Natural history and evolutionary principles of gene duplication in fungi

By I. Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev. Nature, 2007

664 citations recorded by the source corpus.

Subfields: Cell Biology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ac5de4a32acc64e8616ee6f203e8eaed9cbd98c8

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In Cell Biology

Kenneth H. Wolfe

In Molecular Biology

Citations in the corpus

Structural determinants of protein evolution are context-sensitive at the residue level. (2009, background): “To assess the evolutionary constraint imposed on a residue by each property, we first identified positions exhibiting a substitution in any of three closely related yeast species.”
The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse (2013, background): “We found no significant change in the status of H3K27me3 at the promoters of the heart control genes analyzed, while the H3K4me3 mark of the Gata6 and Nkx2-5, but not Gata4 or Tbx5 promoters was increased (Figure 3B).”
Single-cell RNA sequencing technologies and bioinformatics pipelines (2018, background): “Maximum parsimony is the basic principle that infers cellular dynamics and has been widely used in phylogenetic tree reconstruction in evolutionary biology 86,87 .”
Turning a hobby into a job: How duplicated genes find new functions (2008, background): “Not making this distinction is a potential concern as WGD and SSD can produce different kinds of adaptation”
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy (2015, background): “Here an orthogroup by definition contains both orthologues and paralogues, and in this context is frequently used as a unit of comparison for comparative genomics [10–12].”
Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation (2008, background): “Stress-related genes are also more volatile with respect to gene duplications and losses than growth-related genes in yeast”
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data (2011, neutral): “Some of the most highly expressed transcripts in S. pombe are derived from paralogous genes with very similar sequences (e.g., those encoding ribosomal proteins 21 ), yet were resolved by Trinity.”