Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization

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Why Should We Care about Molecular Coevolution?

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Phylogenetic evidence for cladogenetic polyploidization in land plants

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Has the connection between polyploidy and diversification actually been tested?

(2016) Elizabeth A Kellogg   CURRENT OPINION IN PLANT BIOLOGY

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex

(2015) Kathy Scienski et al.   Genome Biology and Evolution

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

(2015) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

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Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time

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Comparative Genomics as a Time Machine: How Relative Gene Dosage and Metabolic Requirements Shaped the Time-dependent Resolution of Yeast Polyploidy

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Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach

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Two Evolutionarily Distinct Classes of Paleopolyploidy

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An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

(2013) Tanja Slotte et al.   NATURE GENETICS

Large-scale gene function analysis with the PANTHER classification system

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Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

(2013) R. De Smet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales

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The Reference Genome of the Halophytic Plant Eutrema salsugineum

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Ancient whole genome duplications, novelty and diversification: the WGD Radiation Lag-Time Model

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Altered Patterns of Fractionation and Exon Deletions in Brassica rapa Support a Two-Step Model of Paleohexaploidy

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Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

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Very Low Rate of Gene Conversion in the Yeast Genome

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Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa

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Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

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The genome of the extremophile crucifer Thellungiella parvula

(2011) Maheshi Dassanayake et al.   NATURE GENETICS

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints

(2011) Michaël Bekaert et al.   PLANT CELL

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

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Evidence for Network Evolution in an Arabidopsis Interactome Map

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Recently Formed Polyploid Plants Diversify at Lower Rates

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Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners

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The collapse of gene complement following whole genome duplication

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Nonrandom Survival of Gene Conversions among Yeast Ribosomal Proteins Duplicated through Genome Doubling

(2010) A. M. Evangelisti et al.   Genome Biology and Evolution

Characterization of duplicate gene evolution in the recent natural allopolyploidTragopogon miscellusby next-generation sequencing and Sequenom iPLEX MassARRAY genotyping

(2010) RICHARD J. A. BUGGS et al.   MOLECULAR ECOLOGY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

The BioGRID Interaction Database: 2011 update

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Ohnologs in the human genome are dosage balanced and frequently associated with disease

(2010) T. Makino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

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Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

(2009) Patrick P. Edger et al.   CHROMOSOME RESEARCH

Metabolic Adaptation after Whole Genome Duplication

(2009) M. J. A. van Hoek et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

The evolutionary significance of ancient genome duplications

(2009) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

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SeqAn An efficient, generic C++ library for sequence analysis

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Probabilistic Cross-Species Inference of Orthologous Genomic Regions Created by Whole-Genome Duplication in Yeast

(2008) G. C. Conant et al.   GENETICS

How to usefully compare homologous plant genes and chromosomes as DNA sequences

(2008) Eric Lyons et al.   PLANT JOURNAL