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Single-cell analysis of chromatin silencing programs in development and tumor progression

https://doi.org/10.1101/2020.09.04.282418
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What this work says

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

inferredcites →https://doi.org/10.1016/j.ccell.2017.06.003openalex-snapshot
Tumor Evolution of Glioma-Intrinsic Gene Expression Subtypes Associates with Immunological Changes in the Microenvironment
inferredcites →https://doi.org/10.1016/j.ccr.2006.02.019openalex-snapshot
Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis
inferredcites →https://doi.org/10.1016/j.cell.2006.02.043openalex-snapshot
Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2019.05.031openalex-snapshot
Comprehensive Integration of Single-Cell Data
inferredcites →https://doi.org/10.1016/j.celrep.2013.04.021openalex-snapshot
An Aberrant Transcription Factor Network Essential for Wnt Signaling and Stem Cell Maintenance in Glioblastoma
inferredcites →https://doi.org/10.1016/j.celrep.2016.11.056openalex-snapshot
Clonal Variation in Drug and Radiation Response among Glioma-Initiating Cells Is Linked to Proneural-Mesenchymal Transition
inferredcites →https://doi.org/10.1016/j.molcel.2019.05.025openalex-snapshot
Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded
inferredcites →https://doi.org/10.1016/j.stem.2010.03.018openalex-snapshot
Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells
inferredcites →https://doi.org/10.1016/j.stem.2014.05.006openalex-snapshot
Chromatin Repressive Complexes in Stem Cells, Development, and Cancer
inferredcites →https://doi.org/10.1016/j.stem.2015.07.002openalex-snapshot
Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury
inferredcites →https://doi.org/10.1016/j.stem.2016.11.003openalex-snapshot
Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance
inferredcites →https://doi.org/10.1016/j.stem.2019.11.015openalex-snapshot
Outer Radial Glia-like Cancer Stem Cells Contribute to Heterogeneity of Glioblastoma
inferredcites →https://doi.org/10.1038/nature07107openalex-snapshot
Genome-scale DNA methylation maps of pluripotent and differentiated cells
inferredcites →https://doi.org/10.1038/nature09784openalex-snapshot
The Polycomb complex PRC2 and its mark in life
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature21350openalex-snapshot
Scaling single-cell genomics from phenomenology to mechanism
inferredcites →https://doi.org/10.1038/nbt.3383openalex-snapshot
Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state
inferredcites →https://doi.org/10.1038/nbt.4314openalex-snapshot
Dimensionality reduction for visualizing single-cell data using UMAP
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/nrc1991openalex-snapshot
Polycomb silencers control cell fate, development and cancer
inferredcites →https://doi.org/10.1038/s41467-019-09982-5openalex-snapshot
CUT&Tag for efficient epigenomic profiling of small samples and single cells
inferredcites →https://doi.org/10.1038/s41467-020-17186-5openalex-snapshot
Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy
inferredcites →https://doi.org/10.1038/s41467-020-17979-8openalex-snapshot
Author Correction: Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy
inferredcites →https://doi.org/10.1038/s41576-018-0089-8openalex-snapshot
Chromatin accessibility and the regulatory epigenome
inferredcites →https://doi.org/10.1038/s41587-019-0332-7openalex-snapshot
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia
inferredcites →https://doi.org/10.1038/s41588-019-0424-9openalex-snapshot
High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer
inferredcites →https://doi.org/10.1038/s41588-021-00790-6openalex-snapshot
ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
inferredcites →https://doi.org/10.1038/s41592-020-0820-1openalex-snapshot
Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes
inferredcites →https://doi.org/10.1093/bioinformatics/btr260openalex-snapshot
Molecular signatures database (MSigDB) 3.0
inferredcites →https://doi.org/10.1126/science.1254257openalex-snapshot
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
inferredcites →https://doi.org/10.1146/annurev.genet.38.072902.091907openalex-snapshot
Epigenetic Regulation of Cellular Memory by the Polycomb and Trithorax Group Proteins
inferredcites →https://doi.org/10.1186/s13059-016-1033-xopenalex-snapshot
Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm
inferredcites →https://doi.org/10.1186/s13072-018-0182-4openalex-snapshot
Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression
inferredcites →https://doi.org/10.1186/s13072-018-0243-8openalex-snapshot
Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs

What points at this work

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

inferred← citeshttps://doi.org/10.1002/9781119671404.ch12openalex-snapshot
Single‐Cell Transcriptomics and Epigenomics for CRISPR‐Mediated Perturbation Studies
inferred← citeshttps://doi.org/10.1007/978-1-0716-1831-8_3openalex-snapshot
Single-Cell Analysis of the Transcriptome and Epigenome
inferred← citeshttps://doi.org/10.1007/978-1-0716-2525-5_2openalex-snapshot
Single-Cell Genomic and Epigenomic DNA Analyses
inferred← citeshttps://doi.org/10.1038/s41467-021-21765-5openalex-snapshot
Deep learning-based enhancement of epigenomics data with AtacWorks
inferred← citeshttps://doi.org/10.1038/s41587-021-00927-2openalex-snapshot
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells
inferred← citeshttps://doi.org/10.1038/s41587-021-01031-1openalex-snapshot
Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin
inferred← citeshttps://doi.org/10.1038/s41587-022-01560-3openalex-snapshot
scChIX-seq infers dynamic relationships between histone modifications in single cells
inferred← citeshttps://doi.org/10.1083/jcb.202103078openalex-snapshot
High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq)
inferred← citeshttps://doi.org/10.1097/mot.0000000000000836openalex-snapshot
Technical advancements in epigenomics and applications in transplantation
inferred← citeshttps://doi.org/10.1101/2021.04.27.441642openalex-snapshot
Simultaneous profiling of multiple chromatin proteins in the same cells
inferred← citeshttps://doi.org/10.3390/cancers13133152openalex-snapshot
A Systems Approach to Brain Tumor Treatment
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