.1038/s41587-019-0071-9
10.1038/s41587-019-0071-9 · External reference
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10.1038/s41576-021-00341-z · External reference
Unresolved reference
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Unresolved reference
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Quantifying Waddingtonas epigenetic landscape: a comparison of single-cell potency measures
10.1101/257220 · 2018 · External reference
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10.1038/s41586-019-0969-x · External reference
10.1016/j.cell.2019.01.006
10.1016/j.cell.2019.01.006 · External reference
10.1126/science.aax9552
10.1126/science.aax9552 · External reference
10.1101/gr.271080.120
10.1101/gr.271080.120 · External reference
Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
10.1186/s12864-018-4772-0 · 2018 · External reference
RNA velocity of single cells
10.1038/s41586-018-0414-6 · 2018 · External reference
Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis
10.1126/science.aar3131 · 2018 · External reference
Fundamental limits on dynamic inference from single-cell snapshots
10.1073/pnas.1714723115 · 2018 · External reference
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10.1016/j.cell.2021.12.045
10.1016/j.cell.2021.12.045 · External reference
RNA velocity–current challenges and future perspectives
10.15252/msb.202110282 · 2021 · External reference
Protein velocity and acceleration from single-cell multiomics experiments
10.1186/s13059-020-1945-3 · 2020 · External reference
10.1038/s41587-021-01031-1
10.1038/s41587-021-01031-1 · External reference
Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction
2022 · External reference
10.1101/2021.10.01.462818
10.1101/2021.10.01.462818 · External reference
Macrophage development and activation involve coordinated intron retention in key inflammatory regulators
10.1093/nar/gkaa435 · 2020 · External reference
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10.1371/journal.pcbi.1010492 · External reference
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Full-length spatial transcriptomics reveals the unexplored isoform diversity of the myocardium Post-MI
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