Interaction-based evolution: how natural selection and nonrandom mutation work together

Genomes on the Edge: Programmed Genome Instability in Ciliates

(2013) John R. Bracht et al.   CELL

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

(2013) Jean-François Flot et al.   NATURE

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

RNA-mediated genome rearrangement: Hypotheses and evidence

(2012) Wenwen Fang et al.   BIOESSAYS

Transposable element recruitments in the mammalian placenta: impacts and mechanisms

(2012) D. Emera et al.   Briefings in Functional Genomics

Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns

(2012) W. Qu et al.   GENOME RESEARCH

Heterogeneity of the Transition/Transversion Ratio in Drosophila and Hominidae Genomes

(2012) V. B. Seplyarskiy et al.   MOLECULAR BIOLOGY AND EVOLUTION

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

De novo mutations in human genetic disease

(2012) Joris A. Veltman et al.   NATURE REVIEWS GENETICS

Transformation of a transposon into a derived prolactin promoter with function during human pregnancy

(2012) D. Emera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

(2012) Chen Xie et al.   PLoS Genetics

New words in human mutagenesis

(2011) Alexander Y Panchin et al.   BMC BIOINFORMATICS

Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection

(2011) Netta Mendelson Cohen et al.   CELL

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Mutation Rate Distribution Inferred from Coincident SNPs and Coincident Substitutions

(2011) Philip L. F. Johnson et al.   Genome Biology and Evolution

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

Direct and indirect consequences of meiotic recombination: implications for genome evolution

(2011) Matthew T. Webster et al.   TRENDS IN GENETICS

De Novo Origin of Human Protein-Coding Genes

(2011) Dong-Dong Wu et al.   PLoS Genetics

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

(2010) Dan Li et al.   CELL RESEARCH

The Genomic Distribution and Local Context of Coincident SNPs in Human and Chimpanzee

(2010) Alan Hodgkinson et al.   Genome Biology and Evolution

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

The mutational spectrum of non-CpG DNA varies with CpG content

(2010) J.-C. Walser et al.   GENOME RESEARCH

Triggers for genomic rearrangements: insights into genomic, cellular and environmental influences

(2010) Ram-Shankar Mani et al.   NATURE REVIEWS GENETICS

Ten years of genetics and genomics: what have we achieved and where are we heading?

(2010) Edith Heard et al.   NATURE REVIEWS GENETICS

Discrete DNA sites regulate global distribution of meiotic recombination

(2010) Wayne P. Wahls et al.   TRENDS IN GENETICS

A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions

(2010) Chuan-Yun Li et al.   PLoS Computational Biology

The maintenance of mixed mating by cleistogamy in the perennial violet Viola septemloba (Violaceae)

(2009) Alice A. Winn et al.   AMERICAN JOURNAL OF BOTANY

The Biogenesis and Function of PIWI Proteins and piRNAs: Progress and Prospect

(2009) Travis Thomson et al.   Annual Review of Cell and Developmental Biology

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

Is evolution Darwinian or/and Lamarckian?

(2009) Eugene V Koonin et al.   Biology Direct

On the problems of a closed marriage: celebrating Darwin 200

(2009) J. R. Pannell   Biology Letters

Positive selection for the male functionality of a co-retroposed gene in the hominoids

(2009) Yong Zhang et al.   BMC EVOLUTIONARY BIOLOGY

Non-B DNA structure-induced genetic instability and evolution

(2009) Junhua Zhao et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Genetic recombination as a major cause of mutagenesis in the human globin gene clusters

(2009) Joseph Borg et al.   CLINICAL BIOCHEMISTRY

Emergence of a New Gene from an Intergenic Region

(2009) Tobias J.A.J. Heinen et al.   CURRENT BIOLOGY

HYPERMUTABILITY OFHOXA13AAND FUNCTIONAL DIVERGENCE FROM ITS PARALOG ARE ASSOCIATED WITH THE ORIGIN OF A NOVEL DEVELOPMENTAL FEATURE IN ZEBRAFISH AND RELATED TAXA (CYPRINIFORMES)

(2009) Karen D. Crow et al.   EVOLUTION

Human Triallelic Sites: Evidence for a New Mutational Mechanism?

(2009) A. Hodgkinson et al.   GENETICS

Darwinian alchemy: Human genes from noncoding DNA

(2009) A. Siepel   GENOME RESEARCH

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

Complex rearrangements in patients with duplications of MECP2 can occur by fork stalling and template switching

(2009) Claudia M.B. Carvalho et al.   HUMAN MOLECULAR GENETICS

Molecular evolution of the antiretroviral TRIM5 gene

(2009) Welkin E. Johnson et al.   IMMUNOGENETICS

Climbing Mount Probable: Mutation as a Cause of Nonrandomness in Evolution

(2009) A. Stoltzfus et al.   JOURNAL OF HEREDITY

Understanding what determines the frequency and pattern of human germline mutations

(2009) Norman Arnheim et al.   NATURE REVIEWS GENETICS

Role of Mre11 in chromosomal nonhomologous end joining in mammalian cells

(2009) Emilie Rass et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Complex human chromosomal and genomic rearrangements

(2009) Feng Zhang et al.   TRENDS IN GENETICS

Cryptic Variation in the Human Mutation Rate

(2009) Alan Hodgkinson et al.   PLOS BIOLOGY

A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation

(2009) P. J. Hastings et al.   PLoS Genetics

De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae

(2008) J. Cai et al.   GENETICS

On the origin of new genes in Drosophila

(2008) Q. Zhou et al.   GENOME RESEARCH

CpG dinucleotides and the mutation rate of non-CpG DNA

(2008) J.-C. Walser et al.   GENOME RESEARCH

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

(2008) P. M. Kim et al.   GENOME RESEARCH

Origin of Primate Orphan Genes: A Comparative Genomics Approach

(2008) M. Toll-Riera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

RNA-based gene duplication: mechanistic and evolutionary insights

(2008) Henrik Kaessmann et al.   NATURE REVIEWS GENETICS

TRIMCyp expression in Old World primates Macaca nemestrina and Macaca fascicularis

(2008) G. Brennan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Independent genesis of chimeric TRIM5-cyclophilin proteins in two primate species

(2008) C. A. Virgen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins

(2008) I. Voineagu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Independent evolution of an antiviral TRIMCyp in rhesus macaques

(2008) S. J. Wilson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics

Evolution of a TRIM5-CypA Splice Isoform in Old World Monkeys

(2008) Ruchi M. Newman et al.   PLoS Pathogens