Extracting functional trends from whole genome duplication events using comparative genomics

[1]  Mark Newman,et al.  Power‐law distribution , 2017 .

[2]  Steven J. M. Jones,et al.  The Atlantic salmon genome provides insights into rediploidization , 2016, Nature.

[3]  Ashley I. Teufel,et al.  Models for gene duplication when dosage balance works as a transition state to subsequent neo-or sub-functionalization , 2016, BMC Evolutionary Biology.

[4]  Ashley I. Teufel,et al.  A generalized birth and death process for modeling the fates of gene duplication , 2015, BMC Evolutionary Biology.

[5]  R. Nielsen,et al.  Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution. , 2015, Systematic biology.

[6]  J. Schiefelbein,et al.  Conserved Gene Expression Programs in Developing Roots from Diverse Plants , 2015, Plant Cell.

[7]  Jiongtang Li,et al.  The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio) , 2015, Scientific Reports.

[8]  Alessandro Vullo,et al.  Ensembl 2015 , 2014, Nucleic Acids Res..

[9]  Davide Heller,et al.  STRING v10: protein–protein interaction networks, integrated over the tree of life , 2014, Nucleic Acids Res..

[10]  Oliver Eulenstein,et al.  Refining discordant gene trees , 2014, BMC Bioinformatics.

[11]  Jing Zhao,et al.  On Mechanistic Modeling of Gene Content Evolution: Birth-Death Models and Mechanisms of Gene Birth and Gene Retention , 2014, Comput..

[12]  M. Lynch,et al.  Differential retention and divergent resolution of duplicate genes following whole-genome duplication , 2014, Genome research.

[13]  B. Koop,et al.  The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei , 2014, PloS one.

[14]  Karl G. Kugler,et al.  Genome interplay in the grain transcriptome of hexaploid bread wheat , 2014, Science.

[15]  Peter J. Bickel,et al.  Comparative Analysis of the Transcriptome across Distant Species , 2014, Nature.

[16]  S. Kelly,et al.  The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize , 2014, Genome research.

[17]  D. Chalopin,et al.  The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates , 2014, Nature Communications.

[18]  Arnold Kuzniar,et al.  Selectome update: quality control and computational improvements to a database of positive selection , 2013, Nucleic Acids Res..

[19]  Rasmus Nielsen,et al.  Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within-species variation. , 2014, Molecular biology and evolution.

[20]  M. Van Montagu,et al.  Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants , 2013, Proceedings of the National Academy of Sciences.

[21]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[22]  Krister M. Swenson,et al.  Gene trees and species trees: irreconcilable differences , 2012, BMC Bioinformatics.

[23]  David R. Kelley,et al.  Mis-Assembled “Segmental Duplications” in Two Versions of the Bos taurus Genome , 2012, PloS one.

[24]  Johan A. Grahnen,et al.  Toward a General Model for the Evolutionary Dynamics of Gene Duplicates , 2011, Genome biology and evolution.

[25]  Martin Goodson,et al.  Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. , 2011, Genome research.

[26]  Ramón Doallo,et al.  ProtTest 3: fast selection of best-fit models of protein evolution , 2011, Bioinform..

[27]  Francesca D. Ciccarelli,et al.  Modification of Gene Duplicability during the Evolution of Protein Interaction Network , 2011, PLoS Comput. Biol..

[28]  Oliver Eulenstein,et al.  Reconciling Phylogenetic Trees , 2011 .

[29]  Ari Löytynoja,et al.  webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser , 2010, BMC Bioinformatics.

[30]  E. Virginia Armbrust,et al.  pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree , 2010, BMC Bioinformatics.

[31]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[32]  Kai Ye,et al.  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..

[33]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[34]  Bengt Sennblad,et al.  The gene evolution model and computing its associated probabilities , 2009, JACM.

[35]  Kousha Etessami,et al.  Recursive Markov chains, stochastic grammars, and monotone systems of nonlinear equations , 2005, JACM.

[36]  K. Gharbi,et al.  Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon) , 2008, BMC Genomics.

[37]  D. Liberles,et al.  Whole-Genome Duplications in the Ancestral Vertebrate Are Detectable in the Distribution of Gene Family Sizes of Tetrapod Species , 2008, Journal of Molecular Evolution.

[38]  Nadia El-Mabrouk,et al.  Gene Family Evolution by Duplication, Speciation and Loss , 2022 .

[39]  David A. Liberles,et al.  The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families. , 2008, Gene.

[40]  Arne Elofsson,et al.  Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia , 2007, Genome Biology.

[41]  Lars Arvestad,et al.  Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. , 2007, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[42]  Brian C. Thomas,et al.  Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. , 2006, Genome research.

[43]  A. Elofsson,et al.  What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? , 2006, Genome Biology.

[44]  M. Lynch,et al.  On the formation of novel genes by duplication in the Caenorhabditis elegans genome. , 2006, Molecular biology and evolution.

[45]  Matthew J. Betts,et al.  Optimal Gene Trees from Sequences and Species Trees Using a Soft Interpretation of Parsimony , 2006, Journal of Molecular Evolution.

[46]  A. Meyer,et al.  From 2R to 3R: evidence for a fish-specific genome duplication (FSGD). , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[47]  Philip C J Donoghue,et al.  Genome duplication, extinction and vertebrate evolution. , 2005, Trends in ecology & evolution.

[48]  D. Liberles,et al.  Subfunctionalization of duplicated genes as a transition state to neofunctionalization , 2005, BMC Evolutionary Biology.

[49]  Hirohisa Kishino,et al.  Divergence pattern of duplicate genes in protein-protein interactions follows the power law. , 2005, Molecular biology and evolution.

[50]  Jianzhi Zhang,et al.  Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution , 2005, Genetics.

[51]  Matthew J. Betts,et al.  The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics , 2004, Nucleic Acids Res..

[52]  M. Lynch,et al.  The altered evolutionary trajectories of gene duplicates. , 2004, Trends in genetics : TIG.

[53]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[54]  Richard W. Lusk,et al.  Organismal complexity, protein complexity, and gene duplicability , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[55]  M. Lynch,et al.  The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. , 2003, Genetics.

[56]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[57]  Bengt Sennblad,et al.  Bayesian gene/species tree reconciliation and orthology analysis using MCMC , 2003, ISMB.

[58]  David A Liberles,et al.  The Adaptive Evolution Database (TAED) , 2001, Genome Biology.

[59]  J. Huelsenbeck,et al.  MRBAYES : Bayesian inference of phylogeny , 2001 .

[60]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.