Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates

Multiple large-scale gene and genome duplications during the evolution of hexapods

(2018) Zheng Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The timescale of early land plant evolution

(2018) Jennifer L. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

(2017) Ya Yang et al.   NEW PHYTOLOGIST

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

(2017) Michiel Van Bel et al.   NUCLEIC ACIDS RESEARCH

Reciprocally Retained Genes in the Angiosperm Lineage Show the Hallmarks of Dosage Balance Sensitivity

(2017) Setareh Tasdighian et al.   PLANT CELL

Constraining the timing of whole genome duplication in plant evolutionary history

(2017) James W. Clark et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events

(2017) W. C. Thomas Gregg et al.   SYSTEMATIC BIOLOGY

Revisiting ancestral polyploidy in plants

(2017) Colin Ruprecht et al.   Science Advances

Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data

(2016) George P. Tiley et al.   Genome Biology and Evolution

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

(2016) Zhen Li et al.   PLANT CELL

Draft genome of the living fossil Ginkgo biloba

(2016) Rui Guan et al.   GigaScience

Early genome duplications in conifers and other seed plants

(2015) Z. Li et al.   Science Advances

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary

(2014) Kevin Vanneste et al.   GENOME RESEARCH

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach

(2013) Charles-Elie Rabier et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

Lateral Gene Transfer from the Dead

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

Efficient Exploration of the Space of Reconciled Gene Trees

(2013) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

The Estimation of Tree Posterior Probabilities Using Conditional Clade Probability Distributions

(2013) Bret Larget   SYSTEMATIC BIOLOGY

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

(2012) G. J. Szollosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Guided Tree Topology Proposals for Bayesian Phylogenetic Inference

(2011) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

(2010) M. D. Rasmussen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Piecemeal or big bangs: correlating the vertebrate evolution with proposed models of gene expansion events

(2010) Amir Ali Abbasi   NATURE REVIEWS GENETICS

2R or not 2R is not the question anymore

(2010) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Examples of Adaptive MCMC

(2009) Gareth O. Roberts et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

The gene evolution model and computing its associated probabilities

(2009) Lars Arvestad et al.   JOURNAL OF THE ACM

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

(2009) M. Csuros et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE