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A gene regulatory network controlling the embryonic specification of endoderm
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/dvdy.21978openalex-snapshot
Blocking Dishevelled signaling in the noncanonical Wnt pathway in sea urchins disrupts endoderm formation and spiculogenesis, but not secondary mesoderm formation
inferredcites →https://doi.org/10.1002/gene.20045openalex-snapshot
Nuclear β‐catenin‐dependent Wnt8 signaling in vegetal cells of the early sea urchin embryo regulates gastrulation and differentiation of endoderm and mesodermal cell lineages
inferredcites →https://doi.org/10.1006/dbio.1997.8814openalex-snapshot
Late Specification of Veg1Lineages to Endodermal Fate in the Sea Urchin Embryo
inferredcites →https://doi.org/10.1006/dbio.2000.9941openalex-snapshot
Recovery of Developmentally Defined Gene Sets from High-Density cDNA Macroarrays
inferredcites →https://doi.org/10.1016/j.bbagrm.2008.07.014openalex-snapshot
Visualization, documentation, analysis, and communication of large-scale gene regulatory networks
inferredcites →https://doi.org/10.1016/j.febslet.2009.11.060openalex-snapshot
Modularity and design principles in the sea urchin embryo gene regulatory network
inferredcites →https://doi.org/10.1016/j.modgep.2006.04.009openalex-snapshot
Regulation of spblimp1/krox1a, an alternatively transcribed isoform expressed in midgut and hindgut of the sea urchin gastrula
inferredcites →https://doi.org/10.1016/j.ydbio.2005.09.047openalex-snapshot
cis-Regulatory inputs of the wnt8 gene in the sea urchin endomesoderm network
inferredcites →https://doi.org/10.1016/j.ydbio.2006.05.037openalex-snapshot
cis-regulatory processing of Notch signaling input to the sea urchin glial cells missing gene during mesoderm specification
inferredcites →https://doi.org/10.1016/j.ydbio.2006.08.012openalex-snapshot
Identification and developmental expression of the ets gene family in the sea urchin (Strongylocentrotus purpuratus)
inferredcites →https://doi.org/10.1016/j.ydbio.2006.08.032openalex-snapshot
The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development
inferredcites →https://doi.org/10.1016/j.ydbio.2006.08.033openalex-snapshot
Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus
inferredcites →https://doi.org/10.1016/j.ydbio.2006.08.039openalex-snapshot
Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development
inferredcites →https://doi.org/10.1016/j.ydbio.2006.09.031openalex-snapshot
Sea urchin Forkhead gene family: Phylogeny and embryonic expression
inferredcites →https://doi.org/10.1016/j.ydbio.2007.10.042openalex-snapshot
A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo
inferredcites →https://doi.org/10.1016/j.ydbio.2009.10.037openalex-snapshot
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage
inferredcites →https://doi.org/10.1016/s0091-679x(04)74024-8openalex-snapshot
Detection of mRNA by In Situ Hybridization and RT-PCR
inferredcites →https://doi.org/10.1038/nature09645openalex-snapshot
Emerging properties of animal gene regulatory networks
inferredcites →https://doi.org/10.1038/nprot.2008.187openalex-snapshot
A protocol for unraveling gene regulatory networks
inferredcites →https://doi.org/10.1073/pnas.0705324104openalex-snapshot
A missing link in the sea urchin embryo gene regulatory network: hesC and the double-negative specification of micromeres
inferredcites →https://doi.org/10.1073/pnas.0711220105openalex-snapshot
Global regulatory logic for specification of an embryonic cell lineage
inferredcites →https://doi.org/10.1073/pnas.1004824107openalex-snapshot
Information processing at the foxa node of the sea urchin endomesoderm specification network
inferredcites →https://doi.org/10.1126/science.1146524openalex-snapshot
A Gene Regulatory Network Subcircuit Drives a Dynamic Pattern of Gene Expression
inferredcites →https://doi.org/10.1242/dev.044149openalex-snapshot
Dynamics of Delta/Notch signaling on endomesoderm segregation in the sea urchin embryo
inferredcites →https://doi.org/10.1242/dev.113.4.1085openalex-snapshot
Macromere cell fates during sea urchin development
inferredcites →https://doi.org/10.1242/dev.124.11.2213openalex-snapshot
The allocation of early blastomeres to the ectoderm and endoderm is variable in the sea urchin embryo
inferredcites →https://doi.org/10.1242/dev.126.2.345openalex-snapshot
Nuclear β-catenin is required to specify vegetal cell fates in the sea urchin embryo
inferredcites →https://doi.org/10.1242/dev.126.23.5255openalex-snapshot
The role of micromere signaling in Notch activation and mesoderm specification during sea urchin embryogenesis
inferredcites →https://doi.org/10.1242/dev.126.8.1703openalex-snapshot
LvNotch signaling mediates secondary mesenchyme specification in the sea urchin embryo
inferredcites →https://doi.org/10.1242/dev.129.8.1945openalex-snapshot
LvDelta is a mesoderm-inducing signal in the sea urchin embryo and can endow blastomeres with organizer-like properties
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids
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Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo
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Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos
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microRNAs regulate β-catenin of the Wnt signaling pathway in early sea urchin development
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Eric Davidson: Steps to a gene regulatory network for development
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microRNA-31 regulates skeletogenesis by direct suppression of Eve and Wnt1
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microRNA-124 directly suppresses Nodal and Notch to regulate mesodermal development
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Unique metabolic regulation of micromeres contributes to gastrulation in the sea urchin embryo
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Segregation of endoderm and mesoderm germ layer identities in the diploblast Nematostella vectensis
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Dpp-induced Egfr signaling triggers postembryonic wing development in Drosophila
inferred← citeshttps://doi.org/10.1073/pnas.1323105111openalex-snapshot
Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo
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Specific functions of the Wnt signaling system in gene regulatory networks throughout the early sea urchin embryo
inferred← citeshttps://doi.org/10.1073/pnas.1509845112openalex-snapshot
Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses
inferred← citeshttps://doi.org/10.1073/pnas.1610605114openalex-snapshot
Gene regulatory networks and cell lineages that underlie the formation of skeletal muscle
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Assessing regulatory information in developmental gene regulatory networks
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Divergence of ectodermal and mesodermal gene regulatory network linkages in early development of sea urchins
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Dynamics of Drosophila endoderm specification
inferred← citeshttps://doi.org/10.1086/bblv224n3p192openalex-snapshot
A Shift in Germ Layer Allocation Is Correlated With Large Egg Size and Facultative Planktotrophy in the Echinoid Clypeaster rosaceus
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Regulatory states in the developmental control of gene expression
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SPREd: a simulation-supervised neural network tool for gene regulatory network reconstruction
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Chromosomal-Level Genome Assembly of the Antarctic Sea Urchin Sterechinus neumayeri: A Model for Antarctic Invertebrate Biology
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Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma
inferred← citeshttps://doi.org/10.1093/genetics/iyad145openalex-snapshot
Widespread priming of transcriptional regulatory elements by incipient accessibility or RNA polymerase II pause in early embryos of the sea urchin Strongylocentrotus purpuratus
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Evo-Devo in the Era of Gene Regulatory Networks
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Inference of Developmental Gene Regulatory Networks Beyond Classical Model Systems: New Approaches in the Post-genomic Era
inferred← citeshttps://doi.org/10.1093/molbev/msad222openalex-snapshot
Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species
inferred← citeshttps://doi.org/10.1093/oso/9780195125689.003.0001openalex-snapshot
Reconstructing History
inferred← citeshttps://doi.org/10.1097/moh.0000000000000628openalex-snapshot
How haematopoiesis research became a fertile ground for regulatory network biology as pioneered by Eric Davidson
inferred← citeshttps://doi.org/10.1098/rsob.150053openalex-snapshot
Tunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley
inferred← citeshttps://doi.org/10.1098/rsta.2016.0338openalex-snapshot
Coarse-graining as a downward causation mechanism
inferred← citeshttps://doi.org/10.1098/rstb.2011.0214openalex-snapshot
Multiple time-scales and the developmental dynamics of social systems
inferred← citeshttps://doi.org/10.1101/2022.06.27.497786openalex-snapshot
Prioritizing transcription factor perturbations from single-cell transcriptomics
inferred← citeshttps://doi.org/10.1101/2023.01.09.523299openalex-snapshot
Evolutionary history of the Brachyury gene in Hydrozoa: duplications, divergence and neofunctionalization
inferred← citeshttps://doi.org/10.1101/2024.10.29.620801openalex-snapshot
Notch, β-catenin and MAPK signaling segregate endoderm and mesoderm in the diploblast Nematostella vectensis
inferred← citeshttps://doi.org/10.1101/gr.139170.112openalex-snapshot
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis
inferred← citeshttps://doi.org/10.1101/gr.167668.113openalex-snapshot
General approach for in vivo recovery of cell type-specific effector gene sets
inferred← citeshttps://doi.org/10.1109/tcyb.2023.3237635openalex-snapshot
Gradient-Based Local Causal Structure Learning
inferred← citeshttps://doi.org/10.1111/dgd.12329openalex-snapshot
Transcriptional and post‐transcriptional regulation of histone variant H2A.Z during sea urchin development
inferred← citeshttps://doi.org/10.1111/ede.12273openalex-snapshot
Canonical Wnt/β‐catenin and Notch signaling regulate animal/vegetal axial patterning in the cephalochordate amphioxus
inferred← citeshttps://doi.org/10.1111/j.1525-142x.2012.00532.xopenalex-snapshot
Population genetics of cis‐regulatory sequences that operate during embryonic development in the sea urchin S trongylocentrotus purpuratus
inferred← citeshttps://doi.org/10.1126/sciadv.abo2416openalex-snapshot
Homologous gene regulatory networks control development of apical organs and brains in Bilateria
inferred← citeshttps://doi.org/10.1126/science.1212867openalex-snapshot
Sequential Signaling Crosstalk Regulates Endomesoderm Segregation in Sea Urchin Embryos
inferred← citeshttps://doi.org/10.1146/annurev-cellbio-111315-125218openalex-snapshot
Transcriptional Control of Developmental Cell Behaviors
inferred← citeshttps://doi.org/10.1146/annurev-genom-091212-153423openalex-snapshot
Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development
inferred← citeshttps://doi.org/10.1155/2012/270425openalex-snapshot
Hematopoietic Stem Cell Development, Niches, and Signaling Pathways
inferred← citeshttps://doi.org/10.1186/1471-2105-16-s16-s1openalex-snapshot
Sieve-based relation extraction of gene regulatory networks from biological literature
inferred← citeshttps://doi.org/10.1186/1752-0509-8-64openalex-snapshot
Latent phenotypes pervade gene regulatory circuits
inferred← citeshttps://doi.org/10.1186/2041-9139-3-19openalex-snapshot
Sequencing and analysis of the gastrula transcriptome of the brittle star Ophiocoma wendtii
inferred← citeshttps://doi.org/10.1186/2041-9139-5-39openalex-snapshot
Molecular conservation of metazoan gut formation: evidence from expression of endomesoderm genes in Capitella teleta (Annelida)
inferred← citeshttps://doi.org/10.1186/gb-2014-15-5-r74openalex-snapshot
SoxNeuro orchestrates central nervous system specification and differentiation in Drosophila and is only partially redundant with Dichaete
inferred← citeshttps://doi.org/10.1186/s12859-015-0460-0openalex-snapshot
Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data
inferred← citeshttps://doi.org/10.1186/s12861-017-0145-1openalex-snapshot
Nodal and BMP expression during the transition to pentamery in the sea urchin Heliocidaris erythrogramma: insights into patterning the enigmatic echinoderm body plan
inferred← citeshttps://doi.org/10.1186/s12864-021-07936-0openalex-snapshot
Identification and prediction of developmental enhancers in sea urchin embryos
inferred← citeshttps://doi.org/10.1186/s13227-023-00214-yopenalex-snapshot
Feedback circuits are numerous in embryonic gene regulatory networks and offer a stabilizing influence on evolution of those networks
inferred← citeshttps://doi.org/10.1201/9781003217503-17openalex-snapshot
Echinoderms : Focus on the Sea Urchin Model in Cellular and Developmental Biology
inferred← citeshttps://doi.org/10.1242/bio.059216openalex-snapshot
The temporal dynamics of the sea urchin regulome
inferred← citeshttps://doi.org/10.1242/dev.075051openalex-snapshot
Axial patterning interactions in the sea urchin embryo: suppression of nodal by Wnt1 signaling
inferred← citeshttps://doi.org/10.1242/dev.113043openalex-snapshot
Dose-dependent nuclear β-catenin response segregates endomesoderm along the sea star primary axis
inferred← citeshttps://doi.org/10.1242/dev.117986openalex-snapshot
Geometric control of ciliated band regulatory states in the sea urchin embryo
inferred← citeshttps://doi.org/10.1242/dev.119396openalex-snapshot
Temporal ordering and registration of images in studies of developmental dynamics
inferred← citeshttps://doi.org/10.1242/dev.127746openalex-snapshot
Genome-wide assessment of differential effector gene use in embryogenesis
inferred← citeshttps://doi.org/10.1242/dev.140822openalex-snapshot
Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network
inferred← citeshttps://doi.org/10.1242/dev.167130openalex-snapshot
Inhibition of microRNA suppression of Dishevelled results in Wnt pathway-associated developmental defects in sea urchin
inferred← citeshttps://doi.org/10.1242/dev.167288openalex-snapshot
Conserved regulatory state expression controlled by divergent developmental gene regulatory networks in echinoids
inferred← citeshttps://doi.org/10.1242/dev.168799openalex-snapshot
A biphasic role of non-canonical Wnt16 signaling during early anterior-posterior patterning and morphogenesis of the sea urchin embryo
inferred← citeshttps://doi.org/10.1242/dev.191197openalex-snapshot
An early global role for Axin is required for correct patterning of the anterior-posterior axis in the sea urchin embryo
inferred← citeshttps://doi.org/10.1242/dev.195859openalex-snapshot
The tolerance to hypoxia is defined by a time-sensitive response of the gene regulatory network in sea urchin embryos
inferred← citeshttps://doi.org/10.1242/dev.198614openalex-snapshot
Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo
inferred← citeshttps://doi.org/10.1242/dev.203015openalex-snapshot
Contrasting the development of larval and adult body plans during the evolution of biphasic lifecycles in sea urchins
inferred← citeshttps://doi.org/10.1242/dev.203152openalex-snapshot
Reprogramming of cells during embryonic transfating: overcoming a reprogramming block
inferred← citeshttps://doi.org/10.1242/dev.205272openalex-snapshot
Wnt dynamics at the blastopore and stomodeum during sea urchin gastrulation
inferred← citeshttps://doi.org/10.12688/f1000research.7381.1openalex-snapshot
Developmental gene regulatory networks in sea urchins and what we can learn from them
inferred← citeshttps://doi.org/10.1353/pbm.2014.0009openalex-snapshot
Brief Notes on the Meaning of a Genomic Control System for Animal Embryogenesis
inferred← citeshttps://doi.org/10.1353/pbm.2015.0025openalex-snapshot
Genomics, “Discovery Science,” Systems Biology, and Causal Explanation: What Really Works?
inferred← citeshttps://doi.org/10.1371/journal.pbio.1001696openalex-snapshot
The Impact of Gene Expression Variation on the Robustness and Evolvability of a Developmental Gene Regulatory Network
inferred← citeshttps://doi.org/10.1371/journal.pbio.1002391openalex-snapshot
Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005073openalex-snapshot
Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes
inferred← citeshttps://doi.org/10.1371/journal.pgen.1002649openalex-snapshot
Transcriptional Regulation of Rod Photoreceptor Homeostasis Revealed by In Vivo NRL Targetome Analysis
inferred← citeshttps://doi.org/10.1371/journal.pgen.1003164openalex-snapshot
A Framework for the Establishment of a Cnidarian Gene Regulatory Network for “Endomesoderm” Specification: The Inputs of ß-Catenin/TCF Signaling
inferred← citeshttps://doi.org/10.1371/journal.pgen.1005435openalex-snapshot
Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics
inferred← citeshttps://doi.org/10.1371/journal.pone.0035934openalex-snapshot
Barcoded DNA-Tag Reporters for Multiplex Cis-Regulatory Analysis
inferred← citeshttps://doi.org/10.1371/journal.pone.0080693openalex-snapshot
Differential Regulation of Disheveled in a Novel Vegetal Cortical Domain in Sea Urchin Eggs and Embryos: Implications for the Localized Activation of Canonical Wnt Signaling
inferred← citeshttps://doi.org/10.1371/journal.pone.0103341openalex-snapshot
A Computational Approach towards a Gene Regulatory Network for the Developing Nematostella vectensis Gut
inferred← citeshttps://doi.org/10.1371/journal.pone.0133860openalex-snapshot
Tissue Regeneration and Biomineralization in Sea Urchins: Role of Notch Signaling and Presence of Stem Cell Markers
inferred← citeshttps://doi.org/10.1387/ijdb.140095mbopenalex-snapshot
Sipuncula: an emerging model of spiralian development and evolution
inferred← citeshttps://doi.org/10.1387/ijdb.160331sbopenalex-snapshot
Regulatory heterochronies and loose temporal scaling between sea star and sea urchin regulatory circuits
inferred← citeshttps://doi.org/10.2142/biophysico.13.0_295openalex-snapshot
Itinerary profiling to analyze a large number of protein-folding trajectories
inferred← citeshttps://doi.org/10.2217/fnl-2019-0014openalex-snapshot
Chronic Stress, Physiological Adaptation and Developmental Programming of the Neuroendocrine Stress System
inferred← citeshttps://doi.org/10.3389/fcell.2022.876825openalex-snapshot
Limb Mesoderm and Head Ectomesenchyme Both Express a Core Transcriptional Program During Chondrocyte Differentiation
inferred← citeshttps://doi.org/10.3389/fgene.2016.00016openalex-snapshot
Robustness and Accuracy in Sea Urchin Developmental Gene Regulatory Networks
inferred← citeshttps://doi.org/10.3389/fimmu.2022.903475openalex-snapshot
SFRP1 Negatively Modulates Pyroptosis of Fibroblast‐Like Synoviocytes in Rheumatoid Arthritis: A Review
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