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Evolution of regulatory networks associated with traits under selection in cichlids

https://doi.org/10.1101/496034
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
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Evolution of Gene Regulatory Networks Controlling Body Plan Development
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Satb1 Regulates Contactin 5 to Pattern Dendrites of a Mammalian Retinal Ganglion Cell
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Common developmental pathways link tooth shape to regeneration
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Visual pigments of African cichlid fishes: evidence for ultraviolet vision from microspectrophotometry and DNA sequences
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A conserved retinoic acid response element required for early expression of the homeobox gene Hoxb-1
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Speciation through sensory drive in cichlid fish
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The evolution of gene expression levels in mammalian organs
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Ecological opportunity and sexual selection together predict adaptive radiation
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The genomic substrate for adaptive radiation in African cichlid fish
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Competing signals drive telencephalon diversity
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Regulatory changes underlying expression differences within and between Drosophila species
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Network motifs in the transcriptional regulation network of Escherichia coli
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The evolution of genetic regulatory systems in bacteria
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Adaptive evolution and explosive speciation: the cichlid fish model
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Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow
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Understanding explosive diversification through cichlid fish genomics
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Behavioral evolution contributes to hindbrain diversification among Lake Malawi cichlid fish
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Gene regulatory networks for development
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Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape
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Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes
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Two Types of Molecular Evolution. Evidence from Studies of Interspecific Hybridization
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Identification of cis-Acting Elements Repressing Blue Opsin Expression in Zebrafish UV Cones and Pineal Cells
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A benchmark of gene expression tissue-specificity metrics
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Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
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BEDTools: a flexible suite of utilities for comparing genomic features
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FIMO: scanning for occurrences of a given motif
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InterProScan 5: genome-scale protein function classification
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Cytoscape.js: a graph theory library for visualisation and analysis
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DyNet: visualization and analysis of dynamic molecular interaction networks
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Altered visual function and interneuron survival in Atrx knockout mice: inference for the human syndrome
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Tbx2a Modulates Switching of RH2 and LWS Opsin Gene Expression
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Age of Cichlids: New Dates for Ancient Lake Fish Radiations
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PAML 4: Phylogenetic Analysis by Maximum Likelihood
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Parallel Evolution of Opsin Gene Expression in African Cichlid Fishes
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
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UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions
inferredcites →https://doi.org/10.1093/nar/gkv362openalex-snapshot
RSAT 2015: Regulatory Sequence Analysis Tools
inferredcites →https://doi.org/10.1093/nar/gkv416openalex-snapshot
The MEME Suite
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A prior-based integrative framework for functional transcriptional regulatory network inference
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GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments
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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
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TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees
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A quantitative model for characterizing the evolutionary history of mammalian gene expression
inferredcites →https://doi.org/10.1101/gr.093815.109openalex-snapshot
Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
inferredcites →https://doi.org/10.1101/gr.146233.112openalex-snapshot
Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1111/j.1749-4877.2008.00137.xopenalex-snapshot
Cichlid fish visual systems: mechanisms of spectral tuning
inferredcites →https://doi.org/10.1111/mec.12887openalex-snapshot
Towards a gene regulatory network perspective on phenotypic plasticity, genetic accommodation and genetic assimilation
inferredcites →https://doi.org/10.1126/science.1090005openalex-snapshot
Evolution at Two Levels in Humans and Chimpanzees
inferredcites →https://doi.org/10.1126/science.1182213openalex-snapshot
Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer
inferredcites →https://doi.org/10.1126/science.1230612openalex-snapshot
The Evolutionary Landscape of Alternative Splicing in Vertebrate Species
inferredcites →https://doi.org/10.1126/science.860134openalex-snapshot
Evolution and Tinkering
inferredcites →https://doi.org/10.1126/science.aao6809openalex-snapshot
Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish radiations
inferredcites →https://doi.org/10.1146/annurev-genom-090413-025412openalex-snapshot
The Evolutionary Genomics of Cichlid Fishes: Explosive Speciation and Adaptation in the Postgenomic Era
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2148-11-120openalex-snapshot
Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes
inferredcites →https://doi.org/10.1186/1741-7007-6-22openalex-snapshot
Visual sensitivities tuned by heterochronic shifts in opsin gene expression
inferredcites →https://doi.org/10.1186/s12861-017-0146-0openalex-snapshot
A compendium of developmental gene expression in Lake Malawi cichlid fishes
inferredcites →https://doi.org/10.1186/s12864-016-3046-yopenalex-snapshot
Comparative transcriptomics of anal fin pigmentation patterns in cichlid fishes
inferredcites →https://doi.org/10.1186/s12864-018-5328-zopenalex-snapshot
Multiple trans QTL and one cis-regulatory deletion are associated with the differential expression of cone opsins in African cichlids
inferredcites →https://doi.org/10.1242/dev.01366openalex-snapshot
Dynactin is required to maintain nuclear position within postmitotic Drosophila photoreceptor neurons
inferredcites →https://doi.org/10.1242/jeb.193.1.191openalex-snapshot
Retinoic Acid Modulates Retinal Development in the Juveniles of a Teleost Fish
inferredcites →https://doi.org/10.1371/journal.pbio.0030363openalex-snapshot
Rapid Behavioral and Genomic Responses to Social Opportunity
inferredcites →https://doi.org/10.1371/journal.pbio.1000031openalex-snapshot
An Ancient Gene Network Is Co-opted for Teeth on Old and New Jaws
inferredcites →https://doi.org/10.1371/journal.pbio.1000266openalex-snapshot
The Eyes Have It: Regulatory and Structural Changes Both Underlie Cichlid Visual Pigment Diversity
inferredcites →https://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
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Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm
inferredcites →https://doi.org/10.7554/elife.01114openalex-snapshot
Correction: Evolutionary principles of modular gene regulation in yeasts

What points at this work

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

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Rewiring Network Plasticity to Improve Crops
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The use of trade data to predict the source and spread of food safety outbreaks: An innovative mathematical modelling approach
inferred← citeshttps://doi.org/10.1101/851394openalex-snapshot
microRNA profiling in the Weddell Seal suggests novel regulatory mechanisms contributing to diving adaptation
inferred← citeshttps://doi.org/10.1186/s12864-020-6675-0openalex-snapshot
microRNA profiling in the Weddell seal suggests novel regulatory mechanisms contributing to diving adaptation
inferred← citeshttps://doi.org/10.21203/rs.3.rs-15753/v2openalex-snapshot
microRNA profiling in the Weddell Seal suggests novel regulatory mechanisms contributing to diving adaptation
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