Related references
Note: Only part of the references are listed.From Drift to Draft: How Much Do Beneficial Mutations Actually Contribute to Predictions of Ohta's Slightly Deleterious Model of Molecular Evolution?
Jun Chen et al.
GENETICS (2020)
The Evolutionary Forces Shaping Cis- and Trans-Regulation of Gene Expression within a Population of Outcrossing Plants
Emily B. Josephs et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
An inferred fitness consequence map of the rice genome
Zoe Joly-Lopez et al.
NATURE PLANTS (2020)
Transposable Elements Are Important Contributors to Standing Variation in Gene Expression in Capsella Grandiflora
Jasmina Uzunovic et al.
MOLECULAR BIOLOGY AND EVOLUTION (2019)
Impact of demography on linked selection in two outcrossing Brassicaceae species
Tiina M. Mattila et al.
ECOLOGY AND EVOLUTION (2019)
polyDFEv2.0: testing for invariance of the distribution of fitness effects within and across species
Paula Tataru et al.
BIOINFORMATICS (2019)
The importance of the Neutral Theory in 1968 and 50 years on: A response to Kern and Hahn 2018
Jeffrey D. Jensen et al.
EVOLUTION (2019)
The prevalence, evolution and chromatin signatures of plant regulatory elements
Zefu Lu et al.
NATURE PLANTS (2019)
Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana
Cristina M. Alexandre et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules
Kelsey A. Maher et al.
PLANT CELL (2018)
Inferring the Probability of the Derived vs. the Ancestral Allelic State at a Polymorphic Site
Peter D. Keightley et al.
GENETICS (2018)
The Neutral Theory in Light of Natural Selection
Andrew D. Kern et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Inferring the Probability of the Derived vs. the Ancestral Allelic State at a Polymorphic Site
Peter D. Keightley et al.
GENETICS (2018)
Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data
Paula Tataru et al.
GENETICS (2017)
The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora
Robert Horvath et al.
Genome Biology and Evolution (2017)
The Relationship between Selection, Network Connectivity, and Regulatory Variation within a Population of Capsella grandiflora
Emily B. Josephs et al.
GENOME BIOLOGY AND EVOLUTION (2017)
Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora
Kim A. Steige et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Inference of Distribution of Fitness Effects and Proportion of Adaptive Substitutions from Polymorphism Data
Paula Tataru et al.
GENETICS (2017)
PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq
Robert Kofler et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
deepTools2: a next generation web server for deep-sequencing data analysis
Fidel Ramirez et al.
NUCLEIC ACIDS RESEARCH (2016)
Open chromatin reveals the functional maize genome
Eli Rodgers-Melnick et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
The 'dark matter' in the plant genomes: non-coding and unannotated DNA sequences associated with open chromatin
Jiming Jiang
CURRENT OPINION IN PLANT BIOLOGY (2015)
Single-cell chromatin accessibility reveals principles of regulatory variation
Jason D. Buenostro et al.
NATURE (2015)
Association mapping reveals the role of purifying selection in the maintenance of genomic variation in gene expression
Emily B. Josephs et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris
Gavin M. Douglas et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
Differential Nuclease Sensitivity Profiling of Chromatin Reveals Biochemical Footprints Coupled to Gene Expression and Functional DNA Elements in Maize
Daniel L. Vera et al.
PLANT CELL (2014)
Evidence for Widespread Positive and Negative Selection in Coding and Conserved Noncoding Regions of Capsella grandiflora
Robert J. Williamson et al.
PLOS GENETICS (2014)
Genetic Diversity in the Interference Selection Limit
Benjamin H. Good et al.
PLOS GENETICS (2014)
Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
Alice Pajoro et al.
GENOME BIOLOGY (2014)
Patterns of Selection in Plant Genomes
Josh Hough et al.
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 44 (2013)
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
Annabelle Haudry et al.
NATURE GENETICS (2013)
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
Tanja Slotte et al.
NATURE GENETICS (2013)
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
Jason D. Buenrostro et al.
NATURE METHODS (2013)
Strong Purifying Selection at Synonymous Sites in D. melanogaster
David S. Lawrie et al.
PLOS GENETICS (2013)
Selection on Synonymous Sites for Increased Accessibility around miRNA Binding Sites in Plants
Wanjun Gu et al.
MOLECULAR BIOLOGY AND EVOLUTION (2012)
A map of the cis-regulatory sequences in the mouse genome
Yin Shen et al.
NATURE (2012)
The variant call format and VCFtools
Petr Danecek et al.
BIOINFORMATICS (2011)
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
Heng Li
BIOINFORMATICS (2011)
A Method for Inferring the Rate of Occurrence and Fitness Effects of Advantageous Mutations
Adrian Schneider et al.
GENETICS (2011)
Significant Selective Constraint at 4-Fold Degenerate Sites in the Avian Genome and Its Consequence for Detection of Positive Selection
Axel Kunstner et al.
GENOME BIOLOGY AND EVOLUTION (2011)
Positive and Negative Selection on Noncoding DNA Close to Protein-Coding Genes in Wild House Mice
Athanasios Kousathanas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2011)
Contrasting demographic history and population structure in Capsella rubella and Capsella grandiflora, two closely related species with different mating systems
Kate R. St Onge et al.
MOLECULAR ECOLOGY (2011)
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
Xiao-Yong Li et al.
GENOME BIOLOGY (2011)
Fast and accurate long-read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2010)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna et al.
GENOME RESEARCH (2010)
Distributions of Selectively Constrained Sites and Deleterious Mutation Rates in the Hominid and Murid Genomes
Lel Eory et al.
MOLECULAR BIOLOGY AND EVOLUTION (2010)
Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species
Toni I. Gossmann et al.
MOLECULAR BIOLOGY AND EVOLUTION (2010)
Genome-Wide Evidence for Efficient Positive and Purifying Selection in Capsella grandiflora, a Plant Species with a Large Effective Population Size
Tanja Slotte et al.
MOLECULAR BIOLOGY AND EVOLUTION (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Conserved noncoding sequences (CNSs) in higher plants
Michael Freeling et al.
CURRENT OPINION IN PLANT BIOLOGY (2009)
Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
Jesse D. Hollister et al.
GENOME RESEARCH (2009)
Estimating the Rate of Adaptive Molecular Evolution in the Presence of Slightly Deleterious Mutations and Population Size Change
Adam Eyre-Walker et al.
MOLECULAR BIOLOGY AND EVOLUTION (2009)
Recent speciation associated with the evolution of selfing in Capsella
John Paul Foxe et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Recent Advances in the Computational Discovery of Transcription Factor Binding Sites
Tung T. Nguyen et al.
ALGORITHMS (2009)
The Impact of Natural Selection on the Genome: Emerging Patterns in Drosophila and Arabidopsis
Stephen I. Wright et al.
ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS (2008)
The loci of evolution: How predictable is genetic evolution ?
David L. Stern et al.
EVOLUTION (2008)
Revealing the architecture of gene regulation: the promise of eQTL studies
Yoav Gilad et al.
TRENDS IN GENETICS (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations
J. M. Comeron et al.
HEREDITY (2008)
Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
Peter D. Keightley et al.
GENETICS (2007)
The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations
Jane Charlesworth et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)
The distribution of fitness effects of new mutations
Adam Eyre-Walker et al.
NATURE REVIEWS GENETICS (2007)
Transcription-related mutations and GC content drive variation in nucleotide substitution rates across the genomes of Arabidopsis thaliana and Arabidopsis lyrata
Leah J. DeRose-Wilson et al.
BMC EVOLUTIONARY BIOLOGY (2007)
The evolutionary significance of cis-regulatory mutations
Gregory A. Wray
NATURE REVIEWS GENETICS (2007)
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
Daniel L. Halligan et al.
GENOME RESEARCH (2006)
Hearing silence: non-neutral evolution at synonymous sites in mammals
JV Chamary et al.
NATURE REVIEWS GENETICS (2006)
Adaptive evolution of non-coding DNA in Drosophila
P Andolfatto
NATURE (2005)
CpG mutation rates in the human genome are highly dependent on local GC content
KJ Fryxell et al.
MOLECULAR BIOLOGY AND EVOLUTION (2005)
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
JV Chamary et al.
GENOME BIOLOGY (2005)
Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila
DL Halligan et al.
GENOME RESEARCH (2004)
Near-neutrality in evolution of genes and gene regulation
T Ohta
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
Share Paper
