De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa

Derived alleles of two axis proteins affect meiotic traits in autotetraploid Arabidopsis arenosa

(2020) Chris Morgan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selective Sweeps

(2019) Wolfgang Stephan   GENETICS

Standing genetic variation as the predominant source for adaptation of a songbird

(2019) Yu-Ting Lai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

(2019) Kathleen T. Xie et al.   SCIENCE

Modular epistasis and the compensatory evolution of gene deletion mutants

(2019) José I. Rojas Echenique et al.   PLoS Genetics

Parallel adaptation of rabbit populations to myxoma virus

(2019) Joel M. Alves et al.   SCIENCE

Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa

(2019) Patrick Monnahan et al.   Nature Ecology & Evolution

Adaptive introgression enables evolutionary rescue from extreme environmental pollution

(2019) Elias M. Oziolor et al.   SCIENCE

Positive Selection and Functional Divergence at Meiosis Genes That Mediate Crossing Over Across the Drosophila Phylogeny

(2019) Cara L. Brand et al.   G3-Genes Genomes Genetics

Estimating Time to the Common Ancestor for a Beneficial Allele

(2018) Joel Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance

(2018) Meng Wu et al.   MOLECULAR ECOLOGY

The rate and potential relevance of new mutations in a colonizing plant lineage

(2018) Moises Exposito-Alonso et al.   PLoS Genetics

Evolutionary footprint of epistasis

(2018) Gabriele Pedruzzi et al.   PLoS Computational Biology

Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell

(2018) Jeff J. Doyle et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Evolution at two time frames: Polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution

(2018) Steven M. Van Belleghem et al.   PLoS Genetics

Current Strategies of Polyploid Plant Genome Sequence Assembly

(2018) Maria Kyriakidou et al.   Frontiers in Plant Science

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Multidrug-resistant bacteria compensate for the epistasis between resistances

(2017) Jorge Moura de Sousa et al.   PLOS BIOLOGY

Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

(2017) Zachary Baker et al.   eLife

The challenge of evolving stable polyploidy: could an increase in “crossover interference distance” play a central role?

(2016) Kirsten Bomblies et al.   CHROMOSOMA

Structural Basis and IP 6 Requirement for Pds5-Dependent Cohesin Dynamics

(2016) Zhuqing Ouyang et al.   MOLECULAR CELL

Northern glacial refugia and altitudinal niche divergence shape genome-wide differentiation in the emerging plant modelArabidopsis arenosa

(2016) Filip Kolář et al.   MOLECULAR ECOLOGY

Structure of the Pds5-Scc1 Complex and Implications for Cohesin Function

(2016) Kyle W. Muir et al.   Cell Reports

Multi-nucleotide de novo Mutations in Humans

(2016) Søren Besenbacher et al.   PLoS Genetics

The Role of Standing Variation in Geographic Convergent Adaptation

(2015) Peter L. Ralph et al.   AMERICAN NATURALIST

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum

(2015) Sebastian Matuszewski et al.   GENETICS

The multifaceted roles of the HORMA domain in cellular signaling

(2015) Scott C. Rosenberg et al.   JOURNAL OF CELL BIOLOGY

Single Geographic Origin of a Widespread Autotetraploid Arabidopsis arenosa Lineage Followed by Interploidy Admixture

(2015) Brian Arnold et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring the age of a fixed beneficial allele

(2015) Louise Ormond et al.   MOLECULAR ECOLOGY

Meiosis evolves: adaptation to external and internal environments

(2015) Kirsten Bomblies et al.   NEW PHYTOLOGIST

Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

(2015) Vimal Rawat et al.   PLoS One

A Conserved Domain in the Scc3 Subunit of Cohesin Mediates the Interaction with Both Mcd1 and the Cohesin Loader Complex

(2015) Ola Orgil et al.   PLoS Genetics

Catch Me if You Can: Adaptation from Standing Genetic Variation to a Moving Phenotypic Optimum

(2015) Sebastian Matuszewski et al.   GENETICS

Polyploidy in the Arabidopsis genus

(2014) Kirsten Bomblies et al.   CHROMOSOME RESEARCH

Structure and function of cohesin's Scc3/SA regulatory subunit

(2014) Maurici B. Roig et al.   FEBS LETTERS

Error-prone polymerase activity causes multinucleotide mutations in humans

(2014) Kelley Harris et al.   GENOME RESEARCH

Selection on Meiosis Genes in Diploid and Tetraploid Arabidopsis arenosa

(2014) Kevin M. Wright et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genomic Landscape of Compensatory Evolution

(2014) Béla Szamecz et al.   PLOS BIOLOGY

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

Meiotic Adaptation to Genome Duplication in Arabidopsis arenosa

(2013) Levi Yant et al.   CURRENT BIOLOGY

Meiosis and Its Deviations in Polyploid Animals

(2013) P. Stenberg et al.   CYTOGENETIC AND GENOME RESEARCH

Estimating and interpreting FST: The impact of rare variants

(2013) G. Bhatia et al.   GENOME RESEARCH

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

Estimating the Strength of Selective Sweeps from Deep Population Diversity Data

(2012) P. W. Messer et al.   GENETICS

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Adaptive evolution: evaluating empirical support for theoretical predictions

(2012) Carrie F. Olson-Manning et al.   NATURE REVIEWS GENETICS

Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosa

(2012) Jesse D. Hollister et al.   PLoS Genetics

Pervasive Multinucleotide Mutational Events in Eukaryotes

(2011) Daniel R. Schrider et al.   CURRENT BIOLOGY

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

(2011) Tina T Hu et al.   NATURE GENETICS

Functional conservation of Mei4 for meiotic DNA double-strand break formation from yeasts to mice

(2010) R. Kumar et al.   GENES & DEVELOPMENT

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Evolutionary consequences of autopolyploidy

(2010) Christian Parisod et al.   NEW PHYTOLOGIST

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Genetic regulation of meiosis in polyploid species: new insights into an old question

(2009) Marta Cifuentes et al.   NEW PHYTOLOGIST

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The McDonald-Kreitman Test and Slightly Deleterious Mutations

(2008) J. Charlesworth et al.   MOLECULAR BIOLOGY AND EVOLUTION

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION