Association of Intron Loss with High Mutation Rate in Arabidopsis: Implications for Genome Size Evolution

Can ENCODE tell us how much junk DNA we carry in our genome?

(2012) Deng-Ke Niu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Origin and evolution of spliceosomal introns

(2012) Igor B Rogozin et al.   Biology Direct

Fast-Forward Genetics Identifies Plant CPL Phosphatases as Regulators of miRNA Processing Factor HYL1

(2012) Pablo A. Manavella et al.   CELL

The C-value paradox, junk DNA and ENCODE

(2012) Sean R. Eddy   CURRENT BIOLOGY

ENCODE explained

(2012) Joseph R. Ecker et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Associative transcriptomics of traits in the polyploid crop species Brassica napus

(2012) Andrea L Harper et al.   NATURE BIOTECHNOLOGY

ENCODE Project Writes Eulogy for Junk DNA

(2012) E. Pennisi   SCIENCE

Genetic consequences of seed banks in the perennial herb Arabidopsis lyrata subsp. petraea (Brassicaceae)

(2011) Mohsen Falahati-Anbaran et al.   AMERICAN JOURNAL OF BOTANY

The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates

(2011) Brandon Gaut et al.   Annual Review of Ecology Evolution and Systematics

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

(2011) Michael Lynch et al.   Annual Review of Genomics and Human Genetics

Why eukaryotic cells use introns to enhance gene expression: Splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity

(2011) Deng-Ke Niu et al.   Biology Direct

Introns within Ribosomal Protein Genes Regulate the Production and Function of Yeast Ribosomes

(2011) Julie Parenteau et al.   CELL

A guided tour of large genome size in animals: what we know and where we are heading

(2011) France Dufresne et al.   CHROMOSOME RESEARCH

NONADAPTIVE EVOLUTION OF MITOCHONDRIAL GENOME SIZE

(2011) Bastien Boussau et al.   EVOLUTION

Causes and Consequences of Genome Expansion in Fungi

(2011) Yogeshwar D. Kelkar et al.   Genome Biology and Evolution

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

Higher Intron Loss Rate in Arabidopsis thaliana Than A. lyrata Is Consistent with Stronger Selection for a Smaller Genome

(2011) J. A. Fawcett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

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

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

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

(2011) Tina T Hu et al.   NATURE GENETICS

Functional consequences of developmentally regulated alternative splicing

(2011) Auinash Kalsotra et al.   NATURE REVIEWS GENETICS

Journey through the past: 150 million years of plant genome evolution

(2011) Sebastian Proost et al.   PLANT JOURNAL

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

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

Impact of a stress-inducible switch to mutagenic repair of DNA breaks on mutation in Escherichia coli

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

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

(2011) Miklos Csuros et al.   PLoS Computational Biology

Drift and Genome Complexity Revisited

(2011) Kenneth D. Whitney et al.   PLoS Genetics

Statistical Inference on the Mechanisms of Genome Evolution

(2011) Michael Lynch   PLoS Genetics

Intron creation and DNA repair

(2010) Hermann Ragg   CELLULAR AND MOLECULAR LIFE SCIENCES

Localized hypermutation and associated gene losses in legume chloroplast genomes

(2010) A. M. Magee et al.   GENOME RESEARCH

Evaluation of Models of the Mechanisms Underlying Intron Loss and Gain in Aspergillus Fungi

(2010) Lei-Ying Zhang et al.   JOURNAL OF MOLECULAR EVOLUTION

The metabolic theory of ecology: prospects and challenges for plant biology

(2010) Charles A. Price et al.   NEW PHYTOLOGIST

Critical association of ncRNA with introns

(2010) David Rearick et al.   NUCLEIC ACIDS RESEARCH

Irremediable Complexity?

(2010) M. W. Gray et al.   SCIENCE

DNA double-strand break repair and the evolution of intron density

(2010) Ashley Farlow et al.   TRENDS IN GENETICS

Did Genetic Drift Drive Increases in Genome Complexity?

(2010) Kenneth D. Whitney et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

A unifying explanation for diverse metabolic scaling in animals and plants

(2009) Douglas S. Glazier   BIOLOGICAL REVIEWS

Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms

(2009) David F Soria-Hernanz et al.   BMC EVOLUTIONARY BIOLOGY

A Universal Nonmonotonic Relationship between Gene Compactness and Expression Levels in Multicellular Eukaryotes

(2009) Liran Carmel et al.   Genome Biology and Evolution

Evolutionary Rates in Veronica L. (Plantaginaceae): Disentangling the Influence of Life History and Breeding System

(2009) Kai Müller et al.   JOURNAL OF MOLECULAR EVOLUTION

Seed banks cause elevated generation times and effective population sizes ofArabidopsis thalianain northern Europe

(2009) SVERRE LUNDEMO et al.   MOLECULAR ECOLOGY

Extensive, Recent Intron Gains in Daphnia Populations

(2009) W. Li et al.   SCIENCE

Exon definition as a potential negative force against intron losses in evolution

(2008) Deng-Ke Niu   Biology Direct

Evidence against the energetic cost hypothesis for the short introns in highly expressed genes

(2008) Yi-Fei Huang et al.   BMC EVOLUTIONARY BIOLOGY

Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression

(2008) A. B. Rose et al.   PLANT CELL

Rapidly regulated genes are intron poor

(2008) Daniel C. Jeffares et al.   TRENDS IN GENETICS

Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes

(2008) Tobias Warnecke et al.   GENOME BIOLOGY

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