Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis

The wondrous cycles of polyploidy in plants

(2015) Jonathan F. Wendel   AMERICAN JOURNAL OF BOTANY

HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species

(2015) Wandrille Duchemin et al.   BMC BIOINFORMATICS

Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms

(2015) Justin T Page et al.   BMC GENETICS

Gene-Expression Novelty in Allopolyploid Cotton: A Proteomic Perspective

(2015) G. Hu et al.   GENETICS

Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis

(2015) Rafael A. Cañas et al.   JOURNAL OF EXPERIMENTAL BOTANY

Persistence of Subgenomes in Paleopolyploid Cotton after 60 My of Evolution

(2015) Simon Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

(2015) Bo Zhu et al.   PLANT CELL

GraP: platform for functional genomics analysis of Gossypium raimondii

(2015) Liwei Zhang et al.   Database-The Journal of Biological Databases and Curation

Gene Network Reconstruction by Integration of Prior Biological Knowledge

(2015) Y. Li et al.   G3-Genes Genomes Genetics

FastRFunctions for Robust Correlations and Hierarchical Clustering

(2015) Peter Langfelder et al.   Journal of Statistical Software

Nonadditive Gene Expression in Polyploids

(2014) Mi-Jeong Yoo et al.   Annual Review of Genetics

Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids

(2014) Tina Sehrish et al.   BMC GENOMICS

Data integration in the era of omics: current and future challenges

(2014) David Gomez-Cabrero et al.   BMC Systems Biology

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

Open Chromatin in Plant Genomes

(2014) Wenli Zhang et al.   CYTOGENETIC AND GENOME RESEARCH

Extensive and Biased Intergenomic Nonreciprocal DNA Exchanges Shaped a Nascent Polyploid Genome, Gossypium (Cotton)

(2014) Hui Guo et al.   GENETICS

Ancient Gene Duplicates in Gossypium (Cotton) Exhibit Near-Complete Expression Divergence

(2014) Simon Renny-Byfield et al.   Genome Biology and Evolution

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

(2014) Thomas E. Hughes et al.   GENOME RESEARCH

Genome-Wide Disruption of Gene Expression in Allopolyploids but Not Hybrids of Rice Subspecies

(2014) Chunming Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bridging physiological and evolutionary time-scales in a gene regulatory network

(2014) Gwenaëlle Marchand et al.   NEW PHYTOLOGIST

Ecological studies of polyploidy in the 100 years following its discovery

(2014) J. Ramsey et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Polyploidy and novelty: Gottlieb's legacy

(2014) Pamela S. Soltis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Extensive Translational Regulation of Gene Expression in an Allopolyploid (Glycine dolichocarpa)

(2014) J. E. Coate et al.   PLANT CELL

A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana

(2014) K. S. Heyndrickx et al.   PLANT CELL

mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

(2014) A. Li et al.   PLANT CELL

Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.)

(2014) Guanjing Hu et al.   PLANTA

Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape

(2014) Y. Ichihashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

Genome interplay in the grain transcriptome of hexaploid bread wheat

(2014) M. Pfeifer et al.   SCIENCE

Polyploidy and small RNA regulation of cotton fiber development

(2014) Xueying Guan et al.   TRENDS IN PLANT SCIENCE

Chromatin accessibility: a window into the genome

(2014) Maria Tsompana et al.   Epigenetics & Chromatin

Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome

(2014) Mi-Jeong Yoo et al.   PLoS Genetics

HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids

(2013) Aziz Mithani et al.   BMC GENOMICS

Genetic and Epigenetic Aspects of Polyploid Evolution in Plants

(2013) A. Madlung et al.   CYTOGENETIC AND GENOME RESEARCH

Composition and Expression of Conserved MicroRNA Genes in Diploid Cotton (Gossypium) Species

(2013) Lei Gong et al.   Genome Biology and Evolution

Putative Cationic Cell-Wall-Bound Peroxidase Homologues in Arabidopsis, AtPrx2, AtPrx25, and AtPrx71, Are Involved in Lignification

(2013) Jun Shigeto et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

Proteomic profiling of developing cotton fibers from wild and domesticatedGossypium barbadense

(2013) Guanjing Hu et al.   NEW PHYTOLOGIST

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

Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

(2013) Justin T. Page et al.   G3-Genes Genomes Genetics

PolyCat: A Resource for Genome Categorization of Sequencing Reads From Allopolyploid Organisms

(2013) Justin T. Page et al.   G3-Genes Genomes Genetics

Polyploidy associated with altered and broader ecological niches in the Claytonia perfoliata (Portulacaceae) species complex

(2012) Patrick J. McIntyre   AMERICAN JOURNAL OF BOTANY

Genomic expression dominance in allopolyploids

(2012) Ryan A Rapp et al.   BMC BIOLOGY

Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton

(2012) Lex E Flagel et al.   BMC GENOMICS

Redundancy and rewiring of genetic networks following genome-wide duplication events

(2012) Riet De Smet et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2012) H. Tang et al.   GENETICS

Allopolyploidization Lays the Foundation for Evolution of Distinct Populations: Evidence From Analysis of Synthetic Arabidopsis Allohexaploids

(2012) S. C. Matsushita et al.   GENETICS

Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant

(2012) T. Makino et al.   GENOME RESEARCH

Transgressive physiological and transcriptomic responses to light stress in allopolyploid Glycine dolichocarpa (Leguminosae)

(2012) J E Coate et al.   HEREDITY

Homoeolog expression bias and expression level dominance in allopolyploid cotton

(2012) M-J Yoo et al.   HEREDITY

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents

(2012) Jin Koh et al.   NEW PHYTOLOGIST

Homoeolog expression bias and expression level dominance in allopolyploids

(2012) C. E. Grover et al.   NEW PHYTOLOGIST

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

(2012) W. Zhang et al.   PLANT CELL

Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication

(2012) M. Abrouk et al.   PLANT CELL

The fate of duplicated genes in a polyploid plant genome

(2012) Anne Roulin et al.   PLANT JOURNAL

Reshaping of the maize transcriptome by domestication

(2012) R. Swanson-Wagner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

(2012) M. Chester et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polyploidy in fungi: evolution after whole-genome duplication

(2012) W. Albertin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

(2012) Xiaoli Shi et al.   Nature Communications

Cotton fiber: a powerful single-cell model for cell wall and cellulose research

(2012) Candace H. Haigler et al.   Frontiers in Plant Science

A systems genetic analysis of high density lipoprotein metabolism and network preservation across mouse models

(2011) Peter Langfelder et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Transcriptomic Shock Generates Evolutionary Novelty in a Newly Formed, Natural Allopolyploid Plant

(2011) Richard J.A. Buggs et al.   CURRENT BIOLOGY

Coordinated histone modifications are associated with gene expression variation within and between species

(2011) M. Ha et al.   GENOME RESEARCH

Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors

(2011) D W-K Ng et al.   HEREDITY

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Differential contributions to the transcriptome of duplicated genes in response to abiotic stresses in natural and synthetic polyploids

(2011) Shaowei Dong et al.   NEW PHYTOLOGIST

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

(2011) Michaël Bekaert et al.   PLANT CELL

Epigenetic Predictor of Age

(2011) Sven Bocklandt et al.   PLoS One

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

Measuring the evolutionary rate of protein-protein interaction

(2011) W. Qian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium)

(2011) Y. Bao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

(2011) Z. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polyploidy and ecological adaptation in wild yarrow

(2011) J. Ramsey   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence for Network Evolution in an Arabidopsis Interactome Map

(2011) et al.   SCIENCE

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

(2011) Peter L Chang et al.   GENOME BIOLOGY

Gene Conversion in Angiosperm Genomes with an Emphasis on Genes Duplicated by Polyploidization

(2011) Xi-Yin Wang et al.   Genes

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication

(2010) Ryan A Rapp et al.   BMC BIOLOGY

Histone variants and modifications in plant gene regulation

(2010) Roger B Deal et al.   CURRENT OPINION IN PLANT BIOLOGY

DNA methylation systems and targets in plants

(2010) Peter Meyer   FEBS LETTERS

The plant formin AtFH4 interacts with both actin and microtubules, and contains a newly identified microtubule-binding domain

(2010) M. J. Deeks et al.   JOURNAL OF CELL SCIENCE

Phylogenetically Distinct Cellulose Synthase Genes Support Secondary Wall Thickening in Arabidopsis Shoot Trichomes and Cotton Fiber

(2010) Lissete Betancur et al.   Journal of Integrative Plant Biology

Identification of Novel Proteins Involved in Plant Cell-Wall Synthesis Based on Protein−Protein Interaction Data

(2010) Chan Zhou et al.   JOURNAL OF PROTEOME RESEARCH

Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae)

(2010) Houda Chelaifa et al.   NEW PHYTOLOGIST

Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus

(2010) Richard J. A. Buggs et al.   NEW PHYTOLOGIST

Arabidopsis VILLIN1 and VILLIN3 Have Overlapping and Distinct Activities in Actin Bundle Formation and Turnover

(2010) P. Khurana et al.   PLANT CELL

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

(2010) Margaret R. Woodhouse et al.   PLOS BIOLOGY

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells

(2009) Mike J Mason et al.   BMC GENOMICS

Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids

(2009) R J A Buggs et al.   HEREDITY

Metabolic Adaptation after Whole Genome Duplication

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

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

The evolutionary significance of ancient genome duplications

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

Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

Homoeologous nonreciprocal recombination in polyploid cotton

(2009) Armel Salmon et al.   NEW PHYTOLOGIST

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

The frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)

(2009) Mingxiong Pang et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: Confirmed actors and newcomers

(2008) Muhammad Irshad et al.   BMC PLANT BIOLOGY

Global analysis of gene expression in cotton fibers from wild and domesticatedGossypium barbadense

(2008) Bhupendra Chaudhary et al.   EVOLUTION & DEVELOPMENT

Parallel Domestication, Convergent Evolution and Duplicated Gene Recruitment in Allopolyploid Cotton

(2008) R. Hovav et al.   GENETICS

Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years

(2008) M. S. Barker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

(2008) Zhongfu Ni et al.   NATURE

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

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

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

Transcriptome Analyses Show Changes in Gene Expression to Accompany Pollen Germination and Tube Growth in Arabidopsis

(2008) Y. Wang et al.   PLANT PHYSIOLOGY

The Evolution of Spinnable Cotton Fiber Entailed Prolonged Development and a Novel Metabolism

(2008) Ran Hovav et al.   PLoS Genetics

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE