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Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data

https://doi.org/10.1101/534800
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf02289565openalex-snapshot
Multidimensional Scaling by Optimizing Goodness of Fit to a Nonmetric Hypothesis
inferredcites →https://doi.org/10.1038/nature12593openalex-snapshot
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
inferredcites →https://doi.org/10.1038/nature23001openalex-snapshot
Cell-cycle dynamics of chromosomal organization at single-cell resolution
inferredcites →https://doi.org/10.1038/nature23884openalex-snapshot
The 4D nucleome project
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.4155openalex-snapshot
Massively multiplex single-cell Hi-C
inferredcites →https://doi.org/10.1038/s41592-019-0367-1openalex-snapshot
cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data
inferredcites →https://doi.org/10.1073/pnas.0307752101openalex-snapshot
Finding scientific topics
inferredcites →https://doi.org/10.1073/pnas.1901423116openalex-snapshot
Robust single-cell Hi-C clustering by convolution- and random-walk–based imputation
inferredcites →https://doi.org/10.1080/01621459.1951.10500769openalex-snapshot
The Kolmogorov-Smirnov Test for Goodness of Fit
inferredcites →https://doi.org/10.1093/bioinformatics/bty285openalex-snapshot
Unsupervised embedding of single-cell Hi-C data
inferredcites →https://doi.org/10.1101/370346openalex-snapshot
Cis-topic modelling of single-cell epigenomes
inferredcites →https://doi.org/10.1101/506717openalex-snapshot
HiCluster: A Robust Single-Cell Hi-C Clustering Method Based on Convolution and Random Walk
inferredcites →https://doi.org/10.1101/gr.220640.117openalex-snapshot
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1186/s13059-015-0741-yopenalex-snapshot
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
inferredcites →https://doi.org/10.1186/s40064-016-3252-8openalex-snapshot
An overview of topic modeling and its current applications in bioinformatics
inferredcites →https://doi.org/10.2307/3001968openalex-snapshot
Individual Comparisons by Ranking Methods
inferredcites →https://doi.org/10.48550/arxiv.1802.03426openalex-snapshot
UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction
inferredcites →https://doi.org/10.5555/944919.944937openalex-snapshot
Latent dirichlet allocation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s12561-021-09304-8openalex-snapshot
Penalized Latent Dirichlet Allocation Model in Single-Cell RNA Sequencing
inferred← citeshttps://doi.org/10.1016/j.ceb.2020.04.005openalex-snapshot
Evolving methodologies and concepts in 4D nucleome research
inferred← citeshttps://doi.org/10.1016/j.ymeth.2019.09.012openalex-snapshot
Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells
inferred← citeshttps://doi.org/10.1101/gr.271791.120openalex-snapshot
Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
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