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Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex

https://doi.org/10.1101/2023.04.08.536119
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What this work says

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

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Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
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Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
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DNA-Binding Specificities of Human Transcription Factors
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Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development
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Enhancer Evolution across 20 Mammalian Species
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Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest
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Integrated analysis of multimodal single-cell data
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A single-cell atlas of chromatin accessibility in the human genome
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DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors
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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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The evolution of Great Apes has shaped the functional enhancers' landscape in human embryonic stem cells
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Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila
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In vivo enhancer analysis of human conserved non-coding sequences
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Topological domains in mammalian genomes identified by analysis of chromatin interactions
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Principles of regulatory information conservation between mouse and human
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A comparative encyclopedia of DNA elements in the mouse genome
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Human body epigenome maps reveal noncanonical DNA methylation variation
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Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus
inferredcites →https://doi.org/10.1038/ng.3211openalex-snapshot
LD Score regression distinguishes confounding from polygenicity in genome-wide association studies
inferredcites →https://doi.org/10.1038/nmeth.3035openalex-snapshot
Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
inferredcites →https://doi.org/10.1038/nrg.2016.139openalex-snapshot
Regulatory activities of transposable elements: from conflicts to benefits
inferredcites →https://doi.org/10.1038/nrg2795openalex-snapshot
Next-generation genomics: an integrative approach
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Motor cortex — to act or not to act?
inferredcites →https://doi.org/10.1038/s41467-019-13056-xopenalex-snapshot
The art of using t-SNE for single-cell transcriptomics
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Confronting false discoveries in single-cell differential expression
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Gene expression across mammalian organ development
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Regulatory genomic circuitry of human disease loci by integrative epigenomics
inferredcites →https://doi.org/10.1038/s41586-020-03182-8openalex-snapshot
DNA methylation atlas of the mouse brain at single-cell resolution
inferredcites →https://doi.org/10.1038/s41586-020-2119-xopenalex-snapshot
Spatiotemporal DNA methylome dynamics of the developing mouse fetus
inferredcites →https://doi.org/10.1038/s41586-021-03446-xopenalex-snapshot
Genome-wide enhancer maps link risk variants to disease genes
inferredcites →https://doi.org/10.1038/s41586-021-03465-8openalex-snapshot
Comparative cellular analysis of motor cortex in human, marmoset and mouse
inferredcites →https://doi.org/10.1038/s41586-021-03500-8openalex-snapshot
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
inferredcites →https://doi.org/10.1038/s41586-021-03604-1openalex-snapshot
An atlas of gene regulatory elements in adult mouse cerebrum
inferredcites →https://doi.org/10.1038/s41586-021-03775-xopenalex-snapshot
Molecular architecture of the developing mouse brain
inferredcites →https://doi.org/10.1038/s41586-021-03950-0openalex-snapshot
A multimodal cell census and atlas of the mammalian primary motor cortex
inferredcites →https://doi.org/10.1038/s41588-019-0479-7openalex-snapshot
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells
inferredcites →https://doi.org/10.1038/s41588-019-0538-0openalex-snapshot
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
inferredcites →https://doi.org/10.1038/s41592-019-0502-zopenalex-snapshot
Joint profiling of DNA methylation and chromatin architecture in single cells
inferredcites →https://doi.org/10.1038/s41592-019-0547-zopenalex-snapshot
Simultaneous profiling of 3D genome structure and DNA methylation in single human cells
inferredcites →https://doi.org/10.1038/s41592-019-0619-0openalex-snapshot
Fast, sensitive and accurate integration of single-cell data with Harmony
inferredcites →https://doi.org/10.1038/s41592-021-01252-xopenalex-snapshot
Effective gene expression prediction from sequence by integrating long-range interactions
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Defining diversity, specialization, and gene specificity in transcriptomes through information theory
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Time Tree of Rubiaceae: Phylogeny and Dating the Family, Subfamilies, and Tribes
inferredcites →https://doi.org/10.1093/bioinformatics/btac757openalex-snapshot
GSEApy: a comprehensive package for performing gene set enrichment analysis in Python
inferredcites →https://doi.org/10.1093/bioinformatics/btad457openalex-snapshot
LegNet: a best-in-class deep learning model for short DNA regulatory regions
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/gbe/evx194openalex-snapshot
Gene Regulatory Enhancers with Evolutionarily Conserved Activity Are More Pleiotropic than Those with Species-Specific Activity
inferredcites →https://doi.org/10.1093/molbev/msh010openalex-snapshot
Mammalian Housekeeping Genes Evolve More Slowly than Tissue-Specific Genes
inferredcites →https://doi.org/10.1093/nar/gkj144openalex-snapshot
The UCSC Genome Browser Database: update 2006
inferredcites →https://doi.org/10.1093/nar/gkv1505openalex-snapshot
TopDom: an efficient and deterministic method for identifying topological domains in genomes
inferredcites →https://doi.org/10.1101/523712openalex-snapshot
Transposable elements drive reorganisation of 3D chromatin during early embryogenesis
inferredcites →https://doi.org/10.1101/731877openalex-snapshot
openTSNE: a modular Python library for t-SNE dimensionality reduction and embedding
inferredcites →https://doi.org/10.1101/gr.260844.120openalex-snapshot
Cross-species analysis of enhancer logic using deep learning
inferredcites →https://doi.org/10.1101/gr.3715005openalex-snapshot
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
inferredcites →https://doi.org/10.1126/science.1088328openalex-snapshot
Scanning Human Gene Deserts for Long-Range Enhancers
inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
inferredcites →https://doi.org/10.1126/science.165.3891.349openalex-snapshot
Gene Regulation for Higher Cells: A Theory
inferredcites →https://doi.org/10.1126/science.362.6413.415-kopenalex-snapshot
Cancer chromatin accessibility landscape
inferredcites →https://doi.org/10.1126/science.aaa1934openalex-snapshot
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
inferredcites →https://doi.org/10.1126/science.abg4696openalex-snapshot
Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells
inferredcites →https://doi.org/10.1126/science.abm1741openalex-snapshot
Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH
inferredcites →https://doi.org/10.1145/2020408.2020496openalex-snapshot
Leakage in data mining
inferredcites →https://doi.org/10.1186/1471-2105-14-128openalex-snapshot
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/gb-2010-11-3-r25openalex-snapshot
A scaling normalization method for differential expression analysis of RNA-seq data
inferredcites →https://doi.org/10.1214/aos/1013699998openalex-snapshot
The control of the false discovery rate in multiple testing under dependency
inferredcites →https://doi.org/10.1371/journal.pcbi.1008050openalex-snapshot
Cross-species regulatory sequence activity prediction
inferredcites →https://doi.org/10.21105/joss.00861openalex-snapshot
UMAP: Uniform Manifold Approximation and Projection

What points at this work

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

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Transcriptional conservation and evolutionary divergence of cell types across mammalian hypothalamus development
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SnapATAC2: a fast, scalable and versatile tool for analysis of single-cell omics data
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ProA and ProB repeat sequences shape 3D genome organization in eukaryotes
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A marmoset brain cell census reveals regional specialization of cellular identities
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