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Cis-topic modelling of single-cell epigenomes

https://doi.org/10.1101/370346
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What this work says

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

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Sox8 and Sox10 jointly maintain myelin gene expression in oligodendrocytes
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Nuclear Factor I Isoforms Regulate Gene Expression During the Differentiation of Human Neural Progenitors to Astrocytes
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Analysis of SOX10 Function in Neural Crest-Derived Melanocyte Development: SOX10-Dependent Transcriptional Control of Dopachrome Tautomerase
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Interpreting tree ensembles with inTrees
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The promoter-specific transcription factor Sp1 binds to upstream sequences in the SV40 early promoter
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SOX–partner code for cell specification: Regulatory target selection and underlying molecular mechanisms
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Olig2 Targets Chromatin Remodelers to Enhancers to Initiate Oligodendrocyte Differentiation
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Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
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Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation
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Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics
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Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
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Dynamic properties of sensory stimulation evoked responses in mouse cerebellar granule cell layer and molecular layer
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Genome-Wide Analysis of MEF2 Transcriptional Program Reveals Synaptic Target Genes and Neuronal Activity-Dependent Polyadenylation Site Selection
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Sox9 and NFIA Coordinate a Transcriptional Regulatory Cascade during the Initiation of Gliogenesis
inferredcites →https://doi.org/10.1016/j.neuron.2017.11.033openalex-snapshot
Distinct Inhibitory Circuits Orchestrate Cortical beta and gamma Band Oscillations
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Molecular basis for the genome engagement by Sox proteins
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DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation
inferredcites →https://doi.org/10.1016/j.stemcr.2014.12.002openalex-snapshot
Direct Conversion of Fibroblasts into Functional Astrocytes by Defined Transcription Factors
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From stem cells to neurons and glia: a Soxist's view of neural development
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Early Growth Response Protein 1 (Egr-1): Prototype of a Zinc-finger Family of Transcription Factors
inferredcites →https://doi.org/10.1016/s0092-8674(02)00677-3openalex-snapshot
The bHLH Transcription Factors OLIG2 and OLIG1 Couple Neuronal and Glial Subtype Specification
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Matching SOX: partner proteins and co-factors of the SOX family of transcriptional regulators
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Molecular classification of cutaneous malignant melanoma by gene expression profiling
inferredcites →https://doi.org/10.1038/jid.2014.128openalex-snapshot
SOX10 Promotes Melanoma Cell Invasion by Regulating Melanoma Inhibitory Activity
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A novel hypoxia-associated subset of FN1highMITFlow melanoma cells: identification, characterization, and prognostic value
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The DNA-encoded nucleosome organization of a eukaryotic genome
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Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma
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Single-cell chromatin accessibility reveals principles of regulatory variation
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Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance
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The cis-regulatory dynamics of embryonic development at single-cell resolution
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GREAT improves functional interpretation of cis-regulatory regions
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Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
inferredcites →https://doi.org/10.1038/ncb2535openalex-snapshot
Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma
inferredcites →https://doi.org/10.1038/ncomms7683openalex-snapshot
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state
inferredcites →https://doi.org/10.1038/ng.3646openalex-snapshot
Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
inferredcites →https://doi.org/10.1038/nm.2863openalex-snapshot
MDM4 is a key therapeutic target in cutaneous melanoma
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Embryonic stem cell–based mapping of developmental transcriptional programs
inferredcites →https://doi.org/10.1038/nmeth.3728openalex-snapshot
Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity
inferredcites →https://doi.org/10.1038/nmeth.4396openalex-snapshot
An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
inferredcites →https://doi.org/10.1038/nmeth.4401openalex-snapshot
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
inferredcites →https://doi.org/10.1038/nmeth.4463openalex-snapshot
SCENIC: single-cell regulatory network inference and clustering
inferredcites →https://doi.org/10.1038/nprot.2011.409openalex-snapshot
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs
inferredcites →https://doi.org/10.1038/s41467-017-01573-6openalex-snapshot
The low affinity neurotrophin receptor CD271 regulates phenotype switching in melanoma
inferredcites →https://doi.org/10.1038/s41467-018-04629-3openalex-snapshot
Unsupervised clustering and epigenetic classification of single cells
inferredcites →https://doi.org/10.1038/s41467-018-05887-xopenalex-snapshot
High-throughput chromatin accessibility profiling at single-cell resolution
inferredcites →https://doi.org/10.1038/s41588-019-0362-6openalex-snapshot
Interrogation of human hematopoiesis at single-cell and single-variant resolution
inferredcites →https://doi.org/10.1038/s41593-018-0079-3openalex-snapshot
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
inferredcites →https://doi.org/10.1073/pnas.0307752101openalex-snapshot
Finding scientific topics
inferredcites →https://doi.org/10.1093/bioinformatics/btv145openalex-snapshot
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
inferredcites →https://doi.org/10.1093/bioinformatics/btv715openalex-snapshot
destiny : diffusion maps for large-scale single-cell data in R
inferredcites →https://doi.org/10.1093/bioinformatics/btx315openalex-snapshot
Single-cell regulome data analysis by SCRAT
inferredcites →https://doi.org/10.1093/emboj/cdf676openalex-snapshot
Matrix metalloproteinases in the adult brain physiology: a link between c‐Fos, AP‐1 and remodeling of neuronal connections?
inferredcites →https://doi.org/10.1093/nar/20.5.1087openalex-snapshot
Evolutionary variation of the CCAAT-binding transcription factor NF-Y
inferredcites →https://doi.org/10.1093/nar/21.3.744openalex-snapshot
Seven new members of theSoxgene family expressed during mouse development
inferredcites →https://doi.org/10.1093/nar/30.1.207openalex-snapshot
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
inferredcites →https://doi.org/10.1093/nar/gkg540openalex-snapshot
Cluster-Buster: finding dense clusters of motifs in DNA sequences
inferredcites →https://doi.org/10.1093/nar/gkp950openalex-snapshot
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
inferredcites →https://doi.org/10.1093/nar/gkr1104openalex-snapshot
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
inferredcites →https://doi.org/10.1093/nar/gks543openalex-snapshot
i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules
inferredcites →https://doi.org/10.1093/nar/gku977openalex-snapshot
GBshape: a genome browser database for DNA shape annotations
inferredcites →https://doi.org/10.1093/nar/gkv395openalex-snapshot
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly
inferredcites →https://doi.org/10.1093/nar/gkx1106openalex-snapshot
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
inferredcites →https://doi.org/10.1097/00008390-199410000-00003openalex-snapshot
Levels of dopachrome tautomerase in human melanocytes cultured in vitro
inferredcites →https://doi.org/10.1097/cmr.0b013e32833bd89eopenalex-snapshot
The immunohistochemistry of invasive and proliferative phenotype switching in melanoma: a case report
inferredcites →https://doi.org/10.1101/129247openalex-snapshot
BROCKMAN: Deciphering variance in epigenomic regulators by k -mer factorization
inferredcites →https://doi.org/10.1101/155473openalex-snapshot
Chromatin accessibility dynamics of myogenesis at single cell resolution
inferredcites →https://doi.org/10.1101/286351openalex-snapshot
Profiling of pluripotency factors in individual stem cells and early embryos
inferredcites →https://doi.org/10.1101/316208openalex-snapshot
Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity
inferredcites →https://doi.org/10.1101/gad.13.13.1647openalex-snapshot
NeuroD is required for differentiation of the granule cells in the cerebellum and hippocampus
inferredcites →https://doi.org/10.1101/gad.215802openalex-snapshot
Terminal differentiation of myelin-forming oligodendrocytes depends on the transcription factor Sox10
inferredcites →https://doi.org/10.1109/tpami.2013.69openalex-snapshot
Latent Dirichlet Allocation Models for Image Classification
inferredcites →https://doi.org/10.1111/1523-1747.ep12476630openalex-snapshot
Role of Tyrosinase as the Determinant of Pigmentation in Cultured Human Melanocytes
inferredcites →https://doi.org/10.1111/j.1600-0749.2006.00322.xopenalex-snapshot
Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature
inferredcites →https://doi.org/10.1111/j.1600-0749.2007.00368.xopenalex-snapshot
The tyrosinase enhancer is activated by Sox10 and Mitf in mouse melanocytes
inferredcites →https://doi.org/10.1111/j.1755-148x.2009.00616.xopenalex-snapshot
NRG1 / ERBB3 signaling in melanocyte development and melanoma: inhibition of differentiation and promotion of proliferation
inferredcites →https://doi.org/10.1111/j.1755-148x.2010.00711.xopenalex-snapshot
Sox proteins in melanocyte development and melanoma
inferredcites →https://doi.org/10.1117/1.2819119openalex-snapshot
Book Review: Pattern Recognition and Machine Learning
inferredcites →https://doi.org/10.1126/science.aab1601openalex-snapshot
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
inferredcites →https://doi.org/10.1126/science.aaf1204openalex-snapshot
Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain
inferredcites →https://doi.org/10.1128/mcb.19.7.4711openalex-snapshot
Major Egr3 Isoforms Are Generated via Alternate Translation Start Sites and Differ in Their Abilities To Activate Transcription
inferredcites →https://doi.org/10.1158/0008-5472.can-07-2491openalex-snapshot
In vivo Switching of Human Melanoma Cells between Proliferative and Invasive States
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10.1162/jmlr.2003.3.4-5.993
inferredcites →https://doi.org/10.1186/1471-213x-11-40openalex-snapshot
SOX10 directly modulates ERBB3 transcription via an intronic neural crest enhancer
inferredcites →https://doi.org/10.1186/s13059-015-0844-5openalex-snapshot
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
inferredcites →https://doi.org/10.1186/s13059-016-0950-zopenalex-snapshot
Simultaneous profiling of transcriptome and DNA methylome from a single cell
inferredcites →https://doi.org/10.1186/s40163-017-0074-0openalex-snapshot
Crime topic modeling
inferredcites →https://doi.org/10.1242/dev.02477openalex-snapshot
Replacement of the Sox10 transcription factor by Sox8 reveals incomplete functional equivalence
inferredcites →https://doi.org/10.1371/journal.pcbi.1003731openalex-snapshot
iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
inferredcites →https://doi.org/10.1371/journal.pgen.1006636openalex-snapshot
TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF
inferredcites →https://doi.org/10.1523/jneurosci.2042-13.2013openalex-snapshot
Titration of GLI3 Repressor Activity by Sonic Hedgehog Signaling Is Critical for Maintaining Multiple Adult Neural Stem Cell and Astrocyte Functions
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SOX9 Is an Astrocyte-Specific Nuclear Marker in the Adult Brain Outside the Neurogenic Regions
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Feature Selection with the Boruta Package
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Latent dirichlet allocation
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Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells
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Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

What points at this work

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

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/10.1038/s41587-021-00962-zopenalex-snapshot
High-content single-cell combinatorial indexing
inferred← citeshttps://doi.org/10.1038/s41592-022-01562-8openalex-snapshot
scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks
inferred← citeshttps://doi.org/10.1038/s41598-018-36057-0openalex-snapshot
Chromatin accessibility identifies diversity in mesenchymal stem cells from different tissue origins
inferred← citeshttps://doi.org/10.1101/2019.12.21.885806openalex-snapshot
Prioritization of enhancer mutations by combining allele-specific chromatin accessibility with deep learning
inferred← citeshttps://doi.org/10.1101/2022.08.14.503915openalex-snapshot
Expression QTLs in single-cell sequencing data
inferred← citeshttps://doi.org/10.1101/534800openalex-snapshot
Capturing cell type-specific chromatin structural patterns by applying topic modeling to single-cell Hi-C data
inferred← citeshttps://doi.org/10.1101/637256openalex-snapshot
Improved single-cell ATAC-seq reveals chromatin dynamics of in vitro corticogenesis
inferred← citeshttps://doi.org/10.1101/gr.243725.118openalex-snapshot
The accessible chromatin landscape of the murine hippocampus at single-cell resolution
inferred← citeshttps://doi.org/10.1186/s13059-020-02034-yopenalex-snapshot
APEC: an accesson-based method for single-cell chromatin accessibility analysis
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006555openalex-snapshot
Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps
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