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Studying the dawn of de novo gene emergence in mice reveals fast integration of new genes into functional networks
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/0471250953.bi1110s43openalex-snapshot
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline
inferredcites →https://doi.org/10.1007/s00265-016-2131-1openalex-snapshot
Personality traits are consistent when measured in the field and in the laboratory in African striped mice (Rhabdomys pumilio)
inferredcites →https://doi.org/10.1007/s00335-015-9583-xopenalex-snapshot
Creating reference gene annotation for the mouse C57BL6/J genome assembly
inferredcites →https://doi.org/10.1007/s11248-013-9764-xopenalex-snapshot
Rapid conversion of EUCOMM/KOMP-CSD alleles in mouse embryos using a cell-permeable Cre recombinase
inferredcites →https://doi.org/10.1016/0091-3057(94)90472-3openalex-snapshot
Ethopharmacological analysis of rat behavior on the elevated plus-maze
inferredcites →https://doi.org/10.1016/0091-3057(95)00138-mopenalex-snapshot
Factor analysis of spatiotemporal and ethological measures in the murine elevated plus-maze test of anxiety
inferredcites →https://doi.org/10.1016/0091-3057(95)02171-xopenalex-snapshot
The influence of open arm ledges and maze experience in the elevated plus-maze
inferredcites →https://doi.org/10.1016/j.cell.2017.05.038openalex-snapshot
An Expanded View of Complex Traits: From Polygenic to Omnigenic
inferredcites →https://doi.org/10.1016/j.cub.2009.07.049openalex-snapshot
Emergence of a New Gene from an Intergenic Region
inferredcites →https://doi.org/10.1016/j.jmb.2005.01.071openalex-snapshot
The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins
inferredcites →https://doi.org/10.1016/j.tig.2009.03.007openalex-snapshot
Thirty years of Mus spretus: a promising future
inferredcites →https://doi.org/10.1016/j.tig.2015.02.007openalex-snapshot
Genes from scratch – the evolutionary fate of de novo genes
inferredcites →https://doi.org/10.1016/j.tpb.2017.06.001openalex-snapshot
The infinitesimal model: Definition, derivation, and implications
inferredcites →https://doi.org/10.1016/j.tpb.2017.09.003openalex-snapshot
Commentary: Fisher’s infinitesimal model: A story for the ages
inferredcites →https://doi.org/10.1016/s0031-9384(00)00373-5openalex-snapshot
Behavioral profile of wild mice in the elevated plus-maze test for anxiety
inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot
EMBOSS: The European Molecular Biology Open Software Suite
inferredcites →https://doi.org/10.1038/cr.2010.31openalex-snapshot
A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand
inferredcites →https://doi.org/10.1038/emboj.2012.326openalex-snapshot
Dissecting the mechanisms of Notch induced hyperplasia
inferredcites →https://doi.org/10.1038/nature01262openalex-snapshot
Initial sequencing and comparative analysis of the mouse genome
inferredcites →https://doi.org/10.1038/nature05874openalex-snapshot
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
inferredcites →https://doi.org/10.1038/nature09267openalex-snapshot
Mammalian microRNAs predominantly act to decrease target mRNA levels
inferredcites →https://doi.org/10.1038/nature10413openalex-snapshot
Mouse genomic variation and its effect on phenotypes and gene regulation
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nbt.3122openalex-snapshot
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
inferredcites →https://doi.org/10.1038/ng.847openalex-snapshot
Subspecific origin and haplotype diversity in the laboratory mouse
inferredcites →https://doi.org/10.1038/ni.3115openalex-snapshot
The RNA-binding protein HuR is essential for the B cell antibody response
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot
HISAT: a fast spliced aligner with low memory requirements
inferredcites →https://doi.org/10.1038/nmeth.3688openalex-snapshot
Detecting actively translated open reading frames in ribosome profiling data
inferredcites →https://doi.org/10.1038/nprot.2007.44openalex-snapshot
The use of the elevated plus maze as an assay of anxiety-related behavior in rodents
inferredcites →https://doi.org/10.1038/nrg.2016.78openalex-snapshot
Open questions in the study of de novo genes: what, how and why
inferredcites →https://doi.org/10.1038/nrg3053openalex-snapshot
The evolutionary origin of orphan genes
inferredcites →https://doi.org/10.1038/nrg3521openalex-snapshot
New genes as drivers of phenotypic evolution
inferredcites →https://doi.org/10.1038/s41559-017-0127openalex-snapshot
Random sequences are an abundant source of bioactive RNAs or peptides
inferredcites →https://doi.org/10.1038/s41559-018-0506-6openalex-snapshot
Translation of neutrally evolving peptides provides a basis for de novo gene evolution
inferredcites →https://doi.org/10.1038/s41559-018-0585-4openalex-snapshot
No beneficial fitness effects of random peptides
inferredcites →https://doi.org/10.1038/s41559-018-0586-3openalex-snapshot
Reply to ‘No beneficial fitness effects of random peptides’
inferredcites →https://doi.org/10.1038/s41559-018-0639-7openalex-snapshot
Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover
inferredcites →https://doi.org/10.1038/sdata.2016.75openalex-snapshot
Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus
inferredcites →https://doi.org/10.1038/srep07280openalex-snapshot
Pleiotropy of the de novo-originated gene MDF1
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot
HTSeq—a Python framework to work with high-throughput sequencing data
inferredcites →https://doi.org/10.1093/molbev/msu286openalex-snapshot
Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution
inferredcites →https://doi.org/10.1093/molbev/msw284openalex-snapshot
No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution
inferredcites →https://doi.org/10.1093/nar/gkr483openalex-snapshot
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
inferredcites →https://doi.org/10.1093/nar/gks1193openalex-snapshot
NCBI GEO: archive for functional genomics data sets—update
inferredcites →https://doi.org/10.1093/nar/gkv1145openalex-snapshot
2016 update of the PRIDE database and its related tools
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1101/gr.101386.109openalex-snapshot
Origins, evolution, and phenotypic impact of new genes
inferredcites →https://doi.org/10.1101/gr.187187.114openalex-snapshot
Divergence patterns of genic copy number variation in natural populations of the house mouse ( Mus musculus domesticus ) reveal three conserved genes with major population-specific expansions
inferredcites →https://doi.org/10.1104/pp.17.00577openalex-snapshot
Identification of Novel Growth Regulators in Plant Populations Expressing Random Peptides
inferredcites →https://doi.org/10.1111/1755-0998.12776openalex-snapshot
Using the Mus musculus hybrid zone to assess covariation and genetic architecture of limb bone lengths
inferredcites →https://doi.org/10.1126/science.1196380openalex-snapshot
New Genes in Drosophila Quickly Become Essential
inferredcites →https://doi.org/10.1126/science.aac7368openalex-snapshot
Multiple repressive mechanisms in the hippocampus during memory formation
inferredcites →https://doi.org/10.1146/annurev-genet-111212-133301openalex-snapshot
New Gene Evolution: Little Did We Know
inferredcites →https://doi.org/10.1186/1471-2164-14-117openalex-snapshot
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution
inferredcites →https://doi.org/10.1186/1472-6785-13-49openalex-snapshot
Consistency in boldness, activity and exploration at different stages of life
inferredcites →https://doi.org/10.1186/1742-9994-9-6openalex-snapshot
TINA manual landmarking tool: software for the precise digitization of 3D landmarks
inferredcites →https://doi.org/10.1186/2051-3933-2-12openalex-snapshot
What seeds tell us about birds: a multi-year analysis of acorn woodpecker foraging movements
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
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferredcites →https://doi.org/10.1186/s12859-018-2191-5openalex-snapshot
RnaSeqSampleSize: real data based sample size estimation for RNA sequencing
inferredcites →https://doi.org/10.1186/s12862-018-1232-zopenalex-snapshot
Dealing with the adaptive immune system during de novo evolution of genes from intergenic sequences
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1210/en.2005-0596openalex-snapshot
Demilune Cell and Parotid Protein from Murine Oviductal Epithelium Stimulates Preimplantation Embryo Development
inferredcites →https://doi.org/10.1353/pbm.2014.0006openalex-snapshot
The Discovery of De Novo Gene Evolution
inferredcites →https://doi.org/10.1371/journal.pcbi.1003280openalex-snapshot
Comprehensive Repertoire of Foldable Regions within Whole Genomes
inferredcites →https://doi.org/10.1371/journal.pgen.1002942openalex-snapshot
Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs
inferredcites →https://doi.org/10.1371/journal.pgen.1003860openalex-snapshot
De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences
inferredcites →https://doi.org/10.1523/jneurosci.0084-14.2014openalex-snapshot
Ribosome Profiling Reveals a Cell-Type-Specific Translational Landscape in Brain Tumors
inferredcites →https://doi.org/10.15252/embj.201386855openalex-snapshot
Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice
inferredcites →https://doi.org/10.1534/genetics.107.084491openalex-snapshot
De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.7554/elife.03523openalex-snapshot
Long non-coding RNAs as a source of new peptides
inferredcites →https://doi.org/10.7554/elife.09977openalex-snapshot
Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1093/gbe/evae107openalex-snapshot
The Rapid Evolution of De Novo Proteins in Structure and Complex
inferred← citeshttps://doi.org/10.1101/575837openalex-snapshot
Frequent birth of de novo genes in the compact yeast genome
inferred← citeshttps://doi.org/10.1134/s1062360421060035openalex-snapshot
The Phenomenon of Evolutionary “De Novo Generation” of Genes
inferred← citeshttps://doi.org/10.1186/s12859-019-3023-yopenalex-snapshot
fagin: synteny-based phylostratigraphy and finer classification of young genes
inferred← citeshttps://doi.org/10.3389/fgene.2021.722981openalex-snapshot
Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
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