Genomic Patterns of Positive Selection at the Origin of Rust Fungi

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

Optimization strategies for fast detection of positive selection on phylogenetic trees

(2014) Mario Valle et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Patterns of Positive Selection in Seven Ant Genomes

(2014) Julien Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Early insights into the genome sequence of Uromyces fabae

(2014) Tobias Link et al.   Frontiers in Plant Science

Overview of the functional virulent genome of the coffee leaf rust pathogen Hemileia vastatrix with an emphasis on early stages of infection

(2014) Pedro Talhinhas et al.   Frontiers in Plant Science

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

(2014) Adnane Nemri et al.   Frontiers in Plant Science

Detecting Natural Selection in Genomic Data

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

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors

(2013) Dario Cantu et al.   BMC GENOMICS

DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution

(2013) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

eggNOG v4.0: nested orthology inference across 3686 organisms

(2013) Sean Powell et al.   NUCLEIC ACIDS RESEARCH

The sacred lotus genome provides insights into the evolution of flowering plants

(2013) Yun Wang et al.   PLANT JOURNAL

How to Make a Dolphin: Molecular Signature of Positive Selection in Cetacean Genome

(2013) Mariana F. Nery et al.   PLoS One

Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

(2013) Lei Zhao et al.   PLoS One

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

(2013) H Bradley Shaffer et al.   GENOME BIOLOGY

Obligate mutualism within a host drives the extreme specialization of a fig wasp genome

(2013) Jin-Hua Xiao et al.   GENOME BIOLOGY

The Genomics of Obligate (and Nonobligate) Biotrophs

(2012) Pietro D. Spanu   Annual Review of Phytopathology

Genes under positive selection in a model plant pathogenic fungus, Botrytis

(2012) Gabriela Aguileta et al.   INFECTION GENETICS AND EVOLUTION

Phenotypic comparison of samdc and spe mutants reveals complex relationships of polyamine metabolism in Ustilago maydis

(2012) L. Valdes-Santiago et al.   MICROBIOLOGY-SGM

Accounting For Alignment Uncertainty in Phylogenomics

(2012) Martin Wu et al.   PLoS One

Evolutionary History and Complementary Selective Relaxation of the Duplicated PI Genes in Grasses

(2011) Ruo-Xun Wei et al.   Journal of Integrative Plant Biology

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Consistent Phylogenetic Backbone for the Fungi

(2011) I. Ebersberger et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

Relaxed selection is a precursor to the evolution of phenotypic plasticity

(2011) B. G. Hunt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

(2011) S. Duplessis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The ecological causes of evolution

(2011) Andrew D.C. MacColl   TRENDS IN ECOLOGY & EVOLUTION

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Finding candidate genes under positive selection in Non-model species: examples of genes involved in host specialization in pathogens

(2010) G. AGUILETA et al.   MOLECULAR ECOLOGY

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Rapidly evolving genes in pathogens: Methods for detecting positive selection and examples among fungi, bacteria, viruses and protists

(2009) Gabriela Aguileta et al.   INFECTION GENETICS AND EVOLUTION

Positive selection in AvrP4 avirulence gene homologues across the genus Melampsora

(2009) M. M. Van der Merwe et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The role of positive selection in determining the molecular cause of species differences in disease

(2008) Jessica J Vamathevan et al.   BMC EVOLUTIONARY BIOLOGY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Adaptation from standing genetic variation

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