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List of works by Antonis Rokas

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Genome-scale approaches to resolving incongruence in molecular phylogenies

scientific article (publication date: 23 October 2003)
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

scientific article
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

scientific article
Rare genomic changes as a tool for phylogenetics

scientific article (publication date: November 2000)
Inferring ancient divergences requires genes with strong phylogenetic signals.

scientific article published on 8 May 2013
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene

scientific article (publication date: 20 April 2006)
Dynamics of Pseudomonas aeruginosa genome evolution

scientific article
Bayesian estimation of concordance among gene trees

scientific article published on 9 November 2006
Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

scientific article published on 27 November 2014
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

scientific article
More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy

article
Bushes in the tree of life

scientific article (publication date: November 2006)
Animal evolution and the molecular signature of radiations compressed in time

scientific article published on 01 December 2005
Comparing bootstrap and posterior probability values in the four-taxon case

scientific article published in August 2003
The origins of multicellularity and the early history of the genetic toolkit for animal development

scientific article published on January 2008
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding

scientific article
Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi

article
Novel information theory-based measures for quantifying incongruence among phylogenetic trees

scientific article published on 7 February 2014
Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution

scientific article published in June 2006
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts

scholarly article
Contentious relationships in phylogenomic studies can be driven by a handful of genes

scientific article published on 10 April 2017
Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics

scientific article published on 25 August 2009
Remarkably ancient balanced polymorphisms in a multi-locus gene network

scientific article (publication date: 4 March 2010)
Phylogenetic and transcriptomic analysis of chemosensory receptors in a pair of divergent ant species reveals sex-specific signatures of odor coding

scientific article
Comparative genomics of biotechnologically important yeasts

scientific article
Non-optimal codon usage is a mechanism to achieve circadian clock conditionality.

scientific article published on 17 February 2013
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

scientific article (publication date: 7 December 2016)
Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi

scientific article
Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

scientific article
Evidence for a High Frequency of Simultaneous Double-Nucleotide Substitutions

scientific article published in Science
Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus

scientific article published on July 2011
Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

scientific article
Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in Anopheles gambiae

scientific article published on 29 April 2013
The evolution of fungal metabolic pathways

scientific article (publication date: December 2014)
Recurrent tissue-specific mtDNA mutations are common in humans

scientific article
Evaluating ortholog prediction algorithms in a yeast model clade

scientific article
The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae.

scientific article
Transcriptome-wide analysis of small RNA expression in early zebrafish development

scientific article
Frequent and widespread parallel evolution of protein sequences

scientific article published on 25 June 2008
Horizontal transfer and death of a fungal secondary metabolic gene cluster

scientific article (publication date: 2012)
Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture

scientific article
Conflicting phylogenetic signals at the base of the metazoan tree

scientific article published in July 2003
A maximum-likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae): implications for insect phylogenetic studies

scientific article published in February 2002
Out of Anatolia: longitudinal gradients in genetic diversity support an eastern origin for a circum-Mediterranean oak gallwasp Andricus quercustozae

scientific article published in August 2003
Understanding patterns of genetic diversity in the oak gallwasp Biorhiza pallida: demographic history or a Wolbachia selective sweep?

scientific article published in September 2001
Genomics and the making of yeast biodiversity

scientific article published on 30 November 2015
The molecular origins of multicellular transitions

scientific article published on 14 October 2008
Fungal metabolic gene clusters—caravans traveling across genomes and environments

scientific article published on March 3, 2015
The molecular evolution of the p120-catenin subfamily and its functional associations

scientific article
Evolutionary shifts between host oak sections and host-plant organs in Andricus gallwasps

scientific article published in September 2002

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