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Evolutionary transition in accessible chromatin landscapes during vertebrate embryogenesis

https://doi.org/10.1101/481309
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Outgoing claims: the papers this work cites, builds on, or argues with.

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ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide
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A series of normal stages in the development of the chick embryo
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Evolution‐development congruence in pattern formation dynamics: Bifurcations in gene expression and regulation of networks structures
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Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes
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Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development
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Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo
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Genome sequence of the Brown Norway rat yields insights into mammalian evolution
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
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The medaka draft genome and insights into vertebrate genome evolution
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The amphioxus genome and the evolution of the chordate karyotype
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The genome of a songbird
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A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns
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Gene expression divergence recapitulates the developmental hourglass model
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The genome of the green anole lizard and a comparative analysis with birds and mammals
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A high-resolution map of human evolutionary constraint using 29 mammals
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The African coelacanth genome provides insights into tetrapod evolution
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The zebrafish reference genome sequence and its relationship to the human genome
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Elephant shark genome provides unique insights into gnathostome evolution
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The genomic substrate for adaptive radiation in African cichlid fish
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A comparative encyclopedia of DNA elements in the mouse genome
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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
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Integrative genomics viewer
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Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis
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Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features
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Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes
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Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution
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The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan
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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
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Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
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Centromere evolution and CpG methylation during vertebrate speciation
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Constrained vertebrate evolution by pleiotropic genes
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Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly
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Pairwise comparisons across species are problematic when analyzing functional genomic data
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Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
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The Sequence Alignment/Map format and SAMtools
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BEDTools: a flexible suite of utilities for comparing genomic features
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Trimmomatic: a flexible trimmer for Illumina sequence data
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Integration of the Genetic Map and Genome Assembly of Fugu Facilitates Insights into Distinct Features of Genome Evolution in Teleosts and Mammals
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VISTA Enhancer Browser--a database of tissue-specific human enhancers
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The BioMart community portal: an innovative alternative to large, centralized data repositories
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Ensembl 2018
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Phylogenetic Analysis Under Dollo's Law
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OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
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Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
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REINTERPRETING RECAPITULATION: SYSTEMATICS OF NEEDLEFISHES AND THEIR ALLIES (TELEOSTEI: BELONIFORMES)
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The Theory of Recapitulation: A Critical Re-statement of the Biogenetic Law.
inferredcites →https://doi.org/10.1126/science.1072104openalex-snapshot
Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes
inferredcites →https://doi.org/10.1126/science.1080049openalex-snapshot
The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins
inferredcites →https://doi.org/10.1126/science.1139158openalex-snapshot
Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
inferredcites →https://doi.org/10.1126/science.1169588openalex-snapshot
The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution
inferredcites →https://doi.org/10.1126/science.1173826openalex-snapshot
Evolution of the Turtle Body Plan by the Folding and Creation of New Muscle Connections
inferredcites →https://doi.org/10.1126/science.1183670openalex-snapshot
The Genome of the Western Clawed Frog Xenopus tropicalis
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Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
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Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology
inferredcites →https://doi.org/10.1146/annurev.bi.57.070188.001111openalex-snapshot
NUCLEASE HYPERSENSITIVE SITES IN CHROMATIN
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The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information
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Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/gb-2013-14-2-r15openalex-snapshot
Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
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Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts
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Temporal colinearity and the phylotypic progression: a basis for the stability of a vertebrate Bauplan and the evolution of morphologies through heterochrony
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Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
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Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling
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On von Baerian and Haeckelian Recapitulation
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Über Entwickelungsgeschichte der Thiere : Beobachtung und Reflexion /
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Generelle morphologie der organismen. Allgemeine grundzüge der organischen formen-wissenschaft, mechanisch begründet durch die von Charles Darwin reformirte descendenztheorie, von Ernst Haeckel.
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Über Entwickelungsgeschichte der Thiere. Beobachtung und Reflexion
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The Shape of Life
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