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The Transcriptional Logic of Mammalian Neuronal Diversity

https://doi.org/10.1101/208355

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What this work says

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

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Topographic organization of embryonic motor neurons defined by expression of LIM homeobox genes

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REST: A mammalian silencer protein that restricts sodium channel gene expression to neurons

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Winged helix transcription factor BF-1 is essential for the development of the cerebral hemispheres

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Alternative splicing: Functional diversity among voltage-gated calcium channels and behavioral consequences

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A genome-wide and nonredundant mouse transcription factor database

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Genome-wide Regional Heritability Mapping Identifies a Locus Within the TOX2 Gene Associated With Major Depressive Disorder

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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

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Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells

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Bayesian Sparse Regression Analysis Documents the Diversity of Spinal Inhibitory Interneurons

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Neuronal cell types

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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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Hox Genes: Choreographers in Neural Development, Architects of Circuit Organization

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Gene Length Matters in Neurons

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Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

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Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans

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Hox Genes Promote Neuronal Subtype Diversification through Posterior Induction in Caenorhabditis elegans

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Multi-Scale Molecular Deconstruction of the Serotonin Neuron System

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Hox gene regulation and timing in embryogenesis

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Intron size in mammals: complexity comes to terms with economy

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The problem of neuronal cell types: a physiological genomics approach

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Chapter Six Hox Networks and the Origins of Motor Neuron Diversity

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Gene Ontology: tool for the unification of biology

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Initial sequencing and comparative analysis of the mouse genome

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Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes

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Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition

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Initial sequence of the chimpanzee genome and comparison with the human genome

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Polycomb complexes repress developmental regulators in murine embryonic stem cells

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Generation of neuronal variability and complexity

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An integrated encyclopedia of DNA elements in the human genome

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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

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Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

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Fast gapped-read alignment with Bowtie 2

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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

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Power analysis of single-cell RNA-sequencing experiments

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A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

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Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

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A manual method for the purification of fluorescently labeled neurons from the mammalian brain

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The evolution of cell types in animals: emerging principles from molecular studies

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Single-cell sequencing-based technologies will revolutionize whole-organism science

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The newly identified migration inhibitory protein regulates the radial migration in the developing neocortex

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The impact of amplification on differential expression analyses by RNA-seq

inferredcites →https://doi.org/10.1073/pnas.1002285107openalex-snapshot

Tbr1 regulates regional and laminar identity of postmitotic neurons in developing neocortex

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Dual role for Islet-1 in promoting striatonigral and repressing striatopallidal genetic programs to specify striatonigral cell identity

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High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

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BEDTools: a flexible suite of utilities for comparing genomic features

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STAR: ultrafast universal RNA-seq aligner

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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HTSeq—a Python framework to work with high-throughput sequencing data

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inferredcites →https://doi.org/10.1093/nar/gkt1114openalex-snapshot

RefSeq: an update on mammalian reference sequences

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Genenames.org: the HGNC resources in 2015

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GENCODE: The reference human genome annotation for The ENCODE Project

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From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

inferredcites →https://doi.org/10.1101/gr.169722.113openalex-snapshot

Gene length and expression level shape genomic novelties

inferredcites →https://doi.org/10.1101/gr.229102openalex-snapshot

The Human Genome Browser at UCSC

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Transposon-free regions in mammalian genomes

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Transposition-Driven Genomic Heterogeneity in the Drosophila Brain

inferredcites →https://doi.org/10.1126/science.7871435openalex-snapshot

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inferredcites →https://doi.org/10.1126/science.aaa1934openalex-snapshot

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Regulatory evolution of innate immunity through co-option of endogenous retroviruses

inferredcites →https://doi.org/10.1146/annurev-genet-120213-092412openalex-snapshot

L1 Retrotransposons and Somatic Mosaicism in the Brain

inferredcites →https://doi.org/10.1186/gb-2007-8-6-r127openalex-snapshot

Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome

inferredcites →https://doi.org/10.1186/gb-2014-15-2-r29openalex-snapshot

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

inferredcites →https://doi.org/10.1186/s13059-016-0970-8openalex-snapshot

Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts

inferredcites →https://doi.org/10.1186/s13100-015-0041-9openalex-snapshot

Repbase Update, a database of repetitive elements in eukaryotic genomes

inferredcites →https://doi.org/10.1371/journal.pone.0016493openalex-snapshot

A Quantitative Comparison of Cell-Type-Specific Microarray Gene Expression Profiling Methods in the Mouse Brain

inferredcites →https://doi.org/10.1523/eneuro.0230-16.2016openalex-snapshot

Lhx2 Determines Odorant Receptor Expression Frequency in Mature Olfactory Sensory Neurons

inferredcites →https://doi.org/10.1523/jneurosci.0105-09.2009openalex-snapshot

Transcriptional and Electrophysiological Maturation of Neocortical Fast-Spiking GABAergic Interneurons

inferredcites →https://doi.org/10.1523/jneurosci.0548-15.2015openalex-snapshot

Opposing Role for Egr3 in Nucleus Accumbens Cell Subtypes in Cocaine Action

inferredcites →https://doi.org/10.1523/jneurosci.1134-08.2008openalex-snapshot

Foxg1Is Required for Development of the Vertebrate Olfactory System

inferredcites →https://doi.org/10.1523/jneurosci.1860-14.2014openalex-snapshot

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

inferredcites →https://doi.org/10.1523/jneurosci.2674-14.2014openalex-snapshot

Cell-Type-Specific Repression by Methyl-CpG-Binding Protein 2 Is Biased toward Long Genes

inferredcites →https://doi.org/10.1523/jneurosci.2707-07.2007openalex-snapshot

Targeting Cre Recombinase to Specific Neuron Populations with Bacterial Artificial Chromosome Constructs

inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot

Scikit-learn: Machine Learning in Python

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Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss

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A Mammalian enhancer trap resource for discovering and manipulating neuronal cell types

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Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons

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An intersectional gene regulatory strategy defines subclass diversity of C. elegans motor neurons

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.gpb.2019.03.003openalex-snapshot

Application of Computational Biology to Decode Brain Transcriptomes

inferred← citeshttps://doi.org/10.1523/jneurosci.1930-17.2018openalex-snapshot

Brain Transcriptome Databases: A User's Guide

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