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Multimodal transcriptional control of pattern formation in embryonic development

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What this work says

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

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Regulation of even‐skipped stripe 2 in the Drosophila embryo.

inferredcites →https://doi.org/10.1002/jmor.1050690102openalex-snapshot

Studies on the cytology and early embryology of the egg of Drosophila melanogaster

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Markovian Modeling of Gene-Product Synthesis

inferredcites →https://doi.org/10.1007/978-1-4939-7213-5_23openalex-snapshot

Live Imaging of mRNA Synthesis in Drosophila

inferredcites →https://doi.org/10.1016/0021-9991(76)90041-3openalex-snapshot

A general method for numerically simulating the stochastic time evolution of coupled chemical reactions

inferredcites →https://doi.org/10.1016/0092-8674(77)90278-1openalex-snapshot

Electron microscopic analysis of chromatin replication in the cellular blastoderm drosophila melanogaster embryo

inferredcites →https://doi.org/10.1016/0092-8674(79)90263-0openalex-snapshot

Post-replicative nonribosomal transcription units in D. melanogaster embryos

inferredcites →https://doi.org/10.1016/0092-8674(88)90183-3openalex-snapshot

The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner

inferredcites →https://doi.org/10.1016/0092-8674(92)90405-2openalex-snapshot

Control of Drosophila body pattern by the hunchback morphogen gradient

inferredcites →https://doi.org/10.1016/0092-8674(93)90402-copenalex-snapshot

Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen

inferredcites →https://doi.org/10.1016/bs.mie.2016.03.017openalex-snapshot

Fluctuation Analysis

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Data Mining: Practical Machine Learning Tools and Techniques

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Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule FRET Data

inferredcites →https://doi.org/10.1016/j.bpj.2018.03.031openalex-snapshot

Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells

inferredcites →https://doi.org/10.1016/j.cell.2007.05.026openalex-snapshot

Stability and Nuclear Dynamics of the Bicoid Morphogen Gradient

inferredcites →https://doi.org/10.1016/j.cell.2008.01.053openalex-snapshot

A Quantitative Spatiotemporal Atlas of Gene Expression in the Drosophila Blastoderm

inferredcites →https://doi.org/10.1016/j.cell.2013.07.025openalex-snapshot

Precise Developmental Gene Expression Arises from Globally Stochastic Transcriptional Activity

inferredcites →https://doi.org/10.1016/j.cell.2014.02.009openalex-snapshot

Looping Back to Leap Forward: Transcription Enters a New Era

inferredcites →https://doi.org/10.1016/j.cell.2016.04.034openalex-snapshot

Dynamics of Translation of Single mRNA Molecules In Vivo

inferredcites →https://doi.org/10.1016/j.cell.2016.04.040openalex-snapshot

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells

inferredcites →https://doi.org/10.1016/j.cell.2016.05.025openalex-snapshot

Enhancer Control of Transcriptional Bursting

inferredcites →https://doi.org/10.1016/j.cell.2018.03.069openalex-snapshot

LlamaTags: A Versatile Tool to Image Transcription Factor Dynamics in Live Embryos

inferredcites →https://doi.org/10.1016/j.cell.2018.09.056openalex-snapshot

Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting

inferredcites →https://doi.org/10.1016/j.cell.2019.01.007openalex-snapshot

Optimal Decoding of Cellular Identities in a Genetic Network

inferredcites →https://doi.org/10.1016/j.celrep.2014.05.053openalex-snapshot

Transcription Factors Modulate c-Fos Transcriptional Bursts

inferredcites →https://doi.org/10.1016/j.cub.2009.10.028openalex-snapshot

Visualization of Individual Scr mRNAs during Drosophila Embryogenesis Yields Evidence for Transcriptional Bursting

inferredcites →https://doi.org/10.1016/j.cub.2010.10.021openalex-snapshot

Developmental Control of Late Replication and S Phase Length

inferredcites →https://doi.org/10.1016/j.cub.2013.08.053openalex-snapshot

Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos

inferredcites →https://doi.org/10.1016/j.cub.2013.08.054openalex-snapshot

Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning

inferredcites →https://doi.org/10.1016/j.cub.2017.03.069openalex-snapshot

Rapid Rates of Pol II Elongation in the Drosophila Embryo

inferredcites →https://doi.org/10.1016/j.molcel.2015.03.005openalex-snapshot

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

inferredcites →https://doi.org/10.1016/j.molcel.2016.03.007openalex-snapshot

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

inferredcites →https://doi.org/10.1016/j.tcb.2015.10.007openalex-snapshot

Theory in Biology: Figure 1 or Figure 7?

inferredcites →https://doi.org/10.1016/j.ymeth.2015.05.012openalex-snapshot

Bayesian inference of reaction kinetics from single-cell recordings across a heterogeneous cell population

inferredcites →https://doi.org/10.1016/s0006-3495(01)75949-8openalex-snapshot

Stochasticity in Transcriptional Regulation: Origins, Consequences, and Mathematical Representations

inferredcites →https://doi.org/10.1016/s1097-2765(00)80143-4openalex-snapshot

Localization of ASH1 mRNA Particles in Living Yeast

inferredcites →https://doi.org/10.1017/cbo9781316576533openalex-snapshot

Computer Age Statistical Inference

inferredcites →https://doi.org/10.1038/328440a0openalex-snapshot

Borders of parasegments in Drosophila embryos are delimited by the fushi tarazu and even-skipped genes

inferredcites →https://doi.org/10.1038/msb.2009.97openalex-snapshot

Deciphering a transcriptional regulatory code: modeling short‐range repression in the Drosophila embryo

inferredcites →https://doi.org/10.1038/msb.2012.48openalex-snapshot

A model of spatially restricted transcription in opposing gradients of activators and repressors

inferredcites →https://doi.org/10.1038/msb.2012.72openalex-snapshot

Accurate measurements of dynamics and reproducibility in small genetic networks

inferredcites →https://doi.org/10.1038/nature02678openalex-snapshot

Dynamic control of positional information in the early Drosophila embryo

inferredcites →https://doi.org/10.1038/nature06496openalex-snapshot

Predicting expression patterns from regulatory sequence in Drosophila segmentation

inferredcites →https://doi.org/10.1038/ng.3509openalex-snapshot

Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors

inferredcites →https://doi.org/10.1038/ng.821openalex-snapshot

General properties of transcriptional time series in Escherichia coli

inferredcites →https://doi.org/10.1038/nmeth.1551openalex-snapshot

A transgenic mouse for in vivo detection of endogenous labeled mRNA

inferredcites →https://doi.org/10.1038/nmeth.2019openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nmeth.2089openalex-snapshot

NIH Image to ImageJ: 25 years of image analysis

inferredcites →https://doi.org/10.1038/nmeth.2305openalex-snapshot

Single-molecule analysis of gene expression using two-color RNA labeling in live yeast

inferredcites →https://doi.org/10.1038/nmeth.2794openalex-snapshot

Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings

inferredcites →https://doi.org/10.1038/nmeth.3446openalex-snapshot

Combining protein and mRNA quantification to decipher transcriptional regulation

inferredcites →https://doi.org/10.1038/nsmb.1514openalex-snapshot

Single-RNA counting reveals alternative modes of gene expression in yeast

inferredcites →https://doi.org/10.1039/c5ib00321kopenalex-snapshot

The appeasement of Doug: a synthetic approach to enhancer biology

inferredcites →https://doi.org/10.1039/c6ib00006aopenalex-snapshot

Using synthetic biology to make cells tomorrow's test tubes

inferredcites →https://doi.org/10.1073/pnas.0707904105openalex-snapshot

Transcriptional control of noise in gene expression

inferredcites →https://doi.org/10.1073/pnas.1312310110openalex-snapshot

Stimulus-induced modulation of transcriptional bursting in a single mammalian gene

inferredcites →https://doi.org/10.1073/pnas.1410022111openalex-snapshot

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos

inferredcites →https://doi.org/10.1073/pnas.2627987100openalex-snapshot

Stochastic gene expression as a many-body problem

inferredcites →https://doi.org/10.1091/mbc.e17-06-0408openalex-snapshot

Differential context-specific impact of individual core promoter elements on transcriptional dynamics

inferredcites →https://doi.org/10.1093/bioinformatics/btx180openalex-snapshot

Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification

inferredcites →https://doi.org/10.1093/biostatistics/kxv010openalex-snapshot

A stochastic transcriptional switch model for single cell imaging data

inferredcites →https://doi.org/10.1093/nar/21.1.113openalex-snapshot

Contacts between mammalian RNA polymerase II and the template DNA in a ternary elongation complex

inferredcites →https://doi.org/10.1101/gad.1.10.1226openalex-snapshot

Cytoarchitecture and the patterning of fushi tarazu expression in the Drosophila blastoderm.

inferredcites →https://doi.org/10.1101/gad.1.9.981openalex-snapshot

Complementary patterns of even-skipped and fushi tarazu expression involve their differential regulation by a common set of segmentation genes in Drosophila.

inferredcites →https://doi.org/10.1101/gad.5.2.265openalex-snapshot

Autoregulation of a segmentation gene in Drosophila: combinatorial interaction of the even-skipped homeo box protein with a distal enhancer element.

inferredcites →https://doi.org/10.1101/gad.5.5.827openalex-snapshot

Transcriptional regulation of a pair-rule stripe in Drosophila.

inferredcites →https://doi.org/10.1101/gad.8.15.1829openalex-snapshot

Short-range repression permits multiple enhancers to function autonomously within a complex promoter.

inferredcites →https://doi.org/10.1103/physreve.97.022402openalex-snapshot

Nascent RNA kinetics: Transient and steady state behavior of models of transcription

inferredcites →https://doi.org/10.1103/physrevlett.117.128101openalex-snapshot

Stochastic Kinetics of Nascent RNA

inferredcites →https://doi.org/10.1109/tit.1967.1054010openalex-snapshot

Error bounds for convolutional codes and an asymptotically optimum decoding algorithm

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.1255301openalex-snapshot

Promoter architecture dictates cell-to-cell variability in gene expression

inferredcites →https://doi.org/10.1126/science.aaa3380openalex-snapshot

An RNA biosensor for imaging the first round of translation from single cells to living animals

inferredcites →https://doi.org/10.1126/science.aaf0899openalex-snapshot

Real-time quantification of single RNA translation dynamics in living cells

inferredcites →https://doi.org/10.1126/science.aaf1084openalex-snapshot

Translation dynamics of single mRNAs in live cells and neurons

inferredcites →https://doi.org/10.1126/scisignal.2002077openalex-snapshot

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

inferredcites →https://doi.org/10.1186/gb-2006-7-12-r123openalex-snapshot

Three-dimensional morphology and gene expression in the Drosophilablastoderm at cellular resolution I: data acquisition pipeline

inferredcites →https://doi.org/10.1201/9781134111589openalex-snapshot

Physical Biology of the Cell

inferredcites →https://doi.org/10.1371/journal.pbio.1000596openalex-snapshot

The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized mRNA

inferredcites →https://doi.org/10.1371/journal.pcbi.1001100openalex-snapshot

Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression

inferredcites →https://doi.org/10.1371/journal.pcbi.1004345openalex-snapshot

Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules

inferredcites →https://doi.org/10.1371/journal.pcbi.1005256openalex-snapshot

Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos

inferredcites →https://doi.org/10.1371/journal.pcbi.1005285openalex-snapshot

Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression

inferredcites →https://doi.org/10.1371/journal.pgen.1006169openalex-snapshot

Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei

inferredcites →https://doi.org/10.1371/journal.pone.0151740openalex-snapshot

SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences

inferredcites →https://doi.org/10.1371/journal.pone.0176228openalex-snapshot

Transcriptional bursting in Drosophila development: Stochastic dynamics of eve stripe 2 expression

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

Structure of silent transcription intervals and noise characteristics of mammalian genes

inferredcites →https://doi.org/10.7554/elife.00522openalex-snapshot

Cellular resolution models for even skipped regulation in the entire Drosophila embryo

inferredcites →https://doi.org/10.7554/elife.03939openalex-snapshot

Kinetic competition during the transcription cycle results in stochastic RNA processing

inferredcites →https://doi.org/10.7554/elife.07956openalex-snapshot

Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo

inferredcites →https://doi.org/10.7554/elife.08445openalex-snapshot

Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo

inferredcites →https://doi.org/10.7554/elife.08494openalex-snapshot

Spatially coordinated dynamic gene transcription in living pituitary tissue

inferredcites →https://doi.org/10.7554/elife.12175openalex-snapshot

Single-cell analysis of transcription kinetics across the cell cycle

inferredcites →https://doi.org/10.7554/elife.13051openalex-snapshot

A continuum model of transcriptional bursting

inferredcites →https://doi.org/10.7554/elife.41266openalex-snapshot

Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity

inferredcites →https://doi.org/10.7554/elife.61635openalex-snapshot

Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

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.celrep.2019.01.115openalex-snapshot

Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo

inferred← citeshttps://doi.org/10.1016/j.devcel.2019.07.002openalex-snapshot

Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling

inferred← citeshttps://doi.org/10.1088/1478-3975/ab45bfopenalex-snapshot

Decoding the grammar of transcriptional regulation from RNA polymerase measurements: models and their applications

inferred← citeshttps://doi.org/10.3389/fgene.2024.1451461openalex-snapshot

Transcriptional bursting dynamics in gene expression

inferred← citeshttps://doi.org/10.7554/elife.59351openalex-snapshot

Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic

inferred← citeshttps://doi.org/10.7554/elife.74509openalex-snapshot

Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription

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