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Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

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What this work says

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

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Making lineage decisions with biological noise: Lessons from the early mouse embryo

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Real-Time Kinetics of Gene Activity in Individual Bacteria

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Genome Regulation by Polycomb and Trithorax Proteins

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Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

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RNF12 Is an X-Encoded Dose-Dependent Activator of X Chromosome Inactivation

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Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells

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Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

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Control of Transcript Variability in Single Mammalian Cells

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Enhancer Control of Transcriptional Bursting

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AKT/PKB Signaling: Navigating the Network

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Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

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Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy

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Nuclear Retention of mRNA in Mammalian Tissues

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Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis

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Transcriptional Pulsing of a Developmental Gene

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Bursty Gene Expression in the Intact Mammalian Liver

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Digital Quantification of Proteins and mRNA in Single Mammalian Cells

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Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

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Models of stochastic gene expression

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Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

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Interplay between gene expression noise and regulatory network architecture

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Statistical Total Correlation Spectroscopy: An Exploratory Approach for Latent Biomarker Identification from Metabolic 1 H NMR Data Sets

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Evaluation of the Orthogonal Projection on Latent Structure Model Limitations Caused by Chemical Shift Variability and Improved Visualization of Biomarker Changes in 1 H NMR Spectroscopic Metabonomic Studies

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Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses

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Transcription regulation and animal diversity

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Summing up the noise in gene networks

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Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

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The ground state of embryonic stem cell self-renewal

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Functional roles for noise in genetic circuits

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Global quantification of mammalian gene expression control

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Control of ground-state pluripotency by allelic regulation of Nanog

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Deconstructing transcriptional heterogeneity in pluripotent stem cells

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

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General properties of transcriptional time series in Escherichia coli

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Fiji: an open-source platform for biological-image analysis

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FISH-quant: automatic counting of transcripts in 3D FISH images

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Validation of noise models for single-cell transcriptomics

inferredcites →https://doi.org/10.1038/nmeth.3047openalex-snapshot

Improved vectors and genome-wide libraries for CRISPR screening

inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot

HISAT: a fast spliced aligner with low memory requirements

inferredcites →https://doi.org/10.1038/nmeth.3935openalex-snapshot

A far-red fluorescent protein evolved from a cyanobacterial phycobiliprotein

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Single-molecule mRNA detection and counting in mammalian tissue

inferredcites →https://doi.org/10.1038/s41467-018-02866-0openalex-snapshot

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

inferredcites →https://doi.org/10.1038/s41580-018-0002-5openalex-snapshot

Single-cell transcriptional profiling: a window into embryonic cell-type specification

inferredcites →https://doi.org/10.1038/s41580-018-0010-5openalex-snapshot

Born to run: control of transcription elongation by RNA polymerase II

inferredcites →https://doi.org/10.1038/s41586-018-0836-1openalex-snapshot

Genomic encoding of transcriptional burst kinetics

inferredcites →https://doi.org/10.1038/s41588-018-0175-zopenalex-snapshot

Dynamic interplay between enhancer–promoter topology and gene activity

inferredcites →https://doi.org/10.1038/srep07125openalex-snapshot

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

inferredcites →https://doi.org/10.1073/pnas.1013148108openalex-snapshot

Exploring transcription regulation through cell-to-cell variability

inferredcites →https://doi.org/10.1073/pnas.1213530109openalex-snapshot

Transcriptional burst frequency and burst size are equally modulated across the human genome

inferredcites →https://doi.org/10.1074/jbc.m411283200openalex-snapshot

Monoallelic Expression and Asynchronous Replication of p120 Catenin in Mouse and Human Cells

inferredcites →https://doi.org/10.1089/omi.2011.0118openalex-snapshot

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

inferredcites →https://doi.org/10.1093/bioinformatics/btl565openalex-snapshot

Predicting transcription factor affinities to DNA from a biophysical model

inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot

TopHat: discovering splice junctions with RNA-Seq

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/btx223openalex-snapshot

DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses

inferredcites →https://doi.org/10.1093/bioinformatics/bty078openalex-snapshot

Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression

inferredcites →https://doi.org/10.1093/dnares/dsn030openalex-snapshot

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

inferredcites →https://doi.org/10.1093/nar/gkv624openalex-snapshot

Simultaneous live imaging of the transcription and nuclear position of specific genes

inferredcites →https://doi.org/10.1101/gr.099796.109openalex-snapshot

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis

inferredcites →https://doi.org/10.1101/gr.139378.112openalex-snapshot

Noise–mean relationship in mutated promoters

inferredcites →https://doi.org/10.1111/j.1365-2958.2009.06605.xopenalex-snapshot

A chance at survival: gene expression noise and phenotypic diversification strategies

inferredcites →https://doi.org/10.1126/science.1070919openalex-snapshot

Stochastic Gene Expression in a Single Cell

inferredcites →https://doi.org/10.1126/science.1098641openalex-snapshot

Control of Stochasticity in Eukaryotic Gene Expression

inferredcites →https://doi.org/10.1126/science.1198817openalex-snapshot

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

inferredcites →https://doi.org/10.1126/science.1202142openalex-snapshot

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

inferredcites →https://doi.org/10.1126/science.1242975openalex-snapshot

Genetic Determinants and Cellular Constraints in Noisy Gene Expression

inferredcites →https://doi.org/10.1128/mcb.01432-06openalex-snapshot

The Polycomb Group Protein Suz12 Is Required for Embryonic Stem Cell Differentiation

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

inferredcites →https://doi.org/10.1186/s12859-015-0656-3openalex-snapshot

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-014-0554-4openalex-snapshot

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens

inferredcites →https://doi.org/10.1186/s13059-015-0727-9openalex-snapshot

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution

inferredcites →https://doi.org/10.1186/s13059-016-0938-8openalex-snapshot

CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq

inferredcites →https://doi.org/10.1186/s13059-017-1200-8openalex-snapshot

SCALE: modeling allele-specific gene expression by single-cell RNA sequencing

inferredcites →https://doi.org/10.1242/dev.003798openalex-snapshot

Stochastic patterning in the mouse pre-implantation embryo

inferredcites →https://doi.org/10.1242/dev.102624openalex-snapshot

Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage

inferredcites →https://doi.org/10.1371/journal.pbio.0040309openalex-snapshot

Stochastic mRNA Synthesis in Mammalian Cells

inferredcites →https://doi.org/10.1371/journal.pbio.1001621openalex-snapshot

Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression

inferredcites →https://doi.org/10.1371/journal.pcbi.1000704openalex-snapshot

Effects of Transcriptional Pausing on Gene Expression Dynamics

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.15252/msb.20145704openalex-snapshot

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

inferredcites →https://doi.org/10.15252/msb.20156257openalex-snapshot

Structure of silent transcription intervals and noise characteristics of mammalian genes

inferredcites →https://doi.org/10.1534/genetics.114.165886openalex-snapshot

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

inferredcites →https://doi.org/10.1634/stemcells.2007-0389openalex-snapshot

Laminin-511 but Not -332, -111, or -411 Enables Mouse Embryonic Stem Cell Self-Renewal In Vitro

inferredcites →https://doi.org/10.7554/elife.02407openalex-snapshot

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

What points at this work

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

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Discontinuous transcription of ribosomal DNA in human cells

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Mammalian gene expression variability is explained by underlying cell state

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Bimodality in gene expression without feedback: from Gaussian white noise to log-normal coloured noise

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