Evolution of Gene Regulatory Networks Controlling Body Plan Development

Peter, Isabelle S., Davidson, Eric H.·2011·Cell
DOI 10.1016/j.cell.2011.02.017

Cited by (439)

Items 201–300 of 439

  1. An Essential Regulatory System Originating from Polygenic Transcriptional Rewiring of PhoP-PhoQ of Xanthomonas campestris
    Peng Bao-Yu, Yue Pan, Rujiao Li, Jin‐Wei Wei, Fang Liang, Li Wang, Fangfang Wang, Wei Qian · 2017 · Genetics
  2. Associative conditioning in gene regulatory network models increases integrative causal emergence
    Federico Pigozzi, Adam Goldstein, Michael G. Levin · 2025 · Communications Biology
  3. Feedforward regulatory logic controls the specification-to-differentiation transition and terminal cell fate during Caenorhabditis elegans endoderm development
    Chee Kiang Ewe, Erica M. Sommermann, Josh Kenchel, Sagen E. Flowers, Morris Maduro, Pradeep M. Joshi, Joel H. Rothman · 2022 · Development
  4. Integrative cross-species analysis of GABAergic neuron cell types and their functions in Alzheimer’s disease
    Shiyou Wang, Peiwen Ding, Jingnan Yuan, Haoyu Wang, Xiuqing Zhang, Dongsheng Chen, Dongli Ma, Xingliang Zhang, Fei Wang · 2022 · Scientific Reports
  5. Phenotypic Robustness and the Assortativity Signature of Human Transcription Factor Networks
    Dov A. Pechenick, Joshua L. Payne, Jason H. Moore · 2014 · PLoS Computational Biology
  6. Inference of Developmental Gene Regulatory Networks Beyond Classical Model Systems: New Approaches in the Post-genomic Era
    Selene L. Fernández-Valverde, Felipe Aguilera, René Alexander Ramos-Díaz · 2018 · Integrative and Comparative Biology
  7. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation
    Georgi K. Marinov, Anshul Bharat Kundaje · 2018 · Briefings in Functional Genomics
  8. Evolution of gene regulatory network of C4 photosynthesis in the genus Flaveria reveals the evolutionary status of C3-C4 intermediate species
    Ming‐Ju Amy Lyu, Qiming Tang, Yanjie Wang, Jemâa Essemine, Fa‐Ming Chen, Xiaoxiang Ni, Genyun Chen, Xin‐Guang Zhu · 2022 · Plant Communications
  9. Diversification of spatiotemporal expression and copy number variation of the echinoid hbox12/pmar1/micro1 multigene family
    Vincenzo Cavalieri, Fabiana Geraci, Giovanni Spinelli · 2017 · PLoS ONE
  10. Continuity and change in neural plasticity through embryonic morphogenesis, fetal activity‐dependent synaptogenesis, and infant memory consolidation
    Phan Luu, Don M. Tucker · 2023 · Developmental Psychobiology
  11. Transcription Profiling of CulturedAcropora digitiferaAdult Cells Reveals the Existence of Ancestral Genome Regulatory Modules Underlying Pluripotency and Cell Differentiation in Cnidaria
    Alejandro Reyes-Bermúdez, Michio Hidaka, Alexander S. Mikheyev · 2021 · Genome Biology and Evolution
  12. Nxf1 Natural Variant E610G Is a Semi-dominant Suppressor of IAP-Induced RNA Processing Defects
    Dorothy Concepcion, Kevin D. Ross, Kasey R. Hutt, Gene Wei-Ming Yeo, Bruce A. Hamilton · 2015 · PLoS Genetics
  13. CpG island turnover events predict evolutionary changes in enhancer activity
    Acadia A. Kocher, Emily V. Dutrow, Severin Uebbing, Kristina Yim, María F. Rosales Larios, Marybeth Baumgartner, Timothy Nottoli, James P. Noonan · 2024 · Genome biology
  14. Transcriptomic analysis of Nodal- and BMP-associated genes during juvenile development of the sea urchin Heliocidaris erythrogramma
    2015
  15. Mature maternal mRNAs are longer than zygotic ones and have complex degradation kinetics in sea urchin
    Tsvia Gildor, Assaf Malik, Noa Sher, Smadar Ben‐Tabou de‐Leon · 2016 · Developmental Biology
  16. High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0
    Claudia Skok Gibbs, Christopher A. Jackson, Giuseppe-Antonio Saldi, Andreas Tjärnberg, Aashna Shah, Aaron Watters, Nicholas De Veaux, Konstantine Tchourine, Ren Yi, Tymor Hamamsy et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  17. Reorganization of H3K9me heterochromatin leads to neuronal impairment via the cascading destruction of the KDM3B-centered epigenomic network
    Mi-Jin An, Jiyoung Kim, Jinho Kim, Dae-Hyun Kim, Geun-Seup Shin, Hyun-Min Lee, Ah-Ra Jo, Yuna Park, Yujeong Hwangbo, Chul-Hong Kim et al. · 2024 · iScience
  18. Suboptimal Intermediates Underlie Evolution of the Bicoid Homeodomain
    Pınar Önal, Himari Imaya Gunasinghe, Kristaley Yui Umezawa, Michael Zheng, Ling Jia, Leen Azeez, Anecine Dalmeus, Tasmima Tazin, Stephen Small · 2021 · Molecular Biology and Evolution
  19. Deuterostome Ancestors and Chordate Origins
    Billie J. Swalla · 2024 · Integrative and Comparative Biology
  20. Interspecies Gene Transfer as a Method for Understanding the Genetic Basis for Evolutionary Change: Progress, Pitfalls, and Prospects
    Lachezar A. Nikolov, Miltos Tsiantis · 2015 · Frontiers in Plant Science
  21. Variable levels of drift in tunicate cardiopharyngeal gene regulatory elements
    William N. Colgan, Alexis Leanza, Ariel Hwang, Melissa B. DeBiasse, Isabel Llosa, Daniel Rodrigues, Hriju Adhikari, Guillermo Barreto Corona, Saskia Bock, Amanda Carillo-Perez et al. · 2019 · EvoDevo
  22. System Principles Governing the Organization, Architecture, Dynamics, and Evolution of Gene Regulatory Networks
    Julio Augusto Freyre-González, Juan M. Escorcia-Rodríguez, Luis F. Gutiérrez-Mondragón, Jerónimo Martí-Vértiz, Camila N. Torres-Franco, Andrea Zorro-Aranda · 2022 · Frontiers in Bioengineering and Biotechnology
  23. What’s next for computational systems biology?
    Eberhard O. Voit, Ashti M. Shah, Daniel V. Olivença, Yoram Vodovotz B · 2023 · Frontiers in Systems Biology
  24. Gene regulatory networks: from correlative models to causal explanations
    Rory J. Maizels, James Briscoe · 2026 · Nature Reviews Genetics
  25. Multi-layered transcriptional control of cranial neural crest development
    Ivan Candido-Ferreira, Martyna Lukoseviciute, Tatjana Sauka‐Spengler · 2022 · Seminars in Cell and Developmental Biology
  26. Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins
    Kiran Rafiq, Tanvi Shashikant, C. Joel McManus, Charles A. Ettensohn · 2014 · Development
  27. Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks
    Federico Gaiti, William L. Hatleberg, Miloš Tanurdžić, Bernard M. Degnan · 2018 · Non-Coding RNA
  28. Cis-regulation and conserved non-coding elements in amphioxus
    Laura Beaster‐Jones · 2012 · Briefings in Functional Genomics
  29. Evolutionary Transformations of the Metazoan Body Plan: Genomic-Morphogenetic Correlations
    Valeria V. Isaeva, С. В. Рожнов · 2021 · Paleontological Journal
  30. Substituting mouse transcription factor Pou4f2 with a sea urchin orthologue restores retinal ganglion cell development
    Chai‐An Mao, Cavit Ağca, Julie A. Mocko, Jing Wang, Esther Ullrich-Lüter, Ping Pan, Steven W. Wang, Maria Ina Arnone, Laura J. Frishman, William H. Klein · 2016 · Proceedings of the Royal Society B Biological Sciences
  31. Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids
    Tarang K. Mehta, Luca Penso-Dolfin, Will J. Nash, Sushmita Roy, Federica Di Palma, Wilfried Haerty · 2022 · Molecular Biology and Evolution
  32. Transcriptional Network Logic
    Isabelle S. Peter, Eric H. Davidson · 2012 · Elsevier eBooks
  33. DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks
    Daifeng Wang, Fei He, Sergei Maslov · 2016 · PLoS Computational Biology
  34. Identification and Characterization of Small RNA Markers of Age in the Blow Fly Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae)
    Carl E. Hjelmen, Ye Yuan, Jonathan J. Parrott · 2022 · Insects
  35. Looking Beyond the Genes
    Séverine Urdy, Nicolas Goudemand, Sophie Pantalacci · 2016 · Current topics in developmental biology/Current Topics in Developmental Biology
  36. Adaptive protein divergence of BMP ligands takes place under developmental and evolutionary constraints
    2016
  37. Functional and Adaptive Significance of Promoter Mutations That Affect Divergent Myocardial Expressions of TRIM72 in Primates
    Yuanqing Feng, Hongzhan Xu, Jinghao Liu, Ning Xie, Lei Gao, Yanyun He, Yuan Yao, Fengxiang Lv, Yan Zhang, Jian Lü et al. · 2021 · Molecular Biology and Evolution
  38. Characterization of the Pristionchus pacificus “epigenetic toolkit” reveals the evolutionary loss of the histone methyltransferase complex PRC2
    Audrey Brown, Adriaan B. Meiborg, Mirita Franz‐Wachtel, Boris Maček, Spencer Gordon, Ofer Rog, Cameron J. Weadick, Michael S. Werner · 2024 · Genetics
  39. Comparative Analysis of Gene Regulatory Network Components in the Auditory Hindbrain of Mice and Chicken
    Benjamin Pawlik, Tina Schlüter, Heiner Hartwich, Saskia Breuel, Lennart Heepmann, Hans Gerd Nothwang · 2016 · Brain Behavior and Evolution
  40. Whence Blobs? Phylogenetics of functional protein condensates
    2020
  41. Sea Urchin Embryo: Specification of Cell Fates
    2012
  42. Expression pattern of cochlear microRNAs in the mammalian auditory hindbrain
    Constanze Krohs, Mor Bordeynik‐Cohen, Naama Messika-Gold, Ran Elkon, Karen B. Avraham, Hans Gerd Nothwang · 2020 · Cell and Tissue Research
  43. Self-Organization at Different Levels of Metazoan Complexity in Comparative Genomic–Phenomic Context
    Valeria V. Isaeva · 2022 · Evolutionary Biology/Evolutionary biology
  44. Evolutionary Development of Marine Larvae
    2017 · Oxford University Press eBooks
  45. Dysregulated YY1/PRMT5 axis promotes the progression and metastasis of laryngeal cancer by targeting Hippo pathway
    Nan Wang, Di Wu, Long Qian, Yue Yan, Xiaoqi Chen, Zheng Zhao, Honghong Yan, Xinrui Zhang, Meilan Xu, Wuguo Deng et al. · 2020 · Journal of Cellular and Molecular Medicine
  46. Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin Strongylocentrotus purpuratus
    Nick Panyushev, Larisa S. Okorokova, Lavrentii G. Danilov, Адонин Леонид Сергеевич · 2021 · Biomedicines
  47. Cuvierian Functionalism
    Aaron Novick · 2019 · Philosophy Theory and Practice in Biology
  48. Direct Molecular Evidence for an Ancient, Conserved Developmental Toolkit Controlling Posttranscriptional Gene Regulation in Land Plants
    Haiyan Jia, Kelsey Aadland, Oralia M. Kolaczkowski, Bryan D. Kolaczkowski · 2021 · Molecular Biology and Evolution
  49. Comparative Studies of Gene Expression Kinetics: Methodologies and Insights on Development and Evolution
    Tsvia Gildor, Ben-Tabou de-Leon Smadar · 2018 · Frontiers in Genetics
  50. Hierarchical decomposition of dynamically evolving regulatory networks
    Ahmet Ali Ay, Dihong Gong, Tamer Kahveci · 2015 · BMC Bioinformatics
  51. RegEnrich: An R package for gene regulator enrichment analysis reveals key role of ETS transcription factor family in interferon signaling
    Weiyang Tao, Timothy R. D. J. Radstake, Aridaman Pandit · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  52. Evolution of CpG island promoter function underlies changes in KChIP2 potassium channel subunit gene expression in mammalian heart
    2012
  53. Molecular and Cell Biological Considerations in the Initiation and Development of Sporadic Non-Hereditary Solid Cancers
    Vladimir F. Niculescu · 2018 · Journal of Cancer Genetics and Biomarkers
  54. Dynamical Modularity of the Genotype-Phenotype Map
    Johannes Jaeger, Nick Monk · 2021 · Springer eBooks
  55. The Developmental Hourglass in the Evolution of Embryogenesis
    2019
  56. The Genome in Development
    Eric H. Davidson, Isabelle S. Peter · 2015 · Elsevier eBooks
  57. Genetic, morphometric, and molecular analyses of interspecies differences in head shape and hybrid developmental defects in the wasp genus Nasonia
    Lorna Cohen, Rachel Jewell, Dyese Moody, Deanna Arsala, John H. Werren, Jeremy Lynch · 2021 · G3 Genes Genomes Genetics
  58. The enigmatic relationship between epiphyseal fusion and bone development in primates
    Conrad Stephen Brimacombe · 2017 · Evolutionary Anthropology Issues News and Reviews
  59. A sensitive mNeonGreen reporter system to measure transcriptional dynamics in Drosophila development
    Stefano Ceolin, Monika Hanf, Marta Bozek, Andrea Ennio Storti, Nicolas Gompel, Ulrich Unnerstall, Christophe Jung, Ulrike Gaul · 2020 · Communications Biology
  60. Neural crest gene regulatory networks as drivers of development, diversification and disease
    Jan Štundl, Desingu Ayyappa Raja, Marianne E. Bronner-Fraser · 2026 · Nature Reviews Molecular Cell Biology
  61. Stasis
    Scott Lidgard, Melanie Jane Hopkins · 2015
  62. Toward new Drosophila paradigms
    Luiz Paulo Moura Andrioli · 2012 · genesis
  63. A role for epigenetic changes in the development of retinal neurodegenerative conditions
    Heather R. Pelzel, Robert W. Nickells · 2011 · Journal of ocular biology, diseases, and informatics
  64. Evolution of regulatory networks associated with traits under selection in cichlids
    2018
  65. The proximity-based protein interactome and regulatory logics of the transcription factor p65 NF-κB/RELA
    2025
  66. The evolution of cultural gadgets
    Daniel Dor, Simona Ginsburg, Eva Jablonka · 2019 · Mind & Language
  67. Fostering synergy between cell biology and systems biology
    James A. Eddy, Cory C. Funk, Nathan D. Price · 2015 · Trends in Cell Biology
  68. Analysis of immune cell activation in patients with diabetes foot ulcer from the perspective of single cell
    Lehoanganh Vu, Fei Xu, Ting Li, Qikai Hua, Xiaocong Kuang, Yongqiang Jiang, Yanfei Liang, Xing Niu, Yixuan Chen, Chengyu Huang et al. · 2024 · European journal of medical research
  69. Animals are both radially and bilaterally symmetrical: Accommodating seemingly mutually exclusive paradigms
    Gábor Holló · 2014 · BioEssays
  70. Generating anatomical variation through mutations in networks – implications for evolution
    Jonathan Bard · 2014 · Journal of Anatomy
  71. MICA: A multi-omics method to predict gene regulatory networks in early human embryos
    Gregorio Alanis‐Lobato, Thomas E. Bartlett, Qiulin Huang, Claire S. Simon, Afshan McCarthy, Kay T. Elder, Phil Snell, Leila Christie, Kathy K. Niakan · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  72. Spatially and Temporally Distributed Complexity—A Refreshed Framework for the Study of GRN Evolution
    Alessandro Minelli, Alberto Valero‐Gracia · 2022 · Cells
  73. Phenotypic innovation in one tooth induced concerted developmental evolution in another
    Marie Sémon, Klára Steklíková, Marion Mouginot, Manon Peltier, Philippe Veber, Laurent Guéguen, Sophie Pantalacci · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  74. Topology in Biology: Singularities and Surgery Transformations in Metazoan Development and Evolution
    Valeria V. Isaeva, Nickolay V. Kasyanov, Eugene V. Presnov · 2014 · Applied Mathematics
  75. CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks
    Guihai Feng, Xin Qin, Jiahao Zhang, Wuliang Huang, Yiyang Zhang, Wentao Cui, Shirui Li, Chen Yao, Wenhao Liu, Yao Tian et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  76. Regulatory feedback loops bridge the human gene regulatory network and regulate carcinogenesis
    Yun-Ru Chen, Hsuan‐Cheng Huang, Chen-Ching Lin · 2017 · Briefings in Bioinformatics
  77. AI-driven automated discovery tools reveal diverse behavioral competencies of biological networks
    Mayalen Etcheverry, Clément Moulin-Frier, Pierre‐Yves Oudeyer, Michael G. Levin · 2025 · eLife
  78. The Power of Simplicity: Sea Urchin Embryos as in Vivo Developmental Models for Studying Complex Cell-to-cell Signaling Network Interactions
    Ryan Range, Marina Martínez-Bartolomé, Stephanie D. Burr · 2017 · Journal of Visualized Experiments
  79. Development and the Evolution of Plant Form
    Barbara A. Ambrose, Cristina Ferrándiz · 2012 · Wiley eBooks
  80. Molecular Paleobiology of the Echinoderm Skeleton
    Jeffrey R. Thompson · 2022 · Cambridge University Press eBooks
  81. Heterochronies, heterotopies, and cell resources of development in ontogenetic and evolutionary transformations
    Valeria V. Isaeva · 2015 · Paleontological Journal
  82. Tools for Sea Urchin Genomic Analysis
    2014
  83. Early origin and deep conservation of enhancers in animals
    Emily S. W. Wong, Siew Zhuan Tan, Victoria C. Garside, Gilles Claude Vanwalleghem, Federico Gaiti, Ethan K. Scott, Edwina McGlinn, Mathias François, Bernard M. Degnan · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  84. Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos
    Gregory D. McCarthy, Robert A. Drewell, Jacqueline M. Dresch · 2015 · PeerJ
  85. The gene regulatory network of mESC differentiation: a benchmark for reverse engineering methods
    Johannes Meisig, Nils Blüthgen · 2018 · Philosophical Transactions of the Royal Society B Biological Sciences
  86. Distinct Traits of Structural and Regulatory Evolutional Conservation of Human Genes with Specific Focus on Major Cancer Molecular Pathways
    2023
  87. Alternative Vertebrate and Invertebrate Model Organisms Show Similar Sensitivity as Rodents to a Diverse Set of Chemicals
    Gaëlle Hayot, Gavin Rhys Lloyd, Gaurav D. Diwan, Nathan Keith, Shannon R. Smoot, Christina A. Cramer von Clausbruch, Thomas C. Kaufman, Marianne Barnard, Andrew J. Tindall, Stephen Glaholt et al. · 2025 · Environmental Science & Technology
  88. Form, function, mind: What doesn't compute (and what might)
    Stuart A. Newman · 2024 · Biochemical and Biophysical Research Communications
  89. Rapid evolutionary repair by secondary perturbation of a primary disrupted transcriptional network
    Po‐Chen Hsu, Yu‐Hsuan Cheng, Chia‐Wei Liao, Richard Ron R. Litan, Yu‐Ting Jhou, Florica Jean Ganaden Opoc, Ahmed A. A. Amine, Jun‐Yi Leu · 2023 · EMBO Reports
  90. Evolution of Gene Regulatory Networks
    Ajna S. Rivera, Andrea Sajuthi · 2014 · Springer eBooks
  91. Using Sub-Network Combinations to Scale Up an Enumeration Method for Determining the Network Structures of Biological Functions
    2016
  92. Genomic-Morphogenetic Correlations and Evolutionary Trajectories of Bilateria
    2018
  93. Evolutionary Trends in Hox Cluster Genes Utilization: Whether Common Genes Play by General Rules?
    Milana A. Kulakova · 2018 · Paleontological Journal
  94. Gene Network Organization, Mutation, and Selection Collectively Drive Developmental Pattern Evolvability and Predictability
    H. Anne F. Booth, Zena Hadjivasiliou · 2025 · PRX Life
  95. Morphogenetic evolution with physical influences
    Tzu-Yi Huang, Steffen Lemke, Yu‐Chiun Wang · 2026 · Seminars in Cell and Developmental Biology
  96. A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression
    Rashid Minhas, Aleksandra Paterek, Maciej Łapiński, Michał A. Bazała, Vladimir P. Korzh, Cecilia Lanny Winata · 2019 · Developmental Dynamics
  97. In Search of the Ancestral Organization and Phylotypic Stage of Porifera
    Alexander V. Ereskovsky · 2019 · Russian Journal of Developmental Biology
  98. Ciliary photoreceptors in sea urchin larvae indicate pan-deuterostome cell type conservation
    2019
  99. Fitting structure to function in gene regulatory networks
    Ellen V. Rothenberg · 2017 · History & Philosophy of the Life Sciences
  100. Pantropic retroviruses as a transduction tool for sea urchin embryos
    Amanda B. Core, Arlene E. Reyna, Evan A. Conaway, Cynthia A. Bradham · 2012 · Proceedings of the National Academy of Sciences