Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived

Genomic inferences of domestication events are corroborated by written records in Brassica rapa

(2017) Xinshuai Qi et al.   MOLECULAR ECOLOGY

Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower

(2017) Patrick P. Edger et al.   PLANT CELL

Robust Yet Fragile: Expression Noise, Protein Misfolding, and Gene Dosage in the Evolution of Genomes

(2016) J. Chris Pires et al.   Annual Review of Genetics

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

(2016) Carlos Alonso-Blanco et al.   CELL

Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

(2016) Feng Cheng et al.   NATURE GENETICS

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

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

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

(2016) Zhen Li et al.   PLANT CELL

Kinetics genetics: Incorporating the concept of genomic balance into an understanding of quantitative traits

(2016) James A. Birchler et al.   PLANT SCIENCE

Models of buffering of dosage imbalances in protein complexes

(2015) Reiner A. Veitia et al.   Biology Direct

Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences

(2015) Michael Freeling et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Polyploidy and genome evolution in plants

(2015) Pamela S Soltis et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Split-alignment of genomes finds orthologies more accurately

(2015) Martin C Frith et al.   GENOME BIOLOGY

Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence

(2014) T. Arias et al.   AMERICAN JOURNAL OF BOTANY

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

(2014) Gavin C Conant et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2014) Gavin C. Conant   MOLECULAR BIOLOGY AND EVOLUTION

Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids

(2014) M. R. Woodhouse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea

(2014) Isobel AP Parkin et al.   GENOME BIOLOGY

Two Evolutionarily Distinct Classes of Paleopolyploidy

(2013) Olivier Garsmeur et al.   MOLECULAR BIOLOGY AND EVOLUTION

Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

(2013) W.-k. Jiang et al.   PLANT PHYSIOLOGY

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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

(2012) H. Tang et al.   GENETICS

Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed by Whole and Small-Scale Genome Duplications

(2012) Lorenzo Carretero-Paulet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis

(2012) Michaël Bekaert et al.   NEW PHYTOLOGIST

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

(2012) Feng Cheng et al.   PLoS One

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

(2012) J. A. Birchler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Screening synteny blocks in pairwise genome comparisons through integer programming

(2011) Haibao Tang et al.   BMC BIOINFORMATICS

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus

(2011) E. Rodgers-Melnick et al.   GENOME RESEARCH

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

(2011) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang 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

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao 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

Comparative Evolution of Photosynthetic Genes in Response to Polyploid and Nonpolyploid Duplication

(2011) J. E. Coate et al.   PLANT PHYSIOLOGY

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

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional bias in molecular evolution rate of Arabidopsis thaliana

(2010) Andrew S Warren et al.   BMC EVOLUTIONARY BIOLOGY

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis

(2010) C. G. de Oliveira Dal'Molin et al.   PLANT PHYSIOLOGY

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

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

Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales

(2009) Michael S. Barker et al.   Genome Biology and Evolution

The evolutionary significance of ancient genome duplications

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

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

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

(2008) Eric Lyons et al.   PLANT JOURNAL

Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids

(2008) E. Lyons et al.   PLANT PHYSIOLOGY

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology