List of works by Cymon John Cox

A 20-state empirical amino-acid substitution model for green plant chloroplasts

scientific article published on 6 April 2013

A congruent phylogenomic signal places eukaryotes within the Archaea.

scientific article published on 24 October 2012

A transcriptome resource for the copepod Calanus glacialis across a range of culture temperatures.

scientific article published on 8 April 2015

Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms

scientific article published on 10 February 2016

An archaeal origin of eukaryotes supports only two primary domains of life

scientific article

Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants

scientific article

Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

scientific article (publication date: October 2004)

Author Correction: Phylogenomics provides robust support for a two-domains tree of life

scientific article published on 19 October 2020

Biopython: freely available Python tools for computational molecular biology and bioinformatics

scientific article

Chloroplast Phylogeny of Asplenioid Ferns based on rbcL and trnL-F Spacer Sequences (Polypodiidae, Aspleniaceae) and its Implications for Biogeography

article

Circulating small non-coding RNAs provide new insights into vitamin K nutrition and reproductive physiology in teleost fish

scientific article published on 27 September 2018

Comparative analysis of zebrafish bone morphogenetic proteins 2, 4 and 16: molecular and evolutionary perspectives.

scientific article

Compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins

scientific article

Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions

scientific article (publication date: March 2014)

Deep sequencing of Ptilidium (Ptilidiaceae) suggests evolutionary stasis in liverwort plastid genome structure

scientific article published on 25 March 2011

Disentangling knots of rapid evolution: origin and diversification of the moss order Hypnales

scientific article published in September 2012

Distribution and phylogenetic significance of the 71-kb inversion in the plastid genome in Funariidae (Bryophyta)

scientific article

Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulva

scientific article

Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges

scientific article

Evolution of multiple paralogous adenosine kinase genes in the moss genus Hygroamblystegium: phylogenetic implications

scientific article published in May 2004

Evolutionary conservation of TFIIH subunits: implications for the use of zebrafish as a model to study TFIIH function and regulation

scientific article published on 13 April 2014

Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts.

scientific article

First molecular estimate of cyclostome bryozoan phylogeny confirms extensive homoplasy among skeletal characters used in traditional taxonomy

scientific article

Genomic blueprints of sponge-prokaryote symbiosis are shared by low abundant and cultivatable Alphaproteobacteria

scientific article published in Scientific Reports

Geographical range in liverworts: does sex really matter?

Global patterns in peatmoss biodiversity

scientific article

Identification of a fish short-chain dehydrogenase/reductase associated with bone metabolism.

scientific article published on 14 December 2017

Improved phylogeny of brown algae Cystoseira (Fucales) from the Atlantic-Mediterranean region based on mitochondrial sequences

scientific article published in PLoS ONE

Increased diversification rates follow shifts to bisexuality in liverworts

scientific article published on February 2016

Land Plant Molecular Phylogenetics: A Review with Comments on Evaluating Incongruence Among Phylogenies

article

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula.

scientific article published on 14 April 2015

Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias

scientific article

Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery

scientific article

Multilocus genetic analyses provide insight into speciation and hybridization in aquatic grasses, genusRuppia

article

Multiple domestications of Asian rice

scientific article published on 5 April 2016

Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses)

scientific article (publication date: 6 August 2010)

Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.)

scholarly article by Filipe Sousa et al published 7 December 2018 in New Phytologist

Optimal data partitioning, multispecies coalescent and Bayesian concordance analyses resolve early divergences of the grape family (Vitaceae)

scientific article published on 6 February 2017

Ordinal relationships of pleurocarpous mosses, with special emphasis on the Hookeriales

scientific article published in November 2004

Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss).

scientific article

Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?

scientific article

Phylogenetic Relationships among the Mosses Based on Heterogeneous Bayesian Analysis of Multiple Genes from Multiple Genomic Compartments

scientific article published in April 2004

Phylogenetic Relationships of Haplolepideous Mosses (Dicranidae) Inferred from rps4 Gene Sequences

scientific article published in January 2004

Phylogenetic relationships within the moss family Bryaceae based on chloroplast DNA evidence

scientific article published in March 2003

Phylogenetically and spatially close marine sponges harbour divergent bacterial communities

scientific article

Phylogenomics provides robust support for a two-domains tree of life

scientific article published on 09 December 2019

Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis

scientific article published on December 2004

Phylogeny and morphological evolution of the amblystegiaceae (Bryopsida).

scientific article published in April 2002

Phylogeny, Character Evolution, and Biogeography of the Gondwanic Moss Family Hypopterygiaceae (Bryophyta)

scientific article published in March 2008

Phylogeny, Species Delimitation, and Recombination in Sphagnum Section Acutifolia

scientific article published in January 2005

Reconstructing the early evolution of Fungi using a six-gene phylogeny ⬇️

scientific article

Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

scientific article published on 02 April 2019

The Bryophyta (Mosses): Systematic and Evolutionary Inferences from an rps4 Gene (cpDNA) Phylogeny

scientific article published in February 2001

The Interrelationships of Land Plants and the Nature of the Ancestral Embryophyte

scientific article

The archaebacterial origin of eukaryotes

scientific article

The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

scientific article (publication date: 12 August 2009)

Three geographically separate domestications of Asian rice

scientific article published on 2 November 2015

WASABI: an automated sequence processing system for multigene phylogenies.

scientific article published in June 2007

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