Extracting functional trends from whole genome duplication events using comparative genomics

Models for gene duplication when dosage balance works as a transition state to subsequent neo- or sub-functionalization

(2016) Ashley I. Teufel et al.   BMC EVOLUTIONARY BIOLOGY

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

A generalized birth and death process for modeling the fates of gene duplication

(2015) Jing Zhao et al.   BMC EVOLUTIONARY BIOLOGY

Conserved Gene Expression Programs in Developing Roots from Diverse Plants

(2015) Ling Huang et al.   PLANT CELL

Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution

(2015) Rori V. Rohlfs et al.   SYSTEMATIC BIOLOGY

The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio)

(2015) Jiong-Tang Li et al.   Scientific Reports

Refining discordant gene trees

(2014) Pawel Górecki et al.   BMC BIOINFORMATICS

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

(2014) Thomas E. Hughes et al.   GENOME RESEARCH

Differential retention and divergent resolution of duplicate genes following whole-genome duplication

(2014) Casey L. McGrath et al.   GENOME RESEARCH

Comparative analysis of the transcriptome across distant species

(2014) Mark B. Gerstein et al.   NATURE

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei

(2014) Eric B. Rondeau et al.   PLoS One

Genome interplay in the grain transcriptome of hexaploid bread wheat

(2014) M. Pfeifer et al.   SCIENCE

Modeling Gene Expression Evolution with an Extended Ornstein–Uhlenbeck Process Accounting for Within-Species Variation

(2013) Rori V. Rohlfs et al.   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

Selectome update: quality control and computational improvements to a database of positive selection

(2013) Sébastien Moretti et al.   NUCLEIC ACIDS RESEARCH

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

(2013) R. De Smet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mis-Assembled “Segmental Duplications” in Two Versions of the Bos taurus Genome

(2012) Aleksey V. Zimin et al.   PLoS One

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Toward a General Model for the Evolutionary Dynamics of Gene Duplicates

(2011) Anke Konrad et al.   Genome Biology and Evolution

Modification of Gene Duplicability during the Evolution of Protein Interaction Network

(2011) Matteo D'Antonio et al.   PLoS Computational Biology

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The gene evolution model and computing its associated probabilities

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

Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon)

(2008) Roy G Danzmann et al.   BMC GENOMICS

The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families

(2008) Timothy Hughes et al.   GENE

Gene Family Evolution by Duplication, Speciation, and Loss

(2008) Cedric Chauve et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Whole-Genome Duplications in the Ancestral Vertebrate Are Detectable in the Distribution of Gene Family Sizes of Tetrapod Species

(2008) Timothy Hughes et al.   JOURNAL OF MOLECULAR EVOLUTION