Cymon J. Cox
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View article: Establishing the ELIXIR Microbiome Community
Establishing the ELIXIR Microbiome Community Open
Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metaba…
View article: First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples
First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples Open
The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites,…
View article: First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples
First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples Open
The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory among designated European coastal marine sites, s…
View article: Establishing the ELIXIR Microbiome Community
Establishing the ELIXIR Microbiome Community Open
Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metaba…
View article: Selection of bacterial strains to bioaugment granular sludge and improve the removal of recalcitrant pollutants
Selection of bacterial strains to bioaugment granular sludge and improve the removal of recalcitrant pollutants Open
Several advantages are gained by the use of granular sludge in wastewater treatment plants (WWTP), such as higher biomass retention, faster settling properties, lower energy costs and smaller operational land space. However, relatively few…
View article: Data-specific substitution models improve protein-based phylogenetics
Data-specific substitution models improve protein-based phylogenetics Open
Calculating amino-acid substitution models that are specific for individual protein data sets is often difficult due to the computational burden of estimating large numbers of rate parameters. In this study, we tested the computational eff…
View article: European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation
European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation Open
Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across com…
View article: metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data - use case
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data - use case Open
Data products returned by metaGOflow (v1.0.0) and packed as a Research Objecte (RO) Crate, when performed with a real-world seawater metagenomic sample (TARA OCEAN, ERR599171). This Zenodo repo accompanies the metaGOflow paper and more abo…
View article: metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data - use case
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data - use case Open
Data products returned by metaGOflow (v1.0.0) and packed as a Research Object (RO) Crate, when performed with: a seawater metagenomic sample (TARA OCEAN, ERR599171) a fish gut sample (ERR4765907) a human gut sample (SRR9654976) This Zenodo…
View article: metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data - use case
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data - use case Open
Data products returned by metaGOflow (v1.0.0) and packed as a Research Object (RO) Crate, when performed with: a seawater metagenomic sample (TARA OCEAN, ERR599171) a fish gut sample (ERR4765907) a human gut sample (SRR9654976) This Zenodo…
View article: metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data - use case
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data - use case Open
Data products returned by metaGOflow (v1.0.0) when performed with real-world samples. In this version we provide the complete data product file (.zip) for a seawater metagenomic sample (TARA OCEAN, ERR599171) and the ro-crate-metadata.json…
View article: metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data Open
Background Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that co…
View article: Integrated phylogenomic analyses unveil reticulate evolution in <i>Parthenocissus</i> (Vitaceae), highlighting speciation dynamics in the <scp>Himalayan–Hengduan</scp> Mountains
Integrated phylogenomic analyses unveil reticulate evolution in <i>Parthenocissus</i> (Vitaceae), highlighting speciation dynamics in the <span>Himalayan–Hengduan</span> Mountains Open
Summary Hybridization caused by frequent environmental changes can lead both to species diversification (speciation) and to speciation reversal (despeciation), but the latter has rarely been demonstrated. Parthenocissus , a genus with its …
View article: Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus
Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus Open
Background The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter n…
View article: Recoding Amino Acids to a Reduced Alphabet may Increase or Decrease Phylogenetic Accuracy
Recoding Amino Acids to a Reduced Alphabet may Increase or Decrease Phylogenetic Accuracy Open
Common molecular phylogenetic characteristics such as long branches and compositional heterogeneity can be problematic for phylogenetic reconstruction when using amino acid data. Recoding alignments to reduced alphabets before phylogenetic…
View article: EOSC-Life Report on the work of the initial demonstrators
EOSC-Life Report on the work of the initial demonstrators Open
This deliverable 3.2 is a report on the demonstrator projects, the eight scientific and technical pilot projects that were selected to provide concrete scientific use-cases and guide and structure the work done in EOSC-Life to build an ope…
View article: Inferring the Deep Past from Molecular Data
Inferring the Deep Past from Molecular Data Open
There is an expectation that analyses of molecular sequences might be able to distinguish between alternative hypotheses for ancient relationships, but the phylogenetic methods used and types of data analyzed are of critical importance in …
View article: Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals
Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals Open
Background In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phyl…
View article: Thermus-Deinococcus alignment
Thermus-Deinococcus alignment Open
The sequence alignment used in the Deinococcus-Thermus analyses (Figure 1).
View article: Additional file 3 of Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals
Additional file 3 of Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals Open
Additional file 2: Supplementary Table S1. Number of sequence reads per quality control step across all metagenome samples using the MGnify metagenomics pipeline (EMBL-EBI), version 2.0 (project PRJEB13222). Supplementary Table S2. Basic i…
View article: Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants
Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants Open
The early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypoth…
View article: Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central America
Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central America Open
Caecidae is a species-rich family of microsnails with a worldwide distribution. Typical for many groups of gastropods, caecid taxonomy is largely based on overt shell characters. However, identification of species using shell characteristi…
View article: The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models
The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models Open
The colonization of land by descendants of charophyte green algae marked a turning point in Earth history that enabled the development of the diverse terrestrial ecosystems we see today. Early land plants diversified into three gametophyte…
View article: data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models"
data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models" Open
The nucleotide, codon-degenerate and protein concatenated alignments of 83 chloroplast genes, with the respective character sets, in nexus format.
View article: data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models"
data from "The chloroplast land plant phylogeny: analyses employing better-fitting tree- and site-heterogeneous composition models" Open
The nucleotide, codon-degenerate and protein concatenated alignments of 83 chloroplast genes, with the respective character sets, in nexus format.
View article: Peer Review #2 of "The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models (v0.1)"
Peer Review #2 of "The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models (v0.1)" Open
Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics.Recent analyses of both nuclear and chloroplast genome data of land plan…
View article: Peer Review #2 of "The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models (v0.2)"
Peer Review #2 of "The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models (v0.2)" Open
Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics.Recent analyses of both nuclear and chloroplast genome data of land plan…